Faculty Publications
2024
- Genomic epidemiology of West Nile virus in Europe.Koch RT, Erazo D, Folly AJ, Johnson N, Dellicour S, Grubaugh ND, Vogels CBF. One Health. 2024 Jun; 2023 Dec 16. PMID: 38193029.
- Polarized localization of kinesin-1 and RIC-7 drives axonal mitochondria anterograde transport.Wu Y, Ding C, Sharif B, Weinreb A, Swaim G, Hao H, Yogev S, Watanabe S, Hammarlund M. J Cell Biol. 2024 May 6; 2024 Mar 12. PMID: 38470363.
- VEGF-C prophylaxis favors lymphatic drainage and modulates neuroinflammation in a stroke model.Boisserand LSB, Geraldo LH, Bouchart J, El Kamouh MR, Lee S, Sanganahalli BG, Spajer M, Zhang S, Lee S, Parent M, Xue Y, Skarica M, Yin X, Guegan J, Boyé K, Saceanu Leser F, Jacob L, Poulet M, Li M, Liu X, Velazquez SE, Singhabahu R, Robinson ME, Askenase MH, Osherov A, Sestan N, Zhou J, Alitalo K, Song E, Eichmann A, Sansing LH, Benveniste H, Hyder F, Thomas JL. J Exp Med. 2024 Apr 1; 2024 Mar 5. PMID: 38442272.
- IL-10 dampens antitumor immunity and promotes liver metastasis via PD-L1 induction.Shiri AM, Zhang T, Bedke T, Zazara DE, Zhao L, Lücke J, Sabihi M, Fazio A, Zhang S, Tauriello DVF, Batlle E, Steglich B, Kempski J, Agalioti T, Nawrocki M, Xu Y, Riecken K, Liebold I, Brockmann L, Konczalla L, Bosurgi L, Mercanoglu B, Seeger P, Küsters N, Lykoudis PM, Heumann A, Arck PC, Fehse B, Busch P, Grotelüschen R, Mann O, Izbicki JR, Hackert T, Flavell RA, Gagliani N, Giannou AD, Huber S. J Hepatol. 2024 Apr; 2023 Dec 30. PMID: 38160941.
- A scalable and cost-efficient rRNA depletion approach to enrich RNAs for molecular biology investigations.Singh A, Xue A, Tai J, Mbadugha F, Obi P, Mascarenhas R, Tyagi A, Siena A, Chen YG. RNA. 2024 Mar 14; 2024 Mar 14. PMID: 38485192.
- Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes.Castillo HB, Shuster SO, Tarekegn LH, Davis CM. Chem Commun (Camb). 2024 Mar 14; 2024 Mar 14. PMID: 38329230.
- Human iPSC-Based Model of COPD to Investigate Disease Mechanisms, Predict SARS-COV-2 Outcome, and Test Preventive Immunotherapy.Dagher R, Moldobaeva A, Gubbins E, Clark S, Madel Alfajaro M, Wilen CB, Hawkins F, Qu X, Chien Chiang C, Li Y, Clarke L, Ikeda Y, Brown C, Kolbeck R, Ma Q, Rojas M, Koff JL, Ghaedi M. Stem Cells. 2024 Mar 14. PMID: 38183264.
- Factors Associated with Long COVID: Insights from Two Nationwide Surveys.Wu Y, Sawano M, Wu Y, Shah RM, Bishop P, Iwasaki A, Krumholz HM. Am J Med. 2024 Mar 13; 2024 Mar 13. PMID: 38490304.
- De novo-designed transmembrane proteins bind and regulate a cytokine receptor.Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Nat Chem Biol. 2024 Mar 13; 2024 Mar 13. PMID: 38480980.
- Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins.Thaenert A, Sevostyanova A, Chung CZ, Vargas-Rodriguez O, Melnikov SV, Söll D. Proc Natl Acad Sci U S A. 2024 Mar 12; 2024 Mar 5. PMID: 38442159.
- Rational Design of TDP-43 Derived α-Helical Peptide Inhibitors: An In Silico Strategy to Prevent TDP-43 Aggregation in Neurodegenerative Disorders.Salaikumaran MR, Gopal PP. ACS Chem Neurosci. 2024 Mar 11; 2024 Mar 11. PMID: 38466778.
- Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB dependent IFITM3 expression.Munir M, Embry A, Doench JG, Heaton NS, Wilen CB, Orchard RC. J Biol Chem. 2024 Mar 8; 2024 Mar 8. PMID: 38462163.
- microRNA-33 controls hunger signaling in hypothalamic AgRP neurons.Price NL, Fernández-Tussy P, Varela L, Cardelo MP, Shanabrough M, Aryal B, de Cabo R, Suárez Y, Horvath TL, Fernández-Hernando C. Nat Commun. 2024 Mar 8; 2024 Mar 8. PMID: 38459068.
- Adaptive multi-interventional trial platform to improve patient care for fibrotic interstitial lung diseases.Kawano-Dourado L, Kulkarni T, Ryerson CJ, Rivera-Ortega P, Baldi BG, Chaudhuri N, Funke-Chambour M, Hoffmann-Vold AM, Johannson KA, Khor YH, Montesi SB, Piccari L, Prosch H, Molina-Molina M, Sellares Torres J, Bauer-Ventura I, Rajan S, Jacob J, Richards D, Spencer LG, Wendelberger B, Jensen T, Quintana M, Kreuter M, Gordon AC, Martinez FJ, Kaminski N, Cornelius V, Lewis R, Adams W, Jenkins G. Thorax. 2024 Mar 6; 2024 Mar 6. PMID: 38448221.
- Highly Reactive Group I Introns Ubiquitous in Pathogenic Fungi.Liu T, Pyle AM. J Mol Biol. 2024 Mar 5; 2024 Mar 5. PMID: 38447889.
- An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis.Huang R, Irish VF. PLoS Genet. 2024 Mar; 2024 Mar 5. PMID: 38442104.
- Low antibody levels associated with significantly increased rate of SARS-CoV-2 infection in a highly vaccinated population from the US National Basketball Association.Tai CG, Haviland MJ, Kissler SM, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH, Mack CD. J Med Virol. 2024 Mar. PMID: 38465748.
- Beyond reader proteins: RNA binding proteins and RNA modifications in conversation to regulate gene expression.Fagre C, Gilbert W. Wiley Interdiscip Rev RNA. 2024 Mar-Apr. PMID: 38444048.
- Challenges and perspectives in computational deconvolution of genomics data.Garmire LX, Li Y, Huang Q, Xu C, Teichmann SA, Kaminski N, Pellegrini M, Nguyen Q, Teschendorff AE. Nat Methods. 2024 Mar; 2024 Feb 19. PMID: 38374264.
- Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever.Kotliar D, Raju S, Tabrizi S, Odia I, Goba A, Momoh M, Sandi JD, Nair P, Phelan E, Tariyal R, Eromon PE, Mehta S, Robles-Sikisaka R, Siddle KJ, Stremlau M, Jalloh S, Gire SK, Winnicki S, Chak B, Schaffner SF, Pauthner M, Karlsson EK, Chapin SR, Kennedy SG, Branco LM, Kanneh L, Vitti JJ, Broodie N, Gladden-Young A, Omoniwa O, Jiang PP, Yozwiak N, Heuklom S, Moses LM, Akpede GO, Asogun DA, Rubins K, Kales S, Happi AN, Iruolagbe CO, Dic-Ijiewere M, Iraoyah K, Osazuwa OO, Okonkwo AK, Kunz S, McCormick JB, Khan SH, Honko AN, Lander ES, Oldstone MBA, Hensley L, Folarin OA, Okogbenin SA, Günther S, Ollila HM, Tewhey R, Okokhere PO, Schieffelin JS, Andersen KG, Reilly SK, Grant DS, Garry RF, Barnes KG, Happi CT, Sabeti PC. Nat Microbiol. 2024 Mar; 2024 Feb 7. PMID: 38326571.
- Mast-cell expressed membrane protein-1 is expressed in classical monocytes and alveolar macrophages in idiopathic pulmonary fibrosis and regulates cell chemotaxis, adhesion, and migration in a TGFβ-dependent manner.Perrot CY, Karampitsakos T, Unterman A, Adams T, Marlin K, Arsenault A, Zhao A, Kaminski N, Katlaps G, Patel K, Bandyopadhyay D, Herazo-Maya JD. Am J Physiol Cell Physiol. 2024 Mar 1; 2024 Jan 8. PMID: 38189137.
- in silico transcriptome dissection of neocortical excitatory neurogenesis via joint matrix decomposition and transfer learning.Sonthalia S, Li G, Blanco XM, Casella A, Liu J, Stein-O'Brien G, Caffo B, Adkins RS, Orvis J, Hertzano R, Mahurkar A, Gillis J, Werner J, Ma S, Micali N, Sestan N, Rakic P, Santpere G, Ament SA, Colantuoni C. bioRxiv. 2024 Feb 28; 2024 Feb 28. PMID: 38464021.
- Compartmentalized ocular lymphatic system mediates eye-brain immunity.Yin X, Zhang S, Lee JH, Dong H, Mourgkos G, Terwilliger G, Kraus A, Geraldo LH, Poulet M, Fischer S, Zhou T, Mohammed FS, Zhou J, Wang Y, Malloy S, Rohner N, Sharma L, Salinas I, Eichmann A, Thomas JL, Saltzman WM, Huttner A, Zeiss C, Ring A, Iwasaki A, Song E. Nature. 2024 Feb 28; 2024 Feb 28. PMID: 38418880.
- Less-is-more: selecting transcription factor binding regions informative for motif inference.Xu J, Gao J, Ni P, Gerstein M. Nucleic Acids Res. 2024 Feb 28. PMID: 38214231.
- Discovery of novel microRNA mimic repressors of ribosome biogenesis.Bryant CJ, McCool MA, Rosado González GT, Abriola L, Surovtseva YV, Baserga SJ. Nucleic Acids Res. 2024 Feb 28. PMID: 38197221.
- Gene-edited Mtsoc1 triple mutant Medicago plants do not flower.Poulet A, Zhao M, Peng Y, Tham F, Jaudal M, Zhang L, van Wolfswinkel JC, Putterill J. Front Plant Sci. 2024; 2024 Feb 26. PMID: 38469328.
- IL-10 constrains sphingolipid metabolism to limit inflammation.York AG, Skadow MH, Oh J, Qu R, Zhou QD, Hsieh WY, Mowel WK, Brewer JR, Kaffe E, Williams KJ, Kluger Y, Smale ST, Crawford JM, Bensinger SJ, Flavell RA. Nature. 2024 Feb 21; 2024 Feb 21. PMID: 38383790.
- Keratin 17 modulates the immune topography of pancreatic cancer.Delgado-Coka LA, Horowitz M, Torrente-Goncalves M, Roa-Peña L, Leiton CV, Hasan M, Babu S, Fassler D, Oentoro J, Karen Bai JD, Petricoin EF, Matrisian LM, Blais EM, Marchenko N, Allard FD, Jiang W, Larson B, Hendifar A, Chen C, Abousamra S, Samaras D, Kurc T, Saltz J, Escobar-Hoyos LF, Shroyer K. Res Sq. 2024 Feb 20; 2024 Feb 20. PMID: 38464123.
- Anti-Inflammatory Roles of Type I Interferon Signaling in the Lung.Feng J, Liu Y, Kim J, Ahangari F, Kaminski N, Bain WG, Jie Z, Dela Cruz CS, Sharma L. Am J Physiol Lung Cell Mol Physiol. 2024 Feb 20; 2024 Feb 20. PMID: 38375579.
- Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis.Guillen-Guio B, Paynton ML, Allen RJ, Chin DPW, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Ma SF, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. ERJ Open Res. 2024 Jan; 2024 Feb 19. PMID: 38375425.
- North-south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic.Miguel I, Feliz EP, Agramonte R, Martinez PV, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago GA, Muñoz-Jordán JL, Peguero A, Paulino-Ramírez R, Grubaugh ND, de Filippis AMB, Alcantara LCJ, Rico JM, Lourenço J, Franco L, Giovanetti M. medRxiv. 2024 Feb 15; 2024 Feb 15. PMID: 38405721.
- Pulmonary Fibrosis Stakeholder Summit: A Joint NHLBI, Three Lakes Foundation, and Pulmonary Fibrosis Foundation Workshop Report.Montesi SB, Gomez CR, Beers M, Brown R, Chattopadhyay I, Flaherty KR, Garcia CK, Gomperts B, Hariri LP, Hogaboam CM, Jenkins RG, Kaminski N, Kim GHJ, Königshoff M, Kolb M, Kotton DN, Kropski JA, Lasky J, Magin CM, Maher TM, McCormick M, Moore BB, Nickerson-Nutter C, Oldham J, Podolanczuk AJ, Raghu G, Rosas I, Rowe SM, Schmidt WT, Schwartz D, Shore JE, Spino C, Craig JM, Martinez FJ. Am J Respir Crit Care Med. 2024 Feb 15. PMID: 38113442.
- Stem cell migration drives lung repair in living mice.Chioccioli M, Liu S, Magruder S, Tata A, Borriello L, McDonough JE, Konkimalla A, Kim SH, Nouws J, Gonzalez DG, Traub B, Ye X, Yang T, Entenberg DR, Krishnaswamy S, Hendry CE, Kaminski N, Tata PR, Sauler M. Dev Cell. 2024 Feb 14; 2024 Feb 14. PMID: 38377991.
- Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources.Lyon SE, Wencker FDR, Fernando CM, Harris KA, Breaker RR. PNAS Nexus. 2024 Feb; 2024 Feb 12. PMID: 38415217.
- Fluoride transport in Arabidopsis thaliana plants is impaired in Fluoride EXporter (FEX) mutants.Tausta SL, Fontaine K, Hillmer AT, Strobel SA. Plant Mol Biol. 2024 Feb 11; 2024 Feb 11. PMID: 38342783.
- DHCR24-mediated sterol homeostasis during spermatogenesis is required for sperm mitochondrial sheath formation and impacts male fertility over time.Relovska S, Wang H, Zhang X, Fernández-Tussy P, Jeong KJ, Choi J, Suárez Y, McDonald JG, Fernández-Hernando C, Chung JJ. bioRxiv. 2024 Feb 11; 2024 Feb 11. PMID: 38187697.
- Heterogeneity of hepatocyte dynamics restores liver architecture after chemical, physical or viral damage.Ruz-Maldonado I, Gonzalez JT, Zhang H, Sun J, Bort A, Kabir I, Kibbey RG, Suárez Y, Greif DM, Fernández-Hernando C. Nat Commun. 2024 Feb 10; 2024 Feb 10. PMID: 38341404.
- Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. bioRxiv. 2024 Feb 8; 2024 Feb 8. PMID: 38370833.
- Contribution of climate change to the spatial expansion of West Nile virus in Europe.Erazo D, Grant L, Ghisbain G, Marini G, Colón-González FJ, Wint W, Rizzoli A, Van Bortel W, Vogels CBF, Grubaugh ND, Mengel M, Frieler K, Thiery W, Dellicour S. Nat Commun. 2024 Feb 8; 2024 Feb 8. PMID: 38331945.
- The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches.Barth KM, Hiller DA, Strobel SA. Biochemistry. 2024 Feb 8; 2024 Feb 8. PMID: 38329042.
- Persistent SARS-CoV-2 infection: significance and implications.Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Lancet Infect Dis. 2024 Feb 7; 2024 Feb 7. PMID: 38340735.
- Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis.Mazzetto M, Gonzalez LE, Sanchez N, Reinke V. Genome Res. 2024 Feb 7; 2024 Feb 7. PMID: 38164610.
- Lytic bacteriophages interact with respiratory epithelial cells and induce the secretion of antiviral and proinflammatory cytokines.Zamora PF, Reidy TG, Armbruster CR, Sun M, Van Tyne D, Turner PE, Koff JL, Bomberger JM. bioRxiv. 2024 Feb 6; 2024 Feb 6. PMID: 38370761.
- Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation.Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2024 Feb 6; 2024 Feb 2. PMID: 38306478.
- Prior Influenza Infection Mitigates SARS-CoV-2 Disease in Syrian Hamsters.Di Pietro C, Haberman AM, Lindenbach BD, Smith PC, Bruscia EM, Allore HG, Vander Wyk B, Tyagi A, Zeiss CJ. Viruses. 2024 Feb 3; 2024 Feb 3. PMID: 38400021.
- Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University.Würstle S, Lee A, Kortright KE, Winzig F, An W, Stanley GL, Rajagopalan G, Harris Z, Sun Y, Hu B, Blazanin M, Hajfathalian M, Bollyky PL, Turner PE, Koff JL, Chan BK. Sci Rep. 2024 Feb 1; 2024 Feb 1. PMID: 38302552.
- Recent developments in membrane traffic and lipid dynamics.Roux A, Reinisch K. Curr Opin Cell Biol. 2024 Feb; 2024 Jan 11. PMID: 38215517.
- PD-1H/VISTA mediates immune evasion in acute myeloid leukemia.Kim TK, Han X, Hu Q, Vandsemb EN, Fielder CM, Hong J, Kim KW, Mason EF, Plowman RS, Wang J, Wang Q, Zhang JP, Badri T, Sanmamed MF, Zheng L, Zhang T, Alawa J, Lee SW, Zeidan AM, Halene S, Pillai MM, Chandhok NS, Lu J, Xu ML, Gore SD, Chen L. J Clin Invest. 2024 Feb 1; 2024 Feb 1. PMID: 38060328.
- Fossil Industry and Respiratory Societies: Time for a Clear Stand.Piccari L, Kaminski N, Mann ME. Am J Respir Crit Care Med. 2024 Feb 1. PMID: 37796608.
- AAV-mediated delivery of a Sleeping Beauty transposon and an mRNA-encoded transposase for the engineering of therapeutic immune cells.Ye L, Lam SZ, Yang L, Suzuki K, Zou Y, Lin Q, Zhang Y, Clark P, Peng L, Chen S. Nat Biomed Eng. 2024 Feb; 2023 Jul 10. PMID: 37430157.
- A compact regulatory RNA element in mouse Hsp70 mRNA.Wang W, Liu F, Ugalde MV, Pyle AM. NAR Mol Med. 2024 Jan; 2024 Jan 29. PMID: 38318492.
- Single-cell transcriptomic analysis of human pleura reveals stromal heterogeneity and informs in vitro models of mesothelioma.Obacz J, Valer JA, Nibhani R, Adams TS, Schupp JC, Veale N, Lewis-Wade A, Flint J, Hogan J, Aresu G, Coonar AS, Peryt A, Biffi G, Kaminski N, Francies H, Rassl DM, Garnett MJ, Rintoul RC, Marciniak SJ. Eur Respir J. 2024 Jan; 2024 Jan 25. PMID: 38212075.
- tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut.Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard RJ, Gabir H, Patel TR, Stetefeld J, Puglisi J, Söll D. Nucleic Acids Res. 2024 Jan 25. PMID: 38100361.
- Virology-the path forward.Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu S-L, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O'Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A. J Virol. 2024 Jan 23; 2024 Jan 3. PMID: 38168672.
- The FANCI/FANCD2 complex links DNA damage response to R-loop regulation through SRSF1-mediated mRNA export.Olazabal-Herrero A, He B, Kwon Y, Gupta AK, Dutta A, Huang Y, Boddu P, Liang Z, Liang F, Teng Y, Lan L, Chen X, Pei H, Pillai MM, Sung P, Kupfer GM. Cell Rep. 2024 Jan 23; 2024 Jan 1. PMID: 38165804.
- scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding.Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. Brief Bioinform. 2024 Jan 22. PMID: 38493342.
- Binding profiles for 954 Drosophila and C. elegans transcription factors reveal tissue specific regulatory relationships.Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH. bioRxiv. 2024 Jan 20; 2024 Jan 20. PMID: 38293065.
- Transcription regulation by long non-coding RNAs: mechanisms and disease relevance.Ferrer J, Dimitrova N. Nat Rev Mol Cell Biol. 2024 Jan 19; 2024 Jan 19. PMID: 38242953.
- Local and dynamic regulation of neuronal glycolysis in vivo.Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Gonzalez IJ, Hammarlund M, Hyman AA, Stork PJS, Goodman RH, Colón-Ramos DA. Proc Natl Acad Sci U S A. 2024 Jan 16; 2024 Jan 10. PMID: 38198527.
- Spartin-mediated lipid transfer facilitates lipid droplet turnover.Wan N, Hong Z, Parson MAH, Korfhage JL, Burke JE, Melia TJ, Reinisch KM. Proc Natl Acad Sci U S A. 2024 Jan 16; 2024 Jan 8. PMID: 38190532.
- Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis.Leavy OC, Goemans AF, Stockwell AD, Allen RJ, Guillen-Guio B, Hernandez-Beeftink T, Adegunsoye A, Booth HL, Cullinan P, Fahy WA, Fingerlin TE, Virk HS, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, Kaminski N, Ma SF, McAnulty RJ, Sheng XR, Millar AB, Molina-Molina M, Navaratnam V, Neighbors M, Parfrey H, Saini G, Sayers I, Strek ME, Tobin MD, Whyte MK, Zhang Y, Maher TM, Molyneaux PL, Oldham JM, Yaspan BL, Flores C, Martinez F, Reynolds CJ, Schwartz DA, Noth I, Jenkins RG, Wain LV. medRxiv. 2024 Jan 15; 2024 Jan 15. PMID: 38293162.
- Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy.Verma N, Renauer PA, Dong C, Xin S, Lin Q, Zhang F, Glazer PM, Chen S. bioRxiv. 2024 Jan 15; 2024 Jan 15. PMID: 38293095.
- Impact of COVID-19 vaccination on symptoms and immune phenotypes in vaccine-naïve individuals with Long COVID.Grady CB, Bhattacharjee B, Silva J, Jaycox J, Lee LW, Monteiro VS, Sawano M, Massey D, Caraballo C, Gehlhausen JR, Tabachnikova A, Mao T, Lucas C, Peña-Hernandez MA, Xu L, Tzeng TJ, Takahashi T, Herrin J, Güthe DB, Akrami A, Assaf G, Davis H, Harris K, McCorkell L, Schulz WL, Grffin D, Wei H, Ring AM, Guan L, Cruz CD, Iwasaki A, Krumholz HM. medRxiv. 2024 Jan 12; 2024 Jan 12. PMID: 38260484.
- Circulating NK cells establish tissue residency upon acute infection of skin and mediate accelerated effector responses to secondary infection.Torcellan T, Friedrich C, Doucet-Ladevèze R, Ossner T, Solé VV, Riedmann S, Ugur M, Imdahl F, Rosshart SP, Arnold SJ, Gomez de Agüero M, Gagliani N, Flavell RA, Backes S, Kastenmüller W, Gasteiger G. Immunity. 2024 Jan 9; 2023 Dec 28. PMID: 38157853.
- Organ Boundary Circuits Regulate Sox9+ Alveolar Tuft Cells During Post-Pneumonectomy Lung Regeneration.Obata T, Mizoguchi S, Greaney AM, Adams T, Yuan Y, Edelstein S, Leiby KL, Rivero R, Wang N, Kim H, Yang J, Schupp JC, Stitelman D, Tsuchiya T, Levchenko A, Kaminski N, Niklason LE, Brickman Raredon MS. bioRxiv. 2024 Jan 8; 2024 Jan 8. PMID: 38260691.
- Dysregulation of alternative splicing in spinocerebellar ataxia type 1.Olmos V, Thompson EN, Gogia N, Luttik K, Veeranki V, Ni L, Sim S, Chen K, Krause DS, Lim J. Hum Mol Genet. 2024 Jan 7. PMID: 37802886.
- Dynamic metabolism of endothelial triglycerides protects against atherosclerosis in mice.Boutagy NE, Gamez-Mendez A, Fowler JW, Zhang H, Chaube BK, Esplugues E, Kuo A, Lee S, Horikami D, Zhang J, Citrin KM, Singh AK, Coon BG, Lee MY, Suarez Y, Fernandez-Hernando C, Sessa WC. J Clin Invest. 2024 Jan 4; 2024 Jan 4. PMID: 38175710.
- Increased expression of CXCL6 in secretory cells drives fibroblast collagen synthesis and is associated with increased mortality in idiopathic pulmonary fibrosis.Bahudhanapati H, Tan J, Apel RM, Seeliger B, Schupp J, Li X, Sullivan DI, Sembrat J, Rojas M, Tabib T, Valenzi E, Lafyatis R, Mitash N, Hernandez Pineda R, Jawale C, Peroumal D, Biswas P, Tedrow J, Adams T, Kaminski N, Wuyts WA, McDyer JF, Gibson KF, Alder JK, Königshoff M, Zhang Y, Nouraie M, Prasse A, Kass DJ. Eur Respir J. 2024 Jan; 2024 Jan 4. PMID: 37918852.
- Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Nat Commun. 2024 Jan 3; 2024 Jan 3. PMID: 38172101.
- How cell biology can save the planet.Neugebauer KM. Nat Cell Biol. 2024 Jan. PMID: 38228830.
- A multicenter phase Ib trial of the histone deacetylase inhibitor entinostat in combination with pembrolizumab in patients with myelodysplastic syndromes/neoplasms or acute myeloid leukemia refractory to hypomethylating agents.Bewersdorf JP, Shallis RM, Sharon E, Park S, Ramaswamy R, Roe CE, Irish JM, Caldwell A, Wei W, Yacoub A, Madanat YF, Zeidner JF, Altman JK, Odenike O, Yerrabothala S, Kovacsovics T, Podoltsev NA, Halene S, Little RF, Piekarz R, Gore SD, Kim TK, Zeidan AM. Ann Hematol. 2024 Jan; 2023 Dec 1. PMID: 38036712.
- Harnessing the effects of hypoxia-like inhibition on homology-directed DNA repair.Altwerger G, Ghazarian M, Glazer PM. Semin Cancer Biol. 2024 Jan; 2023 Nov 28. PMID: 38029867.
- Guidelines on the use of sex and gender in cardiovascular research.Usselman CW, Lindsey ML, Robinson AT, Habecker BA, Taylor CE, Merryman WD, Kimmerly D, Bender JR, Regensteiner JG, Moreau KL, Pilote L, Wenner MM, O'Brien M, Yarovinsky TO, Stachenfeld NS, Charkoudian N, Denfeld QE, Moreira-Bouchard JD, Pyle WG, DeLeon-Pennell KY. Am J Physiol Heart Circ Physiol. 2024 Jan 1; 2023 Nov 24. PMID: 37999647.
- Bioactive signalling lipids as drivers of chronic liver diseases.Kaffe E, Tisi A, Magkrioti C, Aidinis V, Mehal WZ, Flavell RA, Maccarrone M. J Hepatol. 2024 Jan; 2023 Sep 21. PMID: 37741346.
2023
- A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.Salvail H, Balaji A, Roth A, Breaker RR. Cell Rep. 2023 Dec 26; 2023 Dec 12. PMID: 38096053.
- Differences in syncytia formation by SARS-CoV-2 variants modify host chromatin accessibility and cellular senescence via TP53.Lee JD, Menasche BL, Mavrikaki M, Uyemura MM, Hong SM, Kozlova N, Wei J, Alfajaro MM, Filler RB, Müller A, Saxena T, Posey RR, Cheung P, Muranen T, Heng YJ, Paulo JA, Wilen CB, Slack FJ. Cell Rep. 2023 Dec 26; 2023 Nov 21. PMID: 37991919.
- piRNA generation is associated with the pioneer round of translation in stem cells.Allikka Parambil S, Li D, Zelko M, Poulet A, van Wolfswinkel JC. Nucleic Acids Res. 2023 Dec 24; 2023 Dec 24. PMID: 38142432.
- A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus.Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T Jr, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. Brain. 2023 Dec 21; 2023 Dec 21. PMID: 38128548.
- Genome Engineering for Next-Generation Cellular Immunotherapies.Park JJ, Lee KAV, Lam SZ, Tang K, Chen S. Biochemistry. 2023 Dec 19; 2022 Aug 5. PMID: 35930700.
- Unagi: Deep Generative Model for Deciphering Cellular Dynamics and In-Silico Drug Discovery in Complex Diseases.Zheng Y, Schupp JC, Adams T, Clair G, Justet A, Ahangari F, Yan X, Hansen P, Carlon M, Cortesi E, Vermant M, Vos R, De Sadeleer LJ, Rosas IO, Pineda R, Sembrat J, Königshoff M, McDonough JE, Vanaudenaerde BM, Wuyts WA, Kaminski N, Ding J. Res Sq. 2023 Dec 18; 2023 Dec 18. PMID: 38196613.
- Distinct hypoxia-induced translational profiles of embryonic and adult-derived macrophages.Wilcox NS, Yarovinsky TO, Pandya P, Ramgolam VS, Moro A, Wu Y, Nicoli S, Hirschi KK, Bender JR. iScience. 2023 Dec 15; 2023 Sep 21. PMID: 38047075.
- Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases.Emani PS, Geradi MN, Gürsoy G, Grasty MR, Miranker A, Gerstein MB. Genome Res. 2023 Dec 14; 2023 Dec 14. PMID: 38097386.
- Suppression of angiopoietin-like 4 reprograms endothelial cell metabolism and inhibits angiogenesis.Chaube B, Citrin KM, Sahraei M, Singh AK, de Urturi DS, Ding W, Pierce RW, Raaisa R, Cardone R, Kibbey R, Fernández-Hernando C, Suárez Y. Nat Commun. 2023 Dec 12; 2023 Dec 12. PMID: 38086791.
- Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species.Asin-Garcia E, Garcia-Morales L, Bartholet T, Liang Z, Isaacs FJ, Martins Dos Santos VAP. Nucleic Acids Res. 2023 Dec 11. PMID: 37941137.
- Approaches to pandemic prevention - the chromatin vaccine.Zhang J, Askenase P, Jaenisch R, Crumpacker CS. Front Immunol. 2023; 2023 Dec 8. PMID: 38143744.
- Human-specific features and developmental dynamics of the brain N-glycome.Klarić TS, Gudelj I, Santpere G, Novokmet M, Vučković F, Ma S, Doll HM, Risgaard R, Bathla S, Karger A, Nairn AC, Luria V, Bečeheli I, Sherwood CC, Ely JJ, Hof PR, Sousa AMM, Josić D, Lauc G, Sestan N. Sci Adv. 2023 Dec 8; 2023 Dec 6. PMID: 38055821.
- Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses.Ramos Zapatero M, Tong A, Opzoomer JW, O'Sullivan R, Cardoso Rodriguez F, Sufi J, Vlckova P, Nattress C, Qin X, Claus J, Hochhauser D, Krishnaswamy S, Tape CJ. Cell. 2023 Dec 7. PMID: 38065081.
- hMG addition affects the change in progesterone level during IVF stimulation and LBR: a retrospective cohort study.Wesevich VG, Seckin SI, Kelk DA, Kallen AN, Kodaman PH. Reprod Biol Endocrinol. 2023 Dec 6; 2023 Dec 6. PMID: 38057813.
- Splicing under stress: A matter of time and place.Podszywalow-Bartnicka P, Neugebauer KM. J Cell Biol. 2023 Dec 4; 2023 Nov 21. PMID: 37988026.
- Hemodynamics regulate spatiotemporal artery muscularization in the developing circle of Willis.Cheng S, Xia IF, Wanner R, Abello J, Stratman AN, Nicoli S. bioRxiv. 2023 Dec 2; 2023 Dec 2. PMID: 38077062.
- Examination of eQTL Polymorphisms Associated with Increased Risk of Progressive Complicated Sarcoidosis in European and African Descent Subjects.Casanova NG, Camp SM, Gonzalez-Garay ML, Batai K, Garman L, Montgomery CG, Ellis N, Kittles R, Bime C, Hsu AP, Holland S, Lussier YA, Karnes J, Sweiss N, Maier LA, Koth L, Moller DR, Kaminski N, Garcia JGN. Eur J Respir Med. 2023 Dec. PMID: 38390497.
- Pooled screening with next-generation gene editing tools.Zhou L, Yang L, Feng Y, Chen S. Curr Opin Biomed Eng. 2023 Dec; 2023 Jun 21. PMID: 38222973.
- The H2Bub1-deposition complex is required for human and mouse cardiogenesis.Barish S, Berg K, Drozd J, Berglund-Brown I, Khizir L, Wasson LK, Seidman CE, Seidman JG, Chen S, Brueckner M. Development. 2023 Dec 1; 2023 Dec 1. PMID: 38038666.
- Structural insights into intron catalysis and dynamics during splicing.Xu L, Liu T, Chung K, Pyle AM. Nature. 2023 Dec; 2023 Nov 22. PMID: 37993708.
- Exploring novel HIV-1 reverse transcriptase inhibitors with drug-resistant mutants: A double mutant surprise.Hollander K, Chan AH, Frey KM, Hunker O, Ippolito JA, Spasov KA, Yeh YJ, Jorgensen WL, Ho YC, Anderson KS. Protein Sci. 2023 Dec. PMID: 37861472.
- Somatic Mutations: The Next Frontier in Demystifying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis?Yan X, Kaminski N. Am J Respir Crit Care Med. 2023 Dec 1. PMID: 37856835.
- Site-specific crosslinking reveals Phosphofructokinase-L inhibition drives self-assembly and attenuation of protein interactions.Sivadas A, McDonald EF, Shuster SO, Davis CM, Plate L. Adv Biol Regul. 2023 Dec; 2023 Sep 27. PMID: 37806136.
- Microproteins-Discovery, structure, and function.Mohsen JJ, Martel AA, Slavoff SA. Proteomics. 2023 Dec; 2023 Aug 21. PMID: 37603371.
- Identification and characterization of novel lineage 1 Powassan virus strains in New York State.Lange RE, Dupuis Ii AP, Prusinski MA, Maffei JG, Koetzner CA, Ngo K, Backenson B, Oliver J, Vogels CBF, Grubaugh ND, Kramer LD, Ciota AT. Emerg Microbes Infect. 2023 Dec. PMID: 36503411.
- Spartin-mediated lipid transfer facilitates lipid droplet turnover.Wan N, Hong Z, Parson MAH, Korfhage J, Burke JE, Melia TJ, Reinisch KM. bioRxiv. 2023 Nov 29; 2023 Nov 29. PMID: 38076959.
- Five questions on how biochemistry can combat climate change.Chen K, Guo Y, How K, Acosta A, Documet D, Liang C, Arul D, Wood S, Moon K, Oliver LS, Fajardo EL, Kopyto M, Shine M, Neugebauer KM. BBA Adv. 2023; 2023 Nov 22. PMID: 38075469.
- Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases.Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A. Sci Data. 2023 Nov 20; 2023 Nov 20. PMID: 37985666.
- Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations.Zhao S, Mekbib KY, van der Ent MA, Allington G, Prendergast A, Chau JE, Smith H, Shohfi J, Ocken J, Duran D, Furey CG, Hao LT, Duy PQ, Reeves BC, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu PY, Wang YC, Mane S, Piwowarczyk P, Fehnel KP, See AP, Iskandar BJ, Aagaard-Kienitz B, Moyer QJ, Dennis E, Kiziltug E, Kundishora AJ, DeSpenza T Jr, Greenberg ABW, Kidanemariam SM, Hale AT, Johnston JM, Jackson EM, Storm PB, Lang SS, Butler WE, Carter BS, Chapman P, Stapleton CJ, Patel AB, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay EZ, Zhao H, Moreno-De-Luca A, Proctor MR, Smith ER, Orbach DB, Alper SL, Nicoli S, Boggon TJ, Lifton RP, Gunel M, King PD, Jin SC, Kahle KT. Nat Commun. 2023 Nov 17; 2023 Nov 17. PMID: 37978175.
- Advancing the fitness of gut commensal bacteria.Groisman EA, Han W, Krypotou E. Science. 2023 Nov 17; 2023 Nov 16. PMID: 37972163.
- Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma.Singh AK, Chaube B, Citrin KM, Fowler JW, Lee S, Catarino J, Knight J, Lowery S, Shree S, Boutagy N, Ruz-Maldonado I, Harry K, Shanabrough M, Ross TT, Malaker S, Suárez Y, Fernández-Hernando C, Grabinska K, Sessa WC. bioRxiv. 2023 Nov 15; 2023 Nov 15. PMID: 38014178.
- Circulating Mitochondrial DNA Is Associated With High Levels of Fatigue in Two Independent Sarcoidosis Cohorts.Fiorini V, Hu B, Sun Y, Yu S, McGovern J, Gandhi S, Woo S, Turcotte-Foster SJ, Pivarnik T, Khan Z, Adams T, Herzog E, Kaminski N, Gulati M, Ryu C. Chest. 2023 Nov 15; 2023 Nov 15. PMID: 37977267.
- The neuropeptidergic connectome of C. elegans.Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM 3rd, Hobert O, Beets I, Vértes PE, Schafer WR. Neuron. 2023 Nov 15; 2023 Nov 6. PMID: 37935195.
- MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT.Araujo Tavares RC, Mahadeshwar G, Wan H, Pyle AM. J Mol Biol. 2023 Nov 15; 2023 Oct 4. PMID: 37802215.
- Endothelial nitric oxide synthase (eNOS) S1176 phosphorylation status governs atherosclerotic lesion formation.Nguyen TD, Rahman NT, Sessa WC, Lee MY. Front Cardiovasc Med. 2023; 2023 Nov 14. PMID: 38034389.
- Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence.Wei Y, Davenport TC, Collora JA, Ma HK, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho YC. Immunity. 2023 Nov 14; 2023 Nov 2. PMID: 37922905.
- Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean.Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, Grubaugh ND. medRxiv. 2023 Nov 12; 2023 Nov 12. PMID: 37986857.
- The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization.Wang W, Götte B, Guo R, Pyle AM. Nat Commun. 2023 Nov 11; 2023 Nov 11. PMID: 37951994.
- Post-Vaccination Syndrome: A Descriptive Analysis of Reported Symptoms and Patient Experiences After Covid-19 Immunization.Krumholz HM, Wu Y, Sawano M, Shah R, Zhou T, Arun AS, Khosla P, Kaleem S, Vashist A, Bhattacharjee B, Ding Q, Lu Y, Caraballo C, Warner F, Huang C, Herrin J, Putrino D, Hertz D, Dressen B, Iwasaki A. medRxiv. 2023 Nov 10; 2023 Nov 10. PMID: 37986769.
- Cancer Relevance of Circulating Antibodies Against LINE-1 Antigens in Humans.Vylegzhanina AV, Bespalov IA, Novototskaya-Vlasova KA, Hall BM, Gleiberman AS, Yu H, Leontieva OV, Leonova KI, Kurnasov OV, Osterman AL, Dy GK, Komissarov AA, Vasilieva E, Gehlhausen J, Iwasaki A, Ambrosone CB, Tsuji T, Matsuzaki J, Odunsi K, Andrianova EL, Gudkov AV. Cancer Res Commun. 2023 Nov 8. PMID: 37870410.
- Abl2 repairs microtubules and phase separates with tubulin to promote microtubule nucleation.Duan D, Lyu W, Chai P, Ma S, Wu K, Wu C, Xiong Y, Sestan N, Zhang K, Koleske AJ. Curr Biol. 2023 Nov 6; 2023 Oct 18. PMID: 37858340.
- Intrathecal delivery of nanoparticle PARP inhibitor to the cerebrospinal fluid for the treatment of metastatic medulloblastoma.Khang M, Lee JH, Lee T, Suh HW, Lee S, Cavaliere A, Rushing A, Geraldo LH, Belitzky E, Rossano S, de Feyter HM, Shin K, Huttner A, Roussel MF, Thomas JL, Carson RE, Marquez-Nostra B, Bindra RS, Saltzman WM. Sci Transl Med. 2023 Nov; 2023 Nov 1. PMID: 37910601.
- Author Correction: Regulation of CD8(+) T memory and exhaustion by the mTOR signals.Chen Y, Xu Z, Sun H, Ouyang X, Han Y, Yu H, Wu N, Xie Y, Su B. Cell Mol Immunol. 2023 Nov. PMID: 37821622.
- Distinguishing features of long COVID identified through immune profiling.Klein J, Wood J, Jaycox JR, Dhodapkar RM, Lu P, Gehlhausen JR, Tabachnikova A, Greene K, Tabacof L, Malik AA, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott IM, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng TJ, Xu L, Geraghty AC, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick JD, Kaminski N, Omer SB, Krumholz HM, Guan L, Dela Cruz CS, van Dijk D, Ring AM, Putrino D, Iwasaki A. Nature. 2023 Nov; 2023 Sep 25. PMID: 37748514.
- Classification, risk stratification and response assessment in myelodysplastic syndromes/neoplasms (MDS): A state-of-the-art report on behalf of the International Consortium for MDS (icMDS).Stahl M, Bewersdorf JP, Xie Z, Porta MGD, Komrokji R, Xu ML, Abdel-Wahab O, Taylor J, Steensma DP, Starczynowski DT, Sekeres MA, Sanz G, Sallman DA, Roboz GJ, Platzbecker U, Patnaik MM, Padron E, Odenike O, Nimer SD, Nazha A, Majeti R, Loghavi S, Little RF, List AF, Kim TK, Hourigan CS, Hasserjian RP, Halene S, Griffiths EA, Gore SD, Greenberg P, Figueroa ME, Fenaux P, Efficace F, DeZern AE, Daver NG, Churpek JE, Carraway HE, Buckstein R, Brunner AM, Boultwood J, Borate U, Bejar R, Bennett JM, Wei AH, Santini V, Savona MR, Zeidan AM. Blood Rev. 2023 Nov; 2023 Aug 19. PMID: 37704469.
- Nucleolar structure connects with global nuclear organization.Wang C, Ma H, Baserga SJ, Pederson T, Huang S. Mol Biol Cell. 2023 Nov 1; 2023 Aug 23. PMID: 37610836.
- Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition.Saffer AM, Baskin TI, Verma A, Stanislas T, Oldenbourg R, Irish VF. Plant J. 2023 Nov; 2023 Aug 7. PMID: 37548081.
- Applications of CRISPR technology in cellular immunotherapy.Zhou X, Renauer PA, Zhou L, Fang SY, Chen S. Immunol Rev. 2023 Nov; 2023 Jul 14. PMID: 37449673.
- Mitochondrial DNA and the STING pathway are required for hepatic stellate cell activation.Arumugam S, Li B, Boodapati SLT, Nathanson MH, Sun B, Ouyang X, Mehal WZ. Hepatology. 2023 Nov 1; 2023 Apr 5. PMID: 37013923.
- An integrated platform for high-throughput nanoscopy.Barentine AES, Lin Y, Courvan EM, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace MR, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer KM, Bewersdorf J, Baddeley D. Nat Biotechnol. 2023 Nov; 2023 Mar 13. PMID: 36914886.
- StrokeClassifier: Ischemic Stroke Etiology Classification by Ensemble Consensus Modeling Using Electronic Health Records.Lee HJ, Schwamm LH, Sansing L, Kamel H, de Havenon A, Turner AC, Sheth KN, Krishnaswamy S, Brandt C, Zhao H, Krumholz H, Sharma R. Res Sq. 2023 Oct 31; 2023 Oct 31. PMID: 37961532.
- Developing synthetic tools to decipher the tumor-immune interactome.Weizman OE, Luyten S, Lu P, Song E, Qin K, Mostaghimi D, Ring AM, Iwasaki A. Proc Natl Acad Sci U S A. 2023 Oct 31; 2023 Oct 23. PMID: 37871202.
- ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m(6)A modification-mediated RNA stability control.Gao Y, Zimmer JT, Vasic R, Liu C, Gbyli R, Zheng SJ, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao AZ, Slavoff S, Kibbey RG, Flavell RA, Simon MD, Tebaldi T, Li HB, Halene S. Cell Rep. 2023 Oct 31; 2023 Sep 23. PMID: 37742191.
- Structural basis for translation inhibition by MERS-CoV Nsp1 reveals a conserved mechanism for betacoronaviruses.Devarkar SC, Vetick M, Balaji S, Lomakin IB, Yang L, Jin D, Gilbert WV, Chen S, Xiong Y. Cell Rep. 2023 Oct 31; 2023 Sep 19. PMID: 37733586.
- Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects.Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. BMC Bioinformatics. 2023 Oct 19; 2023 Oct 19. PMID: 37858060.
- Head-to-head comparison of in vitro and in vivo efficacy of pHLIP-conjugated anti-seed gamma peptide nucleic acids.Dhuri K, Duran T, Chaudhuri B, Slack FJ, Vikram A, Glazer PM, Bahal R. Cell Rep Phys Sci. 2023 Oct 18; 2023 Sep 15. PMID: 38144419.
- DNA recognition and induced genome modification by a hydroxymethyl-γ tail-clamp peptide nucleic acid.Oyaghire SN, Quijano E, Perera JDR, Mandl HK, Saltzman WM, Bahal R, Glazer PM. Cell Rep Phys Sci. 2023 Oct 18. PMID: 37920723.
- The SMN complex drives structural changes in human snRNAs to enable snRNP assembly.Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. Nat Commun. 2023 Oct 18; 2023 Oct 18. PMID: 37852981.
- Mucosal immune alterations at the early onset of tissue destruction in chronic obstructive pulmonary disease.de Fays C, Geudens V, Gyselinck I, Kerckhof P, Vermaut A, Goos T, Vermant M, Beeckmans H, Kaes J, Van Slambrouck J, Mohamady Y, Willems L, Aversa L, Cortesi EE, Hooft C, Aerts G, Aelbrecht C, Everaerts S, McDonough JE, De Sadeleer LJ, Gohy S, Ambroise J, Janssens W, Ceulemans LJ, Van Raemdonck D, Vos R, Hackett TL, Hogg JC, Kaminski N, Gayan-Ramirez G, Pilette C, Vanaudenaerde BM. Front Immunol. 2023; 2023 Oct 17. PMID: 37915582.
- Sequence-independent activity of a predicted long disordered segment of the human papillomavirus type 16 L2 capsid protein during virus entry.Oh C, Buckley PM, Choi J, Hierro A, DiMaio D. Proc Natl Acad Sci U S A. 2023 Oct 17; 2023 Oct 11. PMID: 37819982.
- Assessing the global risk of typhoid outbreaks caused by extensively drug resistant Salmonella Typhi.Walker J, Chaguza C, Grubaugh ND, Carey M, Baker S, Khan K, Bogoch II, Pitzer VE. Nat Commun. 2023 Oct 16; 2023 Oct 16. PMID: 37845201.
- Rational design of the genetic code expansion toolkit for in vivo encoding of D-amino acids.Jiang HK, Weng JH, Wang YH, Tsou JC, Chen PJ, Ko AA, Söll D, Tsai MD, Wang YS. Front Genet. 2023; 2023 Oct 13. PMID: 37904728.
- DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus.Vogels CBF, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Morrison AM, Michael SF, Grubaugh ND. medRxiv. 2023 Oct 13; 2023 Oct 13. PMID: 37873191.
- Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon.Micali N, Ma S, Li M, Kim SK, Mato-Blanco X, Sindhu SK, Arellano JI, Gao T, Shibata M, Gobeske KT, Duque A, Santpere G, Sestan N, Rakic P. Science. 2023 Oct 13; 2023 Oct 13. PMID: 37824652.
- A kinesin-1 adaptor complex controls bimodal slow axonal transport of spectrin in Caenorhabditis elegans.Glomb O, Swaim G, Munoz LLancao P, Lovejoy C, Sutradhar S, Park J, Wu Y, Cason SE, Holzbaur ELF, Hammarlund M, Howard J, Ferguson SM, Gramlich MW, Yogev S. Dev Cell. 2023 Oct 9; 2023 Sep 25. PMID: 37751746.
- Oleic acid differentially affects de novo lipogenesis in adipocytes and hepatocytes.Castillo HB, Shuster SO, Tarekegn LH, Davis CM. bioRxiv. 2023 Oct 6; 2023 Oct 6. PMID: 37873279.
- Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy.Poulet A, Kratkiewicz AJ, Li D, van Wolfswinkel JC. Sci Adv. 2023 Oct 6; 2023 Oct 6. PMID: 37801496.
- Viral kinetics of sequential SARS-CoV-2 infections.Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad YH. Nat Commun. 2023 Oct 5; 2023 Oct 5. PMID: 37798265.
- Allosteric inhibition of the T cell receptor by a designed membrane ligand.Ye Y, Morita S, Chang JJ, Buckley PM, Wilhelm KB, DiMaio D, Groves JT, Barrera FN. Elife. 2023 Oct 5; 2023 Oct 5. PMID: 37796108.
- 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage.Hamal Dhakal S, Kavita K, Panchapakesan SSS, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2023 Oct 3; 2023 Sep 25. PMID: 37748066.
- Acetyl-methyllysine marks chromatin at active transcription start sites.Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Machyna M, Pintado-Urbanc AP, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD. Nature. 2023 Oct; 2023 Sep 20. PMID: 37731000.
- Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC).Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ. Nat Immunol. 2023 Oct. PMID: 37723351.
- A cross-species proteomic map reveals neoteny of human synapse development.Wang L, Pang K, Zhou L, Cebrián-Silla A, González-Granero S, Wang S, Bi Q, White ML, Ho B, Li J, Li T, Perez Y, Huang EJ, Winkler EA, Paredes MF, Kovner R, Sestan N, Pollen AA, Liu P, Li J, Piao X, García-Verdugo JM, Alvarez-Buylla A, Liu Z, Kriegstein AR. Nature. 2023 Oct; 2023 Sep 13. PMID: 37704727.
- SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC).Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ. Nat Immunol. 2023 Oct; 2023 Sep 4. PMID: 37667052.
- Alveolar Vascular Remodeling in Nonspecific Interstitial Pneumonia: Replacement of Normal Lung Capillaries with COL15A1-Positive Endothelial Cells.Schupp JC, Manning EP, Chioccioli M, Kamp JC, Christian L, Ryu C, Herzog E, Kühnel MP, Prasse A, Kaminski N, Jonigk DD, Homer RJ. Am J Respir Crit Care Med. 2023 Oct 1. PMID: 37552025.
- Advancing evolution: Bacteria break down gene silencer to express horizontally acquired genes.Groisman EA, Choi J. Bioessays. 2023 Oct; 2023 Aug 3. PMID: 37533411.
- Natural killer cell-mediated contact dermatitis-like reaction induced by treatment with TLR3 ligand poly(I:C).Majewska-Szczepanik M, Kowalczyk P, Askenase PW, Szczepanik M. Contact Dermatitis. 2023 Oct; 2023 Jul 18. PMID: 37463838.
- Activation of Platelet mTORC2/Akt Pathway by Anti-β2GP1 Antibody Promotes Thrombosis in Antiphospholipid Syndrome.Tang Z, Shi H, Chen C, Teng J, Dai J, Ouyang X, Liu H, Hu Q, Cheng X, Ye J, Su Y, Sun Y, Pan H, Wang X, Liu J, Su B, Yang C, Xu Y, Liu T. Arterioscler Thromb Vasc Biol. 2023 Oct; 2023 Jun 29. PMID: 37381985.
- Against the Waves: Blocking the EB3-IP3 Interaction Inhibits Calcium Waves in the Lung Endothelium.Takyar SS. Am J Respir Cell Mol Biol. 2023 Oct. PMID: 37348847.
- Microfluidic Immuno-Serolomic Assay Reveals Systems Level Association with COVID-19 Pathology and Vaccine Protection.Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Small Methods. 2023 Oct; 2023 Jun 13. PMID: 37312418.
- Genetic analyses of chr11p15.5 region identify MUC5AC-MUC5B associated with asthma-related phenotypes.Li X, Li H, Christenson SA, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston BM, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Bleecker ER, Meyers DA. J Asthma. 2023 Oct; 2023 Apr 21. PMID: 36946148.
- High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. Nat Biotechnol. 2023 Oct; 2023 Feb 23. PMID: 36823353.
- Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB.Munir M, Embry A, Doench JG, Heaton NS, Wilen CB, Orchard RC. bioRxiv. 2023 Sep 29; 2023 Sep 29. PMID: 37808733.
- Developing Phage Therapy That Overcomes the Evolution of Bacterial Resistance.Oromí-Bosch A, Antani JD, Turner PE. Annu Rev Virol. 2023 Sep 29; 2023 Jun 2. PMID: 37268007.
- Astrovirus replication is dependent on induction of double-membrane vesicles through a PI3K-dependent, LC3-independent pathway.Bub T, Hargest V, Tan S, Smith M, Vazquez-Pagan A, Flerlage T, Brigleb P, Meliopoulos V, Lindenbach B, Ramanathan HN, Cortez V, Crawford JC, Schultz-Cherry S. J Virol. 2023 Sep 28; 2023 Sep 5. PMID: 37668367.
- Survey of white-footed mice in Connecticut, USA reveals low SARS-CoV-2 seroprevalence and infection with divergent betacoronaviruses.Earnest R, Hahn AM, Feriancek NM, Brandt M, Filler RB, Zhao Z, Breban MI, Vogels CBF, Chen NFG, Koch RT, Porzucek AJ, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber HR, Cantoni JL, Pitzer VE, Olarte Castillo XA, Goodman LB, Wilen CB, Linske MA, Williams SC, Grubaugh ND. bioRxiv. 2023 Sep 27; 2023 Sep 27. PMID: 37808797.
- GEODESIC SINKHORN FOR FAST AND ACCURATE OPTIMAL TRANSPORT ON MANIFOLDS.Huguet G, Tong A, Zapatero MR, Tape CJ, Wolf G, Krishnaswamy S. ArXiv. 2023 Sep 26; 2023 Sep 26. PMID: 37808090.
- Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5.Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh KH, Halaban R, Wang Z, Cao X, Slavoff SA. Cell Rep. 2023 Sep 26; 2023 Sep 19. PMID: 37725512.
- Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans.Khazma T, Grossman A, Guez-Haddad J, Feng C, Dabas H, Sain R, Weitman M, Zalk R, Isupov MN, Hammarlund M, Hons M, Opatowsky Y. Cell Rep. 2023 Sep 26; 2023 Aug 26. PMID: 37635352.
- How Bacterial Pathogens Coordinate Appetite with Virulence.Pokorzynski ND, Groisman EA. Microbiol Mol Biol Rev. 2023 Sep 26; 2023 Jun 26. PMID: 37358444.
- Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior.Kochersberger A, Torkashvand MM, Lee D, Baskoylu S, Sengupta T, Koonce N, Emerson CE, Patel NV, Colón-Ramos D, Flavell S, Horvitz HR, Venkatachalam V, Hammarlund M. bioRxiv. 2023 Sep 25; 2023 Sep 25. PMID: 37745399.
- MicroRNA-1 protects the endothelium in acute lung injury.Korde A, Haslip M, Pednekar P, Khan A, Chioccioli M, Mehta S, Lopez-Giraldez F, Bermejo S, Rojas M, Dela Cruz C, Matthay MA, Pober JS, Pierce RW, Takyar SS. JCI Insight. 2023 Sep 22; 2023 Sep 22. PMID: 37737266.
- SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis.Barbayianni I, Kanellopoulou P, Fanidis D, Nastos D, Ntouskou ED, Galaris A, Harokopos V, Hatzis P, Tsitoura E, Homer R, Kaminski N, Antoniou KM, Crestani B, Tzouvelekis A, Aidinis V. Nat Commun. 2023 Sep 21; 2023 Sep 21. PMID: 37735172.
- Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions.Sivadas A, McDonald EF, Shuster SO, Davis CM, Plate L. bioRxiv. 2023 Sep 20; 2023 Sep 20. PMID: 37781627.
- TNFα increases the degradation of pyruvate dehydrogenase kinase 4 by the Lon protease to support proinflammatory genes.Boutagy NE, Fowler JW, Grabinska KA, Cardone R, Sun Q, Vazquez KR, Whalen MB, Zhu X, Chakraborty R, Martin KA, Simons M, Romanoski CE, Kibbey RG, Sessa WC. Proc Natl Acad Sci U S A. 2023 Sep 19; 2023 Sep 11. PMID: 37695914.
- Resisting efficiency's overreachOptimal Illusions: The False Promise of Optimization Coco Krumme Riverhead Books, 2023. 256 pp.Greenbaum D, Gerstein M. Science. 2023 Sep 15; 2023 Sep 14. PMID: 37708273.
- IFN-λ derived from nonsusceptible enterocytes acts on tuft cells to limit persistent norovirus.Ingle H, Makimaa H, Aggarwal S, Deng H, Foster L, Li Y, Kennedy EA, Peterson ST, Wilen CB, Lee S, Suthar MS, Baldridge MT. Sci Adv. 2023 Sep 15; 2023 Sep 13. PMID: 37703370.
- In Silico Discovery of Group II Intron RNA Splicing Inhibitors.Fedorova O, Arhin G, Pyle AM, Frank AT. ACS Chem Biol. 2023 Sep 15; 2023 Aug 21. PMID: 37602469.
- When Development of the Alveolar Gas Exchange Unit Fails: Universal Single-Cell Lessons from Rare Monogenic Disorders.Schupp JC, Kaminski N. Am J Respir Crit Care Med. 2023 Sep 15. PMID: 37555730.
- Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models.Perry ZR, Pyle AM, Zhang C. J Mol Biol. 2023 Sep 15; 2023 Jul 20. PMID: 37479079.
- New insights into programmed cell death protein 1 blockade-associated cutaneous immune-related adverse events.Micevic G, Daniels A, Flavell RA. Br J Dermatol. 2023 Sep 15. PMID: 37471669.
- Noncanonical Rab9a action supports retromer-mediated endosomal exit of human papillomavirus during virus entry.Choi J, DiMaio D. PLoS Pathog. 2023 Sep; 2023 Sep 13. PMID: 37703297.
- IL-6 trans-signaling in a humanized mouse model of scleroderma.Odell ID, Agrawal K, Sefik E, Odell AV, Caves E, Kirkiles-Smith NC, Horsley V, Hinchcliff M, Pober JS, Kluger Y, Flavell RA. Proc Natl Acad Sci U S A. 2023 Sep 12; 2023 Sep 5. PMID: 37669366.
- Phase separation and pathologic transitions of RNP condensates in neurons: implications for amyotrophic lateral sclerosis, frontotemporal dementia and other neurodegenerative disorders.Naskar A, Nayak A, Salaikumaran MR, Vishal SS, Gopal PP. Front Mol Neurosci. 2023; 2023 Sep 1. PMID: 37720552.
- Lipid scrambling is a general feature of protein insertases.Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. bioRxiv. 2023 Sep 1; 2023 Sep 1. PMID: 37693532.
- Regulation of CD8(+) T memory and exhaustion by the mTOR signals.Chen Y, Xu Z, Sun H, Ouyang X, Han Y, Yu H, Wu N, Xie Y, Su B. Cell Mol Immunol. 2023 Sep; 2023 Aug 15. PMID: 37582972.
- Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels.Wong M, Wei Y, Ho YC. Curr Opin HIV AIDS. 2023 Sep 1; 2023 Jul 17. PMID: 37535039.
- CTLA-4 tail fusion enhances CAR-T antitumor immunity.Zhou X, Cao H, Fang SY, Chow RD, Tang K, Majety M, Bai M, Dong MB, Renauer PA, Shang X, Suzuki K, Levchenko A, Chen S. Nat Immunol. 2023 Sep; 2023 Jul 27. PMID: 37500885.
- Evidence that OLE RNA is a component of a major stress-responsive ribonucleoprotein particle in extremophilic bacteria.Breaker RR, Harris KA, Lyon SE, Wencker FDR, Fernando CM. Mol Microbiol. 2023 Sep; 2023 Jul 20. PMID: 37469248.
- Recoding UAG to selenocysteine in Saccharomyces cerevisiae.Hoffman KS, Chung CZ, Mukai T, Krahn N, Jiang HK, Balasuriya N, O'Donoghue P, Söll D. RNA. 2023 Sep; 2023 Jun 6. PMID: 37279998.
- Evaluation of Plasma Biomarkers to Predict Major Adverse Kidney Events in Hospitalized Patients With COVID-19.Menez S, Coca SG, Moledina DG, Wen Y, Chan L, Thiessen-Philbrook H, Obeid W, Garibaldi BT, Azeloglu EU, Ugwuowo U, Sperati CJ, Arend LJ, Rosenberg AZ, Kaushal M, Jain S, Wilson FP, Parikh CR. Am J Kidney Dis. 2023 Sep; 2023 May 30. PMID: 37263570.
- Massively parallel knock-in engineering of human T cells.Dai X, Park JJ, Du Y, Na Z, Lam SZ, Chow RD, Renauer PA, Gu J, Xin S, Chu Z, Liao C, Clark P, Zhao H, Slavoff S, Chen S. Nat Biotechnol. 2023 Sep; 2023 Jan 26. PMID: 36702900.
- Leveraging insect-specific viruses to elucidate mosquito population structure and dynamics.Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC. PLoS Pathog. 2023 Aug; 2023 Aug 31. PMID: 37651317.
- Humanized mouse liver reveals endothelial control of essential hepatic metabolic functions.Kaffe E, Roulis M, Zhao J, Qu R, Sefik E, Mirza H, Zhou J, Zheng Y, Charkoftaki G, Vasiliou V, Vatner DF, Mehal WZ, Yuval Kluger, Flavell RA. Cell. 2023 Aug 31; 2023 Aug 9. PMID: 37562401.
- An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model.Charkoftaki G, Aalizadeh R, Santos-Neto A, Tan WY, Davidson EA, Nikolopoulou V, Wang Y, Thompson B, Furnary T, Chen Y, Wunder EA, Coppi A, Schulz W, Iwasaki A, Pierce RW, Cruz CSD, Desir GV, Kaminski N, Farhadian S, Veselkov K, Datta R, Campbell M, Thomaidis NS, Ko AI, Thompson DC, Vasiliou V. Hum Genomics. 2023 Aug 29; 2023 Aug 29. PMID: 37641126.
- Editorial: Extracellular vesicles as potent modulators of immunity.Bryniarski K, Fernández-Messina L, Askenase PW, Nazimek K. Front Cell Dev Biol. 2023; 2023 Aug 28. PMID: 37701783.
- Local and dynamic regulation of neuronal glycolysis in vivo.Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Hammarlund M, Hyman A, Stork PJ, Goodman R, Colón-Ramos DA. bioRxiv. 2023 Aug 26; 2023 Aug 26. PMID: 37662365.
- Insights in piRNA targeting rules.van Wolfswinkel JC. Wiley Interdiscip Rev RNA. 2023 Aug 26; 2023 Aug 26. PMID: 37632327.
- iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects.Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. BMC Bioinformatics. 2023 Aug 22; 2023 Aug 22. PMID: 37608264.
- Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ. Mol Cell. 2023 Aug 17. PMID: 37595555.
- Polymer nanoparticles deliver mRNA to the lung for mucosal vaccination.Suberi A, Grun MK, Mao T, Israelow B, Reschke M, Grundler J, Akhtar L, Lee T, Shin K, Piotrowski-Daspit AS, Homer RJ, Iwasaki A, Suh HW, Saltzman WM. Sci Transl Med. 2023 Aug 16; 2023 Aug 16. PMID: 37585505.
- ATG2A-mediated bridge-like lipid transport regulates lipid droplet accumulation.Korfhage JL, Wan N, Elhan H, Kauffman L, Pineda M, Fuller DM, Thiam AR, Reinisch KM, Melia TJ. bioRxiv. 2023 Aug 14; 2023 Aug 14. PMID: 37645754.
- Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer.de Miguel FJ, Gentile C, Feng WW, Silva SJ, Sankar A, Exposito F, Cai WL, Melnick MA, Robles-Oteiza C, Hinkley MM, Tsai JA, Hartley AV, Wei J, Wurtz A, Li F, Toki MI, Rimm DL, Homer R, Wilen CB, Xiao AZ, Qi J, Yan Q, Nguyen DX, Jänne PA, Kadoch C, Politi KA. Cancer Cell. 2023 Aug 14; 2023 Aug 3. PMID: 37541244.
- Integrative genetic and genomic networks identify microRNA associated with COPD and ILD.Pavel AB, Garrison C, Luo L, Liu G, Taub D, Xiao J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Geraci MW, Sciurba F, Schwartz DA, Kaminski N, Beane J, Spira A, Lenburg ME, Campbell JD. Sci Rep. 2023 Aug 11; 2023 Aug 11. PMID: 37567908.
- Machine-guided design of synthetic cell type-specific cis-regulatory elements.Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. bioRxiv. 2023 Aug 9; 2023 Aug 9. PMID: 37609287.
- Immunogenetic Metabolomics Reveals Key Enzymes That Modulate CAR T-cell Metabolism and Function.Renauer P, Park JJ, Bai M, Acosta A, Lee WH, Lin GH, Zhang Y, Dai X, Wang G, Errami Y, Wu T, Clark P, Ye L, Yang Q, Chen S. Cancer Immunol Res. 2023 Aug 3. PMID: 37253111.
- Reproductive and Fertility Knowledge and Attitudes Among Transgender and Gender-Expansive Youth: A Replication and Extension.Halloran J, Smidt AM, Morrison A, Cron J, Kallen AN, Olezeski CL. Transgend Health. 2023 Aug; 2023 Jul 28. PMID: 37525841.
- Haematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic endothelium.Ghersi JJ, Baldissera G, Hintzen J, Luff SA, Cheng S, Xia IF, Sturgeon CM, Nicoli S. Nat Cell Biol. 2023 Aug; 2023 Jul 17. PMID: 37460694.
- Rational nanoparticle design: Optimization using insights from experiments and mathematical models.Richfield O, Piotrowski-Daspit AS, Shin K, Saltzman WM. J Control Release. 2023 Aug; 2023 Jul 22. PMID: 37442201.
- SREBP2 regulates the endothelial response to cytokines via direct transcriptional activation of KLF6.Fowler JWM, Boutagy NE, Zhang R, Horikami D, Whalen MB, Romanoski CE, Sessa WC. J Lipid Res. 2023 Aug; 2023 Jul 10. PMID: 37437844.
- Assay optimization for the objective quantification of human multilineage colony-forming units.Thompson EN, Carlino MJ, Scanlon VM, Grimes HL, Krause DS. Exp Hematol. 2023 Aug; 2023 Jun 2. PMID: 37271449.
- Intestinal B cells license metabolic T-cell activation in NASH microbiota/antigen-independently and contribute to fibrosis by IgA-FcR signalling.Kotsiliti E, Leone V, Schuehle S, Govaere O, Li H, Wolf MJ, Horvatic H, Bierwirth S, Hundertmark J, Inverso D, Zizmare L, Sarusi-Portuguez A, Gupta R, O'Connor T, Giannou AD, Shiri AM, Schlesinger Y, Beccaria MG, Rennert C, Pfister D, Öllinger R, Gadjalova I, Ramadori P, Rahbari M, Rahbari N, Healy ME, Fernández-Vaquero M, Yahoo N, Janzen J, Singh I, Fan C, Liu X, Rau M, Feuchtenberger M, Schwaneck E, Wallace SJ, Cockell S, Wilson-Kanamori J, Ramachandran P, Kho C, Kendall TJ, Leblond AL, Keppler SJ, Bielecki P, Steiger K, Hofmann M, Rippe K, Zitzelsberger H, Weber A, Malek N, Luedde T, Vucur M, Augustin HG, Flavell R, Parnas O, Rad R, Pabst O, Henderson NC, Huber S, Macpherson A, Knolle P, Claassen M, Geier A, Trautwein C, Unger K, Elinav E, Waisman A, Abdullah Z, Haller D, Tacke F, Anstee QM, Heikenwalder M. J Hepatol. 2023 Aug; 2023 May 22. PMID: 37224925.
- Tudor-dimethylarginine interactions: the condensed version.Šimčíková D, Gelles-Watnick S, Neugebauer KM. Trends Biochem Sci. 2023 Aug; 2023 May 6. PMID: 37156649.
- Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity.Focht CM, Hiller DA, Grunseich SG, Strobel SA. RNA. 2023 Aug; 2023 May 2. PMID: 37130702.
- Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases.Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Thorax. 2023 Aug; 2022 Oct 10. PMID: 36216496.
- A statistical framework to identify cell types whose genetically regulated proportions are associated with complex diseases.Liu W, Deng W, Chen M, Dong Z, Zhu B, Yu Z, Tang D, Sauler M, Lin C, Wain LV, Cho MH, Kaminski N, Zhao H. PLoS Genet. 2023 Jul; 2023 Jul 31. PMID: 37523391.
- Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.Ren P, Hu Y, Peng L, Yang L, Suzuki K, Fang Z, Bai M, Zhou L, Feng Y, Zou Y, Xiong Y, Chen S. Signal Transduct Target Ther. 2023 Jul 31; 2023 Jul 31. PMID: 37518189.
- Acetylation of MLH1 by CBP increases cellular DNA mismatch repair activity.Zhang M, Zhao J, Glazer PM, Bai W, Bepler G, Zhang XM. J Biochem. 2023 Jul 31. PMID: 37094360.
- An analysis of the nutritional effects of Schisandra chinensis components based on mass spectrometry technology.Jia M, Zhou L, Lou Y, Yang X, Zhao H, Ouyang X, Huang Y. Front Nutr. 2023; 2023 Jul 25. PMID: 37560060.
- IL-7R licenses a population of epigenetically poised memory CD8(+) T cells with superior antitumor efficacy that are critical for melanoma memory.Micevic G, Daniels A, Flem-Karlsen K, Park K, Talty R, McGeary M, Mirza H, Blackburn HN, Sefik E, Cheung JF, Hornick NI, Aizenbud L, Joshi NS, Kluger H, Iwasaki A, Bosenberg MW, Flavell RA. Proc Natl Acad Sci U S A. 2023 Jul 25; 2023 Jul 17. PMID: 37459511.
- METTL3-mediated m6A methylation orchestrates mRNA stability and dsRNA contents to equilibrate γδ T1 and γδ T17 cells.Xiao Z, Wang S, Tian Y, Lv W, Sheng H, Zhan M, Huang Q, Zhang Z, Zhu L, Zhu C, Zhong H, Wen Q, Liu Z, Tan J, Xu Y, Yang M, Liu Y, Flavell RA, Yang Q, Cao G, Yin Z. Cell Rep. 2023 Jul 25; 2023 Jun 23. PMID: 37355989.
- Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis.Guillen-Guio B, Paynton ML, Allen RJ, Chin DPW, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. medRxiv. 2023 Jul 24; 2023 Jul 24. PMID: 37546732.
- COVID-19 annual update: a narrative review.Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. Hum Genomics. 2023 Jul 24; 2023 Jul 24. PMID: 37488607.
- More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome.Minteer CJ, Thrush K, Gonzalez J, Niimi P, Rozenblit M, Rozowsky J, Liu J, Frank M, McCabe T, Higgins-Chen AT, Hofstatter E, Pusztai L, Beckman K, Gerstein M, Levine ME. Sci Adv. 2023 Jul 21; 2023 Jul 19. PMID: 37467337.
- The promoter as a trip navigator: Guiding alternative polyadenylation site destinations.Bergfort A, Neugebauer KM. Mol Cell. 2023 Jul 20. PMID: 37478824.
- Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 55 from Rivière la Quint in Gonaïves, Haiti.Schwarz JC, An W, Theroux A, Vargas LD, Chan BK, Turner PE, Burmeister AR. Microbiol Resour Announc. 2023 Jul 18; 2023 Jun 5. PMID: 37272828.
- rMSA: A Sequence Search and Alignment Algorithm to Improve RNA Structure Modeling.Zhang C, Zhang Y, Pyle AM. J Mol Biol. 2023 Jul 15; 2022 Dec 1. PMID: 37356900.
- Polarized localization of kinesin-1 and RIC-7 drives axonal mitochondria anterograde transport.Wu Y, Ding C, Weinreb A, Manning L, Swaim G, Yogev S, Colón-Ramos DA, Hammarlund M. bioRxiv. 2023 Jul 12; 2023 Jul 12. PMID: 37502914.
- Acetate controls endothelial-to-mesenchymal transition.Zhu X, Wang Y, Soaita I, Lee HW, Bae H, Boutagy N, Bostwick A, Zhang RM, Bowman C, Xu Y, Trefely S, Chen Y, Qin L, Sessa W, Tellides G, Jang C, Snyder NW, Yu L, Arany Z, Simons M. Cell Metab. 2023 Jul 11; 2023 Jun 15. PMID: 37327791.
- Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin.Pownall ME, Miao L, Vejnar CE, M'Saad O, Sherrard A, Frederick MA, Benitez MDJ, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Science. 2023 Jul 7; 2023 Jul 6. PMID: 37410825.
- The scientific director: A complimentary model for academic leadership.Hendry C, Giraldez AJ. Cell. 2023 Jul 6. PMID: 37419083.
- Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.Lou S, Yang M, Li T, Zhao W, Cevasco H, Yang YT, Gerstein M. PLoS Comput Biol. 2023 Jul; 2023 Jul 6. PMID: 37410793.
- The KDM6A-KMT2D-p300 axis regulates susceptibility to diverse coronaviruses by mediating viral receptor expression.Wei J, Alfajaro MM, Cai WL, Graziano VR, Strine MS, Filler RB, Biering SB, Sarnik SA, Patel S, Menasche BL, Compton SR, Konermann S, Hsu PD, Orchard RC, Yan Q, Wilen CB. PLoS Pathog. 2023 Jul; 2023 Jul 6. PMID: 37410700.
- Gasdermin D licenses MHCII induction to maintain food tolerance in small intestine.He K, Wan T, Wang D, Hu J, Zhou T, Tao W, Wei Z, Lu Q, Zhou R, Tian Z, Flavell RA, Zhu S. Cell. 2023 Jul 6; 2023 Jun 15. PMID: 37327784.
- In vitro Selection and in vivo Testing of Riboswitch-inspired Aptamers.Mohsen MG, Breaker RR. Bio Protoc. 2023 Jul 5; 2023 Jul 5. PMID: 37456339.
- Cell cycle controls long-range calcium signaling in the regenerating epidermis.Moore JL, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Campamà Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V. J Cell Biol. 2023 Jul 3; 2023 Apr 27. PMID: 37102999.
- Autologous humanized PDX modeling for immuno-oncology recapitulates features of the human tumor microenvironment.Chiorazzi M, Martinek J, Krasnick B, Zheng Y, Robbins KJ, Qu R, Kaufmann G, Skidmore Z, Juric M, Henze LA, Brösecke F, Adonyi A, Zhao J, Shan L, Sefik E, Mudd J, Bi Y, Goedegebuure SP, Griffith M, Griffith O, Oyedeji A, Fertuzinhos S, Garcia-Milian R, Boffa D, Detterbeck F, Dhanasopon A, Blasberg J, Judson B, Gettinger S, Politi K, Kluger Y, Palucka K, Fields RC, Flavell RA. J Immunother Cancer. 2023 Jul. PMID: 37487666.
- Murine Norovirus: Additional Protocols for Basic and Antiviral Studies.Wobus CE, Peiper AM, McSweeney AM, Young VL, Chaika M, Lane MS, Lingemann M, Deerain JM, Strine MS, Alfajaro MM, Helm EW, Karst SM, Mackenzie JM, Taube S, Ward VK, Wilen CB. Curr Protoc. 2023 Jul. PMID: 37478303.
- PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection.Xu D, Jiang W, Wu L, Gaudet RG, Park ES, Su M, Cheppali SK, Cheemarla NR, Kumar P, Uchil PD, Grover JR, Foxman EF, Brown CM, Stansfeld PJ, Bewersdorf J, Mothes W, Karatekin E, Wilen CB, MacMicking JD. Nature. 2023 Jul; 2023 Jul 12. PMID: 37438530.
- PD-1 maintains CD8 T cell tolerance towards cutaneous neoantigens.Damo M, Hornick NI, Venkat A, William I, Clulo K, Venkatesan S, He J, Fagerberg E, Loza JL, Kwok D, Tal A, Buck J, Cui C, Singh J, Damsky WE, Leventhal JS, Krishnaswamy S, Joshi NS. Nature. 2023 Jul; 2023 Jun 21. PMID: 37344588.
- Chemical interactions modulate λ(6-85) stability in cells.Knab E, Davis CM. Protein Sci. 2023 Jul. PMID: 37313657.
- Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data.Venkat A, Bhaskar D, Krishnaswamy S. Trends Immunol. 2023 Jul; 2023 Jun 9. PMID: 37301677.
- A T(reg)-specific long noncoding RNA maintains immune-metabolic homeostasis in aging liver.Ding C, Yu Z, Sefik E, Zhou J, Kaffe E, Wang G, Li B, Flavell RA, Hu W, Ye Y, Li HB. Nat Aging. 2023 Jul; 2023 Jun 5. PMID: 37277640.
- The association between evening social media use and delayed sleep may be causal: Suggestive evidence from 120 million Reddit timestamps.Meyerson WU, Fineberg SK, Andrade FC, Corlett P, Gerstein MB, Hoyle RH. Sleep Med. 2023 Jul; 2023 May 3. PMID: 37235891.
- Mistranslation of the genetic code by a new family of bacterial transfer RNAs.Schuntermann DB, Fischer JT, Bile J, Gaier SA, Shelley BA, Awawdeh A, Jahn M, Hoffman KS, Westhof E, Söll D, Clarke CR, Vargas-Rodriguez O. J Biol Chem. 2023 Jul; 2023 May 22. PMID: 37224963.
- Nanoparticles as a Therapeutic Delivery System for Skin Cancer Prevention and Treatment.Chang J, Yu B, Saltzman WM, Girardi M. JID Innov. 2023 Jul; 2023 Mar 16. PMID: 37205301.
- bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.Vock IW, Simon MD. RNA. 2023 Jul; 2023 Apr 7. PMID: 37028916.
- Current landscape of translational and clinical research in myelodysplastic syndromes/neoplasms (MDS): Proceedings from the 1(st) International Workshop on MDS (iwMDS) Of the International Consortium for MDS (icMDS).Bewersdorf JP, Xie Z, Bejar R, Borate U, Boultwood J, Brunner AM, Buckstein R, Carraway HE, Churpek JE, Daver NG, Porta MGD, DeZern AE, Fenaux P, Figueroa ME, Gore SD, Griffiths EA, Halene S, Hasserjian RP, Hourigan CS, Kim TK, Komrokji R, Kuchroo VK, List AF, Loghavi S, Majeti R, Odenike O, Patnaik MM, Platzbecker U, Roboz GJ, Sallman DA, Santini V, Sanz G, Sekeres MA, Stahl M, Starczynowski DT, Steensma DP, Taylor J, Abdel-Wahab O, Xu ML, Savona MR, Wei AH, Zeidan AM. Blood Rev. 2023 Jul; 2023 Mar 11. PMID: 36934059.
- Interferon-induced IL-10 drives systemic T-cell dysfunction during chronic liver injury.Hackstein CP, Spitzer J, Symeonidis K, Horvatic H, Bedke T, Steglich B, Klein S, Assmus LM, Odainic A, Szlapa J, Kessler N, Beyer M, Schmithausen R, Latz E, Flavell RA, Garbi N, Kurts C, Kümmerer BM, Trebicka J, Roers A, Huber S, Schmidt SV, Knolle PA, Abdullah Z. J Hepatol. 2023 Jul; 2023 Mar 2. PMID: 36870611.
- VISTA (PD-1H) Is a Crucial Immune Regulator to Limit Pulmonary Fibrosis.Kim SH, Adams TS, Hu Q, Shin HJ, Chae G, Lee SE, Sharma L, Kwon HK, Lee FY, Park HJ, Huh WJ, Manning E, Kaminski N, Sauler M, Chen L, Song JW, Kim TK, Kang MJ. Am J Respir Cell Mol Biol. 2023 Jul. PMID: 36450109.
- Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation.Burmeister AR, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson RD, Turner PE. Appl Environ Microbiol. 2023 Jun 28; 2023 May 16. PMID: 37191555.
- Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides.Chen Y, Cao X, Loh KH, Slavoff SA. Biochem Soc Trans. 2023 Jun 28. PMID: 37171061.
- An agenda to advance research in myelodysplastic syndromes: a TOP 10 priority list from the first international workshop in MDS.Stahl M, Abdel-Wahab O, Wei AH, Savona MR, Xu ML, Xie Z, Taylor J, Starczynowski D, Sanz GF, Sallman DA, Santini V, Roboz GJ, Patnaik MM, Padron E, Odenike O, Nazha A, Nimer SD, Majeti R, Little RF, Gore S, List AF, Kutchroo V, Komrokji RS, Kim TK, Kim N, Hourigan CS, Hasserjian RP, Halene S, Griffiths EA, Greenberg PL, Figueroa M, Fenaux P, Efficace F, DeZern AE, Della Porta MG, Daver NG, Churpek JE, Carraway HE, Brunner AM, Borate U, Bennett JM, Bejar R, Boultwood J, Loghavi S, Bewersdorf JP, Platzbecker U, Steensma DP, Sekeres MA, Buckstein RJ, Zeidan AM. Blood Adv. 2023 Jun 27. PMID: 36260702.
- Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors-A prospective study and guidelines for clinical testing.Galbraith K, Vasudevaraja V, Serrano J, Shen G, Tran I, Abdallat N, Wen M, Patel S, Movahed-Ezazi M, Faustin A, Spino-Keeton M, Roberts LG, Maloku E, Drexler SA, Liechty BL, Pisapia D, Krasnozhen-Ratush O, Rosenblum M, Shroff S, Boué DR, Davidson C, Mao Q, Suchi M, North P, Hopp A, Segura A, Jarzembowski JA, Parsons L, Johnson MD, Mobley B, Samore W, McGuone D, Gopal PP, Canoll PD, Horbinski C, Fullmer JM, Farooqui MS, Gokden M, Wadhwani NR, Richardson TE, Umphlett M, Tsankova NM, DeWitt JC, Sen C, Placantonakis DG, Pacione D, Wisoff JH, Teresa Hidalgo E, Harter D, William CM, Cordova C, Kurz SC, Barbaro M, Orringer DA, Karajannis MA, Sulman EP, Gardner SL, Zagzag D, Tsirigos A, Allen JC, Golfinos JG, Snuderl M. Neurooncol Adv. 2023 Jan-Dec; 2023 Jun 26. PMID: 37476329.
- An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells.Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk BE, Sessa WC, Liu Y. Nat Commun. 2023 Jun 26; 2023 Jun 26. PMID: 37365174.
- Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients.Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Cell Rep Med. 2023 Jun 20; 2023 May 23. PMID: 37327781.
- Complete Genome Assembly and Annotation of Escherichia coli Bacteriophage 107.Schwarz JC, Chan BK, Turner PE, Burmeister AR. Microbiol Resour Announc. 2023 Jun 20; 2023 May 16. PMID: 37191527.
- mRNA Regulation by RNA Modifications.Gilbert WV, Nachtergaele S. Annu Rev Biochem. 2023 Jun 20; 2023 Apr 5. PMID: 37018844.
- Dynamics of eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.Hill V, Koch RT, Bialosuknia SM, Ngo K, Zink SD, Koetzner CA, Maffei JG, Dupuis AP, Backenson PB, Oliver J, Bransfield AB, Misencik MJ, Petruff TA, Shepard JJ, Warren JL, Gill MS, Baele G, Vogels CBF, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer LD, Armstrong PM, Ciota AT, Grubaugh ND. Curr Biol. 2023 Jun 19; 2023 Jun 8. PMID: 37295427.
- Noncoding translation: Quality control in the BAG.Mohsen JJ, Slavoff SA. Mol Cell. 2023 Jun 15. PMID: 37327774.
- Minor intron splicing is critical for survival of lethal prostate cancer.Augspach A, Drake KD, Roma L, Qian E, Lee SR, Clarke D, Kumar S, Jaquet M, Gallon J, Bolis M, Triscott J, Galván JA, Chen Y, Thalmann GN, Kruithof-de Julio M, Theurillat JP, Wuchty S, Gerstein M, Piscuoglio S, Kanadia RN, Rubin MA. Mol Cell. 2023 Jun 15; 2023 Jun 8. PMID: 37295433.
- Cutting Edge: IL-21 and Tissue-Specific Signals Instruct Tbet+CD11c+ B Cell Development following Viral Infection.Song W, Sanchez GM, Mayer DP, Blackburn HN, Chernova I, Flavell RA, Weinstein JS, Craft J. J Immunol. 2023 Jun 15. PMID: 37133336.
- Toward a global virus genomic surveillance network.Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Cell Host Microbe. 2023 Jun 14; 2023 Mar 6. PMID: 36921604.
- DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner.Strine MS, Cai WL, Wei J, Alfajaro MM, Filler RB, Biering SB, Sarnik S, Chow RD, Patil A, Cervantes KS, Collings CK, DeWeirdt PC, Hanna RE, Schofield K, Hulme C, Konermann S, Doench JG, Hsu PD, Kadoch C, Yan Q, Wilen CB. PLoS Biol. 2023 Jun; 2023 Jun 13. PMID: 37310920.
- Development of an amplicon-based sequencing approach in response to the global emergence of mpox.Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. PLoS Biol. 2023 Jun; 2023 Jun 13. PMID: 37310918.
- In utero delivery of miRNA induces epigenetic alterations and corrects pulmonary pathology in congenital diaphragmatic hernia.Ullrich SJ, Yung NK, Bauer-Pisani TJ, Maassel NL, Guerra ME, Freedman-Weiss M, Ahle SL, Ricciardi AS, Sauler M, Saltzman WM, Piotrowski-Daspit AS, Stitelman DH. Mol Ther Nucleic Acids. 2023 Jun 13; 2023 Apr 23. PMID: 37200861.
- Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq.Patel S, Sexton AN, Strine MS, Wilen CB, Simon MD, Pyle AM. Nat Commun. 2023 Jun 9; 2023 Jun 9. PMID: 37296103.
- Game over for RSV?Strine MS, Wilen CB. Sci Immunol. 2023 Jun 8; 2023 Jun 2. PMID: 37276355.
- Two cold shock domain containing proteins trigger the development of infectious Trypanosoma brucei.Toh JY, Nkouawa A, Dong G, Kolev NG, Tschudi C. PLoS Pathog. 2023 Jun; 2023 Jun 5. PMID: 37276216.
- A Picture Worth a Thousand Words, Created with One Sentence: Using Artificial Intelligence-created Art to Enhance Medical Education.Huston JC, Kaminski N. ATS Sch. 2023 Jun; 2023 May 10. PMID: 37533539.
- Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation.Collora JA, Ho YC. Genome Res. 2023 Jun; 2023 Jun 9. PMID: 37295842.
- An integrated cell atlas of the lung in health and disease.Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. Nat Med. 2023 Jun; 2023 Jun 8. PMID: 37291214.
- Author Correction: LACC1 bridges NOS2 and polyamine metabolism in inflammatory macrophages.Wei Z, Oh J, Flavell RA, Crawford JM. Nature. 2023 Jun. PMID: 37231312.
- Age-associated features of norovirus infection analysed in mice.Kennedy EA, Aggarwal S, Dhar A, Karst SM, Wilen CB, Baldridge MT. Nat Microbiol. 2023 Jun; 2023 May 15. PMID: 37188813.
- HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal.Pierce CA, Loh LN, Steach HR, Cheshenko N, Preston-Hurlburt P, Zhang F, Stransky S, Kravets L, Sidoli S, Philbrick W, Nassar M, Krishnaswamy S, Herold KC, Herold BC. J Clin Invest. 2023 Jun 1; 2023 Jun 1. PMID: 37079384.
- Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMC. Nat Genet. 2023 Jun. PMID: 36944736.
- Molecular and cellular mechanisms of human cortical connectivity.Luria V, Ma S, Shibata M, Pattabiraman K, Sestan N. Curr Opin Neurobiol. 2023 Jun; 2023 Mar 13. PMID: 36921362.
- Vascular-Parenchymal Cross-Talk Promotes Lung Fibrosis through BMPR2 Signaling.Yanagihara T, Tsubouchi K, Zhou Q, Chong M, Otsubo K, Isshiki T, Schupp JC, Sato S, Scallan C, Upagupta C, Revill S, Ayoub A, Chong SG, Dvorkin-Gheva A, Kaminski N, Tikkanen J, Keshavjee S, Paré G, Guignabert C, Ask K, Kolb MRJ. Am J Respir Crit Care Med. 2023 Jun 1. PMID: 36917778.
- Unified views on variant impact across many diseases.Kumar S, Gerstein M. Trends Genet. 2023 Jun; 2023 Feb 28. PMID: 36858880.
- Medical Societies Must Choose Professional Meeting Locations Responsibly in a Post-Roe World.Lee AG, Maley J, Hibbert K, Akgün KM, Hauschildt KE, Law A, Kaminski N, Hayes M, Gesthalter Y, Bosslet GT, Santhosh L, Witkin A, Hills-Dunlap K, Çoruh B, Gershengorn HB, Hardin CC. Ann Am Thorac Soc. 2023 Jun. PMID: 36812378.
- Differences in the immunogenicity of engineered circular RNAs.Tai J, Chen YG. J Mol Cell Biol. 2023 Jun 1. PMID: 36787893.
- PCSK6 and Survival in Idiopathic Pulmonary Fibrosis.Oldham JM, Allen RJ, Lorenzo-Salazar JM, Molyneaux PL, Ma SF, Joseph C, Kim JS, Guillen-Guio B, Hernández-Beeftink T, Kropski JA, Huang Y, Lee CT, Adegunsoye A, Pugashetti JV, Linderholm AL, Vo V, Strek ME, Jou J, Muñoz-Barrera A, Rubio-Rodriguez LA, Hubbard R, Hirani N, Whyte MKB, Hart S, Nicholson AG, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters PJ, Molina-Molina M, Banovich NE, Fahy WA, Martinez FJ, Hall IP, Tobin MD, Maher TM, Blackwell TS, Yaspan BL, Jenkins RG, Flores C, Wain LV, Noth I. Am J Respir Crit Care Med. 2023 Jun 1. PMID: 36780644.
- Emergence of division of labor in tissues through cell interactions and spatial cues.Adler M, Moriel N, Goeva A, Avraham-Davidi I, Mages S, Adams TS, Kaminski N, Macosko EZ, Regev A, Medzhitov R, Nitzan M. Cell Rep. 2023 May 30; 2023 Apr 21. PMID: 37086403.
- MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT.Tavares RCA, Mahadeshwar G, Wan H, Pyle AM. bioRxiv. 2023 May 25; 2023 May 25. PMID: 37292902.
- Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.Salichos L, Warrell J, Cevasco H, Chung A, Gerstein M. Sci Rep. 2023 May 25; 2023 May 25. PMID: 37231011.
- Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.Zimmer JT, Vock IW, Schofield JA, Kiefer L, Moon MH, Simon MD. bioRxiv. 2023 May 24; 2023 May 24. PMID: 37292657.
- My favourite flowering image: Arabidopsis conical petal epidermal cells.Irish VF. J Exp Bot. 2023 May 19. PMID: 36932972.
- The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A. bioRxiv. 2023 May 16; 2023 May 16. PMID: 37292896.
- linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells.Tornini VA, Miao L, Lee HJ, Gerson T, Dube SE, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. Elife. 2023 May 16; 2023 May 16. PMID: 37191016.
- The Upstream Sequence Transcription Complex Dictates Nucleosome Positioning and Promoter Accessibility at piRNA Genes in the C. elegans Germ Line.Sanchez N, Gonzalez LE, Reinke V. bioRxiv. 2023 May 12; 2023 May 12. PMID: 37215016.
- Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system.Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Genome Biol Evol. 2023 May 12; 2023 May 12. PMID: 37170918.
- Calculating the futureQuantum Supremacy: How the Quantum Computer Revolution Will Change Everything Michio Kaku Doubleday, 2023. 352 pp.Greenbaum D, Gerstein M. Science. 2023 May 12; 2023 May 11. PMID: 37167370.
- Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine-associated myocarditis.Barmada A, Klein J, Ramaswamy A, Brodsky NN, Jaycox JR, Sheikha H, Jones KM, Habet V, Campbell M, Sumida TS, Kontorovich A, Bogunovic D, Oliveira CR, Steele J, Hall EK, Pena-Hernandez M, Monteiro V, Lucas C, Ring AM, Omer SB, Iwasaki A, Yildirim I, Lucas CL. Sci Immunol. 2023 May 12; 2023 May 5. PMID: 37146127.
- exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. Cell Genom. 2023 May 10; 2023 Apr 20. PMID: 37228754.
- 7SK methylation by METTL3 promotes transcriptional activity.Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR. Sci Adv. 2023 May 10; 2023 May 10. PMID: 37163588.
- Riboswitches.Salvail H, Breaker RR. Curr Biol. 2023 May 8. PMID: 37160088.
- Single-cell analysis reveals inflammatory interactions driving macular degeneration.Kuchroo M, DiStasio M, Song E, Calapkulu E, Zhang L, Ige M, Sheth AH, Majdoubi A, Menon M, Tong A, Godavarthi A, Xing Y, Gigante S, Steach H, Huang J, Huguet G, Narain J, You K, Mourgkos G, Dhodapkar RM, Hirn MJ, Rieck B, Wolf G, Krishnaswamy S, Hafler BP. Nat Commun. 2023 May 5; 2023 May 5. PMID: 37147305.
- A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression.Narunsky A, Kavita K, Panchapakesan SSS, Fris ME, Breaker RR. Microb Genom. 2023 May. PMID: 37233150.
- Nanoparticle-mediated genome editing in single-cell embryos via peptide nucleic acids.Putman R, Ricciardi AS, Carufe KEW, Quijano E, Bahal R, Glazer PM, Saltzman WM. Bioeng Transl Med. 2023 May; 2022 Dec 2. PMID: 37206203.
- A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis.Ma H, Hu T, Tao W, Tong J, Han Z, Herndler-Brandstetter D, Wei Z, Liu R, Zhou T, Liu Q, Xu X, Zhang K, Zhou R, Cho JH, Li HB, Huang H, Flavell RA, Zhu S. Cell Res. 2023 May; 2023 Apr 13. PMID: 37055591.
- Polyvalent mRNA vaccination elicited potent immune response to monkeypox virus surface antigens.Fang Z, Monteiro VS, Renauer PA, Shang X, Suzuki K, Ling X, Bai M, Xiang Y, Levchenko A, Booth CJ, Lucas C, Chen S. Cell Res. 2023 May; 2023 Mar 6. PMID: 36879038.
- Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis.Unterman A, Zhao AY, Neumark N, Schupp JC, Ahangari F, Cosme C Jr, Sharma P, Flint J, Stein Y, Ryu C, Ishikawa G, Sumida TS, Gomez JL, Herazo-Maya J, Dela Cruz CS, Herzog EL, Kaminski N. medRxiv. 2023 Apr 29; 2023 Apr 29. PMID: 37163015.
- Rational engineering of lung alveolar epithelium.Leiby KL, Yuan Y, Ng R, Raredon MSB, Adams TS, Baevova P, Greaney AM, Hirschi KK, Campbell SG, Kaminski N, Herzog EL, Niklason LE. NPJ Regen Med. 2023 Apr 28; 2023 Apr 28. PMID: 37117221.
- Mapping the in vivo fitness landscape of a tethered ribosome.Radford F, Rinehart J, Isaacs FJ. Sci Adv. 2023 Apr 28; 2023 Apr 28. PMID: 37115918.
- Leveraging base-pair mammalian constraint to understand genetic variation and human disease.Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Science. 2023 Apr 28; 2023 Apr 28. PMID: 37104612.
- Evolutionary constraint and innovation across hundreds of placental mammals.Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Science. 2023 Apr 28; 2023 Apr 28. PMID: 37104599.
- The functional and evolutionary impacts of human-specific deletions in conserved elements.Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK. Science. 2023 Apr 28; 2023 Apr 28. PMID: 37104592.
- Cheating leads to the evolution of multipartite viruses.Leeks A, Young PG, Turner PE, Wild G, West SA. PLoS Biol. 2023 Apr; 2023 Apr 24. PMID: 37093882.
- Thyroid hormone modulates hyperoxic neonatal lung injury and mitochondrial function.Vamesu BM, Nicola T, Li R, Hazra S, Matalon S, Kaminski N, Ambalavanan N, Kandasamy J. JCI Insight. 2023 Apr 24; 2023 Apr 24. PMID: 36917181.
- Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. mSphere. 2023 Apr 20; 2023 Jan 26. PMID: 36700653.
- scRNA-seq profiling of neonatal and adult thymus-derived CD4+ T cells by a T cell origin-time tracing model.Han Y, Ouyang X, Chen Y, Lai S, Sun H, Wu N, Ruan C, Lu L, Su B. J Mol Cell Biol. 2023 Apr 20. PMID: 36542462.
- A Multi-omic Analysis of the Human Lung Reveals Distinct Cell Specific Aging and Senescence Molecular Programs.De Man R, McDonough JE, Adams TS, Manning EP, Myers G, Vos R, Ceulemans L, Dupont L, Vanaudenaerde BM, Wuyts WA, Rosas IO, Hagood JS, Ambalavanan N, Niklason L, Hansen KC, Yan X, Kaminski N. bioRxiv. 2023 Apr 19; 2023 Apr 19. PMID: 37131739.
- Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States.Vogels CBF, Brackney DE, Dupuis AP 2nd, Robich RM, Fauver JR, Brito AF, Williams SC, Anderson JF, Lubelczyk CB, Lange RE, Prusinski MA, Kramer LD, Gangloff-Kaufmann JL, Goodman LB, Baele G, Smith RP, Armstrong PM, Ciota AT, Dellicour S, Grubaugh ND. Proc Natl Acad Sci U S A. 2023 Apr 18; 2023 Apr 11. PMID: 37040418.
- Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants.Moriyama M, Lucas C, Monteiro VS, Iwasaki A. Proc Natl Acad Sci U S A. 2023 Apr 18; 2023 Apr 10. PMID: 37036977.
- Type 2 Dendritic Cells Orchestrate a Local Immune Circuit to Confer Antimetastatic Immunity.Weizman OE, Luyten S, Krykbaeva I, Song E, Mao T, Bosenberg M, Iwasaki A. J Immunol. 2023 Apr 15. PMID: 36881866.
- Spatiotemporal Heterogeneity of De Novo Lipogenesis in Fixed and Living Single Cells.Shuster SO, Burke MJ, Davis CM. J Phys Chem B. 2023 Apr 6; 2023 Mar 28. PMID: 36976708.
- Nonsystematic Reporting Biases of the SARS-CoV-2 Variant Mu Could Impact Our Understanding of the Epidemiological Dynamics of Emerging Variants.Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Holmes EC, Ko AI, Grubaugh ND, Iwasaki A, Wilen CB, Vogels CBF, Fauver JR. Genome Biol Evol. 2023 Apr 5. PMID: 36974986.
- A neural stem cell paradigm of pediatric hydrocephalus.Duy PQ, Rakic P, Alper SL, Robert SM, Kundishora AJ, Butler WE, Walsh CA, Sestan N, Geschwind DH, Jin SC, Kahle KT. Cereb Cortex. 2023 Apr 4. PMID: 36097331.
- PDC: a highly compact file format to store protein 3D coordinates.Zhang C, Pyle AM. Database (Oxford). 2023 Apr 3. PMID: 37010520.
- Transbronchial Lung Cryobiopsy for the Diagnosis of Interstitial Lung Disease: A Right Answer to a Wrong Question Is Still a Wrong Answer.Low SW, Kaminski N, Maldonado F. J Bronchology Interv Pulmonol. 2023 Apr 1; 2023 Apr 1. PMID: 37005378.
- Why we need a deeper understanding of the pathophysiology of long COVID.Iwasaki A, Putrino D. Lancet Infect Dis. 2023 Apr; 2023 Feb 14. PMID: 36967698.
- Epithelial Nlrp10 inflammasome mediates protection against intestinal autoinflammation.Zheng D, Mohapatra G, Kern L, He Y, Shmueli MD, Valdés-Mas R, Kolodziejczyk AA, Próchnicki T, Vasconcelos MB, Schorr L, Hertel F, Lee YS, Rufino MC, Ceddaha E, Shimshy S, Hodgetts RJ, Dori-Bachash M, Kleimeyer C, Goldenberg K, Heinemann M, Stettner N, Harmelin A, Shapiro H, Puschhof J, Chen M, Flavell RA, Latz E, Merbl Y, Abdeen SK, Elinav E. Nat Immunol. 2023 Apr; 2023 Mar 20. PMID: 36941399.
- Effects of androgen excess and body mass index on endothelial function in women with polycystic ovary syndrome.Berbrier DE, Leone CA, Adler TE, Bender JR, Taylor HS, Stachenfeld NS, Usselman CW. J Appl Physiol (1985). 2023 Apr 1; 2023 Mar 2. PMID: 36861670.
- Mature B cells and mesenchymal stem cells control emergency myelopoiesis.Lim VY, Feng X, Miao R, Zehentmeier S, Ewing-Crystal N, Lee M, Tumanov AV, Oh JE, Iwasaki A, Wang A, Choi J, Pereira JP. Life Sci Alliance. 2023 Apr; 2023 Jan 30. PMID: 36717247.
- Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch.Sadeeshkumar H, Balaji A, Sutherland AG, Mootien S, Anthony KG, Breaker RR. Anal Biochem. 2023 Apr 1; 2023 Jan 20. PMID: 36682579.
- Digoxin as an emerging therapy in noncardiac diseases.Dashti F, Jamshed F, Ouyang X, Mehal WZ, Banini BA. Trends Pharmacol Sci. 2023 Apr; 2022 Nov 14. PMID: 36396496.
- Nanoparticle Targeting with Antibodies in the Central Nervous System.Lee JH, Chapman DV, Saltzman WM. BME Front. 2023; 2023 Mar 31. PMID: 37849659.
- Nucleolar structure connects with global nuclear organization.Wang C, Ma H, Baserga SJ, Pederson T, Huang S. bioRxiv. 2023 Mar 31; 2023 Mar 31. PMID: 37034708.
- The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. Cell. 2023 Mar 30. PMID: 37001506.
- New uses for an old remedy: Digoxin as a potential treatment for steatohepatitis and other disorders.Jamshed F, Dashti F, Ouyang X, Mehal WZ, Banini BA. World J Gastroenterol. 2023 Mar 28. PMID: 37032732.
- Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ. bioRxiv. 2023 Mar 19; 2023 Mar 19. PMID: 36993485.
- SH2 Domain-Containing Phosphatase-SHP2 Attenuates Fibrotic Responses through Negative Regulation of Mitochondrial Metabolism in Lung Fibroblasts.Karampitsakos T, Galaris A, Barbayianni I, DeIuliis G, Ahangari F, Sampsonas F, Sotiropoulou V, Aidinis V, Bennett AM, Herazo-Maya JD, Xylourgidis N, Bakakos P, Bouros D, Kaminski N, Tzouvelekis A. Diagnostics (Basel). 2023 Mar 18; 2023 Mar 18. PMID: 36980473.
- Bacteria require phase separation for fitness in the mammalian gut.Krypotou E, Townsend GE, Gao X, Tachiyama S, Liu J, Pokorzynski ND, Goodman AL, Groisman EA. Science. 2023 Mar 17; 2023 Mar 16. PMID: 36927025.
- Immunogenetic metabolomics revealed key enzymes that modulate CAR-T metabolism and function.Renauer P, Park JJ, Bai M, Acosta A, Lee WH, Lin GH, Zhang Y, Dai X, Wang G, Errami Y, Wu T, Clark P, Ye L, Yang Q, Chen S. bioRxiv. 2023 Mar 15; 2023 Mar 15. PMID: 36993638.
- Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages.Ren P, Hu Y, Peng L, Yang L, Suzuki K, Fang Z, Bai M, Zhou L, Feng Y, Zou Y, Xiong Y, Chen S. bioRxiv. 2023 Mar 15; 2023 Mar 15. PMID: 35982661.
- A protocol for capturing RNA-sensing innate immune receptors in multiple conformations by single-particle cryo-EM.Wang W, Fedorova O, Pyle AM. STAR Protoc. 2023 Mar 14; 2023 Mar 14. PMID: 36920909.
- Cross-platform analysis reveals cellular and molecular landscape of glioblastoma invasion.Chen AT, Xiao Y, Tang X, Baqri M, Gao X, Reschke M, Sheu WC, Long G, Zhou Y, Deng G, Zhang S, Deng Y, Bai Z, Kim D, Huttner A, Kunes R, Günel M, Moliterno J, Saltzman WM, Fan R, Zhou J. Neuro Oncol. 2023 Mar 14. PMID: 35901838.
- Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. bioRxiv. 2023 Mar 10; 2023 Mar 10. PMID: 36945512.
- SARS-CoV-2 mRNA vaccines decouple anti-viral immunity from humoral autoimmunity.Jaycox JR, Lucas C, Yildirim I, Dai Y, Wang EY, Monteiro V, Lord S, Carlin J, Kita M, Buckner JH, Ma S, Campbell M, Ko A, Omer S, Lucas CL, Speake C, Iwasaki A, Ring AM. Nat Commun. 2023 Mar 9; 2023 Mar 9. PMID: 36894554.
- Humanized MISTRG as a preclinical in vivo model to study human neutrophil-mediated immune processes.Martinez-Sanz P, Laurent ARG, Slot E, Hoogenboezem M, Bąbała N, van Bruggen R, Rongvaux A, Flavell RA, Tytgat GAM, Franke K, Matlung HL, Kuijpers TW, Amsen D, Karrich JJ. Front Immunol. 2023; 2023 Mar 8. PMID: 36969261.
- Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Consortium P, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. medRxiv. 2023 Mar 6; 2023 Mar 6. PMID: 36945630.
- Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States.Hill V, Koch RT, Bialosuknia SM, Ngo K, Zink SD, Koetzner CA, Maffei JG, Dupuis AP, Backenson PB, Oliver J, Bransfield AB, Misencik MJ, Petruff TA, Shepard JJ, Warren JL, Gill MS, Baele G, Vogels CBF, Gallagher G, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer LD, Armstrong PM, Ciota AT, Grubaugh ND. medRxiv. 2023 Mar 6; 2023 Mar 6. PMID: 36945576.
- Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid RM, von Delius S, Gundling F, Burgkart R, Obermeier A, Mayr U, Ringelhan M, Rasch S, Lahmer T, Geisler F, Turner PE, Chan BK, Spinner CD, Schneider J. Diagnostics (Basel). 2023 Mar 6; 2023 Mar 6. PMID: 36900138.
- Multi-view manifold learning of human brain-state trajectories.Busch EL, Huang J, Benz A, Wallenstein T, Lajoie G, Wolf G, Krishnaswamy S, Turk-Browne NB. Nat Comput Sci. 2023 Mar; 2023 Mar 27. PMID: 37693659.
- Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection.Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Nat Genet. 2023 Mar; 2023 Mar 9. PMID: 36894709.
- Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect.Takahashi T, Stoiljkovic M, Song E, Gao XB, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu ZW, Kristant A, Zhang Y, Sulkowski P, Glazer PM, Kaczmarek LK, Horvath TL, Iwasaki A. Neuron. 2023 Mar 1. PMID: 36863323.
- RSCanner: rapid assessment and visualization of RNA structure content.Mahadeshwar G, Tavares RCA, Wan H, Perry ZR, Pyle AM. Bioinformatics. 2023 Mar 1. PMID: 36857576.
- Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach.Du H, Dong E, Badr HS, Petrone ME, Grubaugh ND, Gardner LM. EBioMedicine. 2023 Mar; 2023 Feb 21. PMID: 36821889.
- Editorial: Molecular advances make the day in myeloid diseases.Halene S. Curr Opin Hematol. 2023 Mar 1. PMID: 36752625.
- Positive-strand RNA viruses-a Keystone Symposia report.Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Ann N Y Acad Sci. 2023 Mar; 2023 Jan 25. PMID: 36697369.
- Is it the time to integrate novel sequencing technologies into clinical practice?VanOudenhove J, Halene S, Mendez L. Curr Opin Hematol. 2023 Mar 1; 2022 Dec 30. PMID: 36602939.
- Expression and T cell regulatory action of the PD-1 immune checkpoint in the ovary and fallopian tube.Johnson J, Kim SY, Sam PK, Asokan R, Cari EL, Bales ES, Luu TH, Perez L, Kallen AN, Nel-Themaat L, Polotsky AJ, Post MD, Orlicky DJ, Jordan KR, Bitler BG. Am J Reprod Immunol. 2023 Mar; 2022 Dec 26. PMID: 36394352.
- Metastatic and multiply relapsed SDH-deficient GIST and paraganglioma displays clinical response to combined poly ADP-ribose polymerase inhibition and temozolomide.Singh C, Bindra RS, Glazer PM, Vasquez JC, Pashankar F. Pediatr Blood Cancer. 2023 Mar; 2022 Sep 24. PMID: 36151992.
- Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. mBio. 2023 Feb 28; 2023 Jan 26. PMID: 36700642.
- Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. J Virol. 2023 Feb 28; 2023 Jan 26. PMID: 36700640.
- NLRP6 deficiency expands a novel CD103(+) B cell population that confers immune tolerance in NOD mice.Pearson JA, Peng J, Huang J, Yu X, Tai N, Hu Y, Sha S, Flavell RA, Zhao H, Wong FS, Wen L. Front Immunol. 2023; 2023 Feb 23. PMID: 36911699.
- microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis.Ahangari F, Price NL, Malik S, Chioccioli M, Bärnthaler T, Adams TS, Kim J, Pradeep SP, Ding S, Cosmos C Jr, Rose KS, McDonough JE, Aurelien NR, Ibarra G, Omote N, Schupp JC, DeIuliis G, Villalba Nunez JA, Sharma L, Ryu C, Dela Cruz CS, Liu X, Prasse A, Rosas I, Bahal R, Fernández-Hernando C, Kaminski N. JCI Insight. 2023 Feb 22; 2023 Feb 22. PMID: 36626225.
- Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Cell Rep Med. 2023 Feb 21; 2023 Jan 27. PMID: 36791724.
- Split aminoacyl-tRNA synthetases for proximity-induced stop codon suppression.Jiang HK, Ambrose NL, Chung CZ, Wang YS, Söll D, Tharp JM. Proc Natl Acad Sci U S A. 2023 Feb 21; 2023 Feb 14. PMID: 36787361.
- Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose.Filardi BA, Monteiro VS, Schwartzmann PV, do Prado Martins V, Zucca LER, Baiocchi GC, Malik AA, Silva J, Hahn AM, Chen NFG, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca RA, Mendez RDR, Bardini Silveira D, Pinto AR, Croda J, Yildirim I, Omer SB, Ko AI, Vermund SH, Grubaugh ND, Iwasaki A, Lucas C, Vogels CBF, Breban M, Koch TR, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry ML, Schulz W. Sci Transl Med. 2023 Feb 15; 2023 Feb 15. PMID: 36791210.
- Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity.Li X, Guerra S, Ledford JG, Kraft M, Li H, Hastie AT, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Meyers DA, Bleecker ER. Am J Respir Crit Care Med. 2023 Feb 15. PMID: 36066606.
- Piwi maintains homeostasis in the Drosophila adult intestine.Tang X, Liu N, Qi H, Lin H. Stem Cell Reports. 2023 Feb 14; 2023 Feb 2. PMID: 36736325.
- Integrated transcriptome and trajectory analysis of cutaneous T-cell lymphoma identifies putative precancer populations.Ren J, Qu R, Rahman NT, Lewis JM, King ALO, Liao X, Mirza FN, Carlson KR, Huang Y, Gigante S, Evans B, Rajendran BK, Xu S, Wang G, Foss FM, Damsky W, Kluger Y, Krishnaswamy S, Girardi M. Blood Adv. 2023 Feb 14. PMID: 35947128.
- Anti-seed PNAs targeting multiple oncomiRs for brain tumor therapy.Wang Y, Malik S, Suh HW, Xiao Y, Deng Y, Fan R, Huttner A, Bindra RS, Singh V, Saltzman WM, Bahal R. Sci Adv. 2023 Feb 10; 2023 Feb 8. PMID: 36753549.
- Lung Cell Atlases in Health and Disease.Adams TS, Marlier A, Kaminski N. Annu Rev Physiol. 2023 Feb 10; 2022 Nov 9. PMID: 36351366.
- Single-cell RNA-seq uncovers cellular heterogeneity and provides a signature for paediatric sleep apnoea.Cortese R, Adams TS, Cataldo KH, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Eur Respir J. 2023 Feb; 2023 Feb 9. PMID: 36356973.
- Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages.Oliveira G, Vogels CBF, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros CO, Agarwal R, Tsetsarkin KA, Harris E, Ebel GD, Wohl S, Grubaugh ND, Andersen KG. PLoS Negl Trop Dis. 2023 Feb; 2023 Feb 8. PMID: 36753510.
- Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti-PD-1 Immunotherapy in Endometrial Carcinoma.Chow RD, Michaels T, Bellone S, Hartwich TMP, Bonazzoli E, Iwasaki A, Song E, Santin AD. Cancer Discov. 2023 Feb 6. PMID: 36301137.
- Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centers.Rayack EJ, Askari HM, Zirinsky E, Lapidus S, Sheikha H, Peno C, Kazemi Y, Yolda-Carr D, Liu C, Grubaugh ND, Ko AI, Wyllie AL, Spatz ES, Oliveira CR, Bei AK. Front Public Health. 2023; 2023 Feb 3. PMID: 36817891.
- Nucleic DHX9 cooperates with STAT1 to transcribe interferon-stimulated genes.Ren X, Wang D, Zhang G, Zhou T, Wei Z, Yang Y, Zheng Y, Lei X, Tao W, Wang A, Li M, Flavell RA, Zhu S. Sci Adv. 2023 Feb 3; 2023 Feb 3. PMID: 36735791.
- Binding peptide generation for MHC Class I proteins with deep reinforcement learning.Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C, Min MR. Bioinformatics. 2023 Feb 3. PMID: 36692135.
- Allobaculum mucilyticum sp. nov. and Allobaculum fili sp. nov., isolated from the human intestinal tract.van Muijlwijk GH, Rice TA, Flavell RA, Palm NW, de Zoete MR. Int J Syst Evol Microbiol. 2023 Feb. PMID: 36748696.
- Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Nature. 2023 Feb. PMID: 36697832.
- Cholinergic control of Th17 cell pathogenicity in experimental autoimmune encephalomyelitis.Nechanitzky R, Nechanitzky D, Ramachandran P, Duncan GS, Zheng C, Göbl C, Gill KT, Haight J, Wakeham AC, Snow BE, Bradaschia-Correa V, Ganguly M, Lu Z, Saunders ME, Flavell RA, Mak TW. Cell Death Differ. 2023 Feb; 2022 Dec 17. PMID: 36528755.
- Randomized Trial of Olaparib With or Without Cediranib for Metastatic Castration-Resistant Prostate Cancer: The Results From National Cancer Institute 9984.Kim JW, McKay RR, Radke MR, Zhao S, Taplin ME, Davis NB, Monk P, Appleman LJ, Lara PN Jr, Vaishampayan UN, Zhang J, Paul AK, Bubley G, Van Allen EM, Unlu S, Huang Y, Loda M, Shapiro GI, Glazer PM, LoRusso PM, Ivy SP, Shyr Y, Swisher EM, Petrylak DP. J Clin Oncol. 2023 Feb 1; 2022 Oct 18. PMID: 36256912.
- Discovering riboswitches: the past and the future.Kavita K, Breaker RR. Trends Biochem Sci. 2023 Feb; 2022 Sep 20. PMID: 36150954.
- Selective inhibition of MCL1 overcomes venetoclax resistance in a murine model of myelodysplastic syndromes.Fischer MA, Song Y, Arrate MP, Gbyli R, Villaume MT, Smith BN, Childress MA, Stricker TP, Halene S, Savona MR. Haematologica. 2023 Feb 1; 2023 Feb 1. PMID: 35979721.
- PD-1(high)CXCR5(-)CD4(+) peripheral helper T cells promote CXCR3(+) plasmablasts in human acute viral infection.Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. Cell Rep. 2023 Jan 31; 2023 Jan 2. PMID: 36596303.
- Macrophage-Derived 25-Hydroxycholesterol Promotes Vascular Inflammation, Atherogenesis, and Lesion Remodeling.Canfrán-Duque A, Rotllan N, Zhang X, Andrés-Blasco I, Thompson BM, Sun J, Price NL, Fernández-Fuertes M, Fowler JW, Gómez-Coronado D, Sessa WC, Giannarelli C, Schneider RJ, Tellides G, McDonald JG, Fernández-Hernando C, Suárez Y. Circulation. 2023 Jan 31; 2022 Nov 23. PMID: 36416142.
- Privacy-preserving cancer type prediction with homomorphic encryption.Sarkar E, Chielle E, Gursoy G, Chen L, Gerstein M, Maniatakos M. Sci Rep. 2023 Jan 30; 2023 Jan 30. PMID: 36717667.
- Exploiting natural riboswitches for aptamer engineering and validation.Mohsen MG, Midy MK, Balaji A, Breaker RR. Nucleic Acids Res. 2023 Jan 25. PMID: 36617976.
- Dual incorporation of non-canonical amino acids enables production of post-translationally modified selenoproteins.Morosky P, Comyns C, Nunes LGA, Chung CZ, Hoffmann PR, Söll D, Vargas-Rodriguez O, Krahn N. Front Mol Biosci. 2023; 2023 Jan 24. PMID: 36762212.
- Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic.Paulino-Ramírez R, Pham K, Breban MI, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh ND, Hahn AM. Microbiol Resour Announc. 2023 Jan 24; 2022 Nov 30. PMID: 36448812.
- Epstein-Barr virus-associated primary intracranial leiomyosarcoma in an immunocompetent patient: illustrative case.Tabor JK, Lei H, Morales-Valero SF, O'Brien J, Gopal PP, Erson-Omay EZ, Fulbright RK, Moliterno J. J Neurosurg Case Lessons. 2023 Jan 23; 2023 Jan 23. PMID: 36692065.
- Machine learning identifies T cell receptor repertoire signatures associated with COVID-19 severity.Park JJ, Lee KAV, Lam SZ, Moon KS, Fang Z, Chen S. Commun Biol. 2023 Jan 20; 2023 Jan 20. PMID: 36670287.
- HPV is a cargo for the COPI sorting complex during virus entry.Harwood MC, Woo TT, Takeo Y, DiMaio D, Tsai B. Sci Adv. 2023 Jan 20; 2023 Jan 20. PMID: 36662862.
- RAMIHM generates fully human monoclonal antibodies by rapid mRNA immunization of humanized mice and BCR-seq.Ren P, Peng L, Yang L, Suzuki K, Fang Z, Renauer PA, Lin Q, Bai M, Li T, Clark P, Klein D, Chen S. Cell Chem Biol. 2023 Jan 19; 2023 Jan 13. PMID: 36640761.
- A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.Deng W, Li B, Wang J, Jiang W, Yan X, Li N, Vukmirovic M, Kaminski N, Wang J, Zhao H. Brief Bioinform. 2023 Jan 19. PMID: 36631398.
- Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys.Meyerson WU, Fineberg SK, Song YK, Faber A, Ash G, Andrade FC, Corlett P, Gerstein MB, Hoyle RH. JMIR Form Res. 2023 Jan 17; 2023 Jan 17. PMID: 36649054.
- Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity.Han W, Peng BZ, Wang C, Townsend GE 2nd, Barry NA, Peske F, Goodman AL, Liu J, Rodnina MV, Groisman EA. EMBO J. 2023 Jan 16; 2022 Dec 6. PMID: 36472247.
- Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. medRxiv. 2023 Jan 13; 2023 Jan 13. PMID: 36299420.
- Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry.Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Res Sq. 2023 Jan 10; 2023 Jan 10. PMID: 36711552.
- Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry.Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. bioRxiv. 2023 Jan 10; 2023 Jan 10. PMID: 36711508.
- T cell-derived interleukin-22 drives the expression of CD155 by cancer cells to suppress NK cell function and promote metastasis.Briukhovetska D, Suarez-Gosalvez J, Voigt C, Markota A, Giannou AD, Schübel M, Jobst J, Zhang T, Dörr J, Märkl F, Majed L, Müller PJ, May P, Gottschlich A, Tokarew N, Lücke J, Oner A, Schwerdtfeger M, Andreu-Sanz D, Grünmeier R, Seifert M, Michaelides S, Hristov M, König LM, Cadilha BL, Mikhaylov O, Anders HJ, Rothenfusser S, Flavell RA, Cerezo-Wallis D, Tejedo C, Soengas MS, Bald T, Huber S, Endres S, Kobold S. Immunity. 2023 Jan 10. PMID: 36630913.
- Tissue resident iNKT17 cells facilitate cancer cell extravasation in liver metastasis via interleukin-22.Giannou AD, Kempski J, Shiri AM, Lücke J, Zhang T, Zhao L, Zazara DE, Cortesi F, Riecken K, Amezcua Vesely MC, Low JS, Xu H, Kaffe E, Garcia-Perez L, Agalioti T, Yamada Y, Jungraithmayr W, Zigmond E, Karstens KF, Steglich B, Wagner J, Konczalla L, Carambia A, Schulze K, von Felden J, May P, Briukhovetska D, Bedke T, Brockmann L, Starzonek S, Lange T, Koch C, Riethdorf S, Pelczar P, Böttcher M, Sabihi M, Huber FJ, Reeh M, Grass JK, Wahib R, Seese H, Stüben BO, Fard-Aghaie M, Duprée A, Scognamiglio P, Plitzko G, Meiners J, Soukou S, Wittek A, Manthey C, Maroulis IC, Arck PC, Perez D, Gao B, Zarogiannis SG, Strowig T, Pasqualini R, Arap W, Gosálvez JS, Kobold S, Prinz I, Guse AH, Tachezy M, Ghadban T, Heumann A, Li J, Melling N, Mann O, Izbicki JR, Pantel K, Schumacher U, Lohse AW, Flavell RA, Gagliani N, Huber S. Immunity. 2023 Jan 10. PMID: 36630911.
- Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors.Shi G, Song C, Torres Robles J, Salichos L, Lou HJ, Lam TT, Gerstein M, Turk BE. Sci Signal. 2023 Jan 10; 2023 Jan 10. PMID: 36626580.
- GENCODE: reference annotation for the human and mouse genomes in 2023.Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron CG, Gonzalez JM, Hardy M, Harrison PW, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin FJ, Gómez LM, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt BM, Schreiber JM, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang YT, Yates A, Zafrulla Z, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Flicek P. Nucleic Acids Res. 2023 Jan 6. PMID: 36420896.
- FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G, Weng Z, Neale B, Sunyaev SR, Lin X. Nucleic Acids Res. 2023 Jan 6. PMID: 36350676.
- BONCAT-based Profiling of Nascent Small and Alternative Open Reading Frame-encoded Proteins.Cao X, Chen Y, Khitun A, Slavoff SA. Bio Protoc. 2023 Jan 5; 2023 Jan 5. PMID: 36789088.
- The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum.Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. Int J Mol Sci. 2023 Jan 5; 2023 Jan 5. PMID: 36674565.
- Platelet-derived TLT-1 promotes tumor progression by suppressing CD8+ T cells.Tyagi T, Jain K, Yarovinsky TO, Chiorazzi M, Du J, Castro C, Griffin J, Korde A, Martin KA, Takyar SS, Flavell RA, Patel AA, Hwa J. J Exp Med. 2023 Jan 2; 2022 Oct 28. PMID: 36305874.
- D-Seq: Genome-wide detection of dihydrouridine modifications in RNA.Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Gilbert WV. Methods Enzymol. 2023; 2023 Sep 22. PMID: 37925185.
- End-to-end RT-PCR of long RNA and highly structured RNA.Guo LT, Pyle AM. Methods Enzymol. 2023; 2023 Jul 27. PMID: 37914451.
- Making RNA: Using T7 RNA polymerase to produce high yields of RNA from DNA templates.Liu T, Patel S, Pyle AM. Methods Enzymol. 2023; 2023 Jul 26. PMID: 37914446.
- RT-based Sanger sequencing of RNAs containing complex RNA repetitive elements.Guo LT, Pyle AM. Methods Enzymol. 2023; 2023 Aug 1. PMID: 37914445.
- The future of evolutionary medicine: sparking innovation in biomedicine and public health.Natterson-Horowitz B, Aktipis A, Fox M, Gluckman PD, Low FM, Mace R, Read A, Turner PE, Blumstein DT. Front Sci. 2023; 2023 Feb 28. PMID: 37869257.
- The Aging Ovary and the Tales Learned Since Fetal Development.Lopez J, Hohensee G, Liang J, Sela M, Johnson J, Kallen AN. Sex Dev. 2023; 2023 Aug 18. PMID: 37598664.
- Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species.Pearce VH, Groisman EA, Townsend GE 2nd. Gut Microbes. 2023 Jan-Dec. PMID: 37358144.
- Creating Selenocysteine-Specific Reporters Using Inteins.Chung CZ, Söll D, Krahn N. Methods Mol Biol. 2023. PMID: 37277625.
- Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing.McCool MA, Bryant CJ, Huang H, Ogawa LM, Farley-Barnes KI, Sondalle SB, Abriola L, Surovtseva YV, Baserga SJ. RNA Biol. 2023 Jan. PMID: 37246770.
- 3D bioprinting of an implantable xeno-free vascularized human skin graft.Baltazar T, Jiang B, Moncayo A, Merola J, Albanna MZ, Saltzman WM, Pober JS. Bioeng Transl Med. 2023 Jan; 2022 Apr 21. PMID: 36684084.
- Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study.Cheemarla NR, Hanron A, Fauver JR, Bishai J, Watkins TA, Brito AF, Zhao D, Alpert T, Vogels CBF, Ko AI, Schulz WL, Landry ML, Grubaugh ND, van Dijk D, Foxman EF. Lancet Microbe. 2023 Jan. PMID: 36586415.
- Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing.Begik O, Diensthuber G, Liu H, Delgado-Tejedor A, Kontur C, Niazi AM, Valen E, Giraldez AJ, Beaudoin JD, Mattick JS, Novoa EM. Nat Methods. 2023 Jan; 2022 Dec 19. PMID: 36536091.
- Recurrent repeat expansions in human cancer genomes.Erwin GS, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, Hoerner CR, White SM, Ramirez L, Vadlakonda A, Vadlakonda A, von Kraut K, Park J, Brannon CM, Sumano DA, Kirtikar RA, Erwin AA, Metzner TJ, Yuen RKC, Fan AC, Leppert JT, Eberle MA, Gerstein M, Snyder MP. Nature. 2023 Jan; 2022 Dec 14. PMID: 36517591.
- Insights from incorporating quantum computing into drug design workflows.Lau B, Emani PS, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein MB, Lam HYK. Bioinformatics. 2023 Jan 1. PMID: 36477833.
- Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES.Raredon MSB, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason LE, Kluger Y. Bioinformatics. 2023 Jan 1. PMID: 36458905.
- Prognostic implications of mono-hit and multi-hit TP53 alterations in patients with acute myeloid leukemia and higher risk myelodysplastic syndromes treated with azacitidine-based therapy.Zeidan AM, Bewersdorf JP, Hasle V, Shallis RM, Thompson E, de Menezes DL, Rose S, Boss I, Halene S, Haferlach T, Fox B. Leukemia. 2023 Jan; 2022 Nov 27. PMID: 36437356.
- Longitudinal lung function and gas transfer in individuals with idiopathic pulmonary fibrosis: a genome-wide association study.Allen RJ, Oldham JM, Jenkins DA, Leavy OC, Guillen-Guio B, Melbourne CA, Ma SF, Jou J, Kim JS, Fahy WA, Oballa E, Hubbard RB, Navaratnam V, Braybrooke R, Saini G, Roach KM, Tobin MD, Hirani N, Whyte MKB, Kaminski N, Zhang Y, Martinez FJ, Linderholm AL, Adegunsoye A, Strek ME, Maher TM, Molyneaux PL, Flores C, Noth I, Gisli Jenkins R, Wain LV. Lancet Respir Med. 2023 Jan; 2022 Aug 16. PMID: 35985358.
2022
- Deciphering the role of RNA structure in translation efficiency.Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. BMC Bioinformatics. 2022 Dec 23; 2022 Dec 23. PMID: 36564729.
- Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter.Winzig F, Gandhi S, Lee A, Würstle S, Stanley GL, Capuano I, Neuringer I, Koff JL, Turner PE, Chan BK. Yale J Biol Med. 2022 Dec; 2022 Dec 22. PMID: 36568830.
- Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein.Lapidus S, Liu F, Casanovas-Massana A, Dai Y, Huck JD, Lucas C, Klein J, Filler RB, Strine MS, Sy M, Deme AB, Badiane AS, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Diagne CT, Vigan-Womas I, Mbengue A, Sadio BD, Diagne MM, Moore AJ, Mangou K, Diallo F, Sene SD, Pouye MN, Faye R, Diouf B, Nery N Jr, Costa F, Reis MG, Muenker MC, Hodson DZ, Mbarga Y, Katz BZ, Andrews JR, Campbell M, Srivathsan A, Kamath K, Baum-Jones E, Faye O, Sall AA, Vélez JCQ, Cappello M, Wilson M, Ben-Mamoun C, Tedder R, McClure M, Cherepanov P, Somé FA, Dabiré RK, Moukoko CEE, Ouédraogo JB, Boum Y 2nd, Shon J, Ndiaye D, Wisnewski A, Parikh S, Iwasaki A, Wilen CB, Ko AI, Ring AM, Bei AK. Sci Rep. 2022 Dec 22; 2022 Dec 22. PMID: 36550362.
- Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells.Kshitiz, Afzal J, Suhail Y, Chang H, Hubbi ME, Hamidzadeh A, Goyal R, Liu Y, Sun P, Nicoli S, Dang CV, Levchenko A. Cell Syst. 2022 Dec 21; 2022 Dec 2. PMID: 36462504.
- Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays.Garrigues JM, Hemarajata P, Lucero B, Alarcón J, Ransohoff H, Marutani AN, Kim M, Marlowe EM, Realegeno SE, Kagan RM, Montero CI, Chen NFG, Grubaugh ND, Vogels CBF, Green NM. J Clin Microbiol. 2022 Dec 21; 2022 Nov 29. PMID: 36445125.
- Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus.Keeler EL, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan KE, Bushman FD, Collman RG, Rosenbach M. Sarcoidosis Vasc Diffuse Lung Dis. 2022 Dec 19; 2022 Dec 19. PMID: 36533601.
- Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq.Biancon G, Busarello E, Joshi P, Lesch BJ, Halene S, Tebaldi T. STAR Protoc. 2022 Dec 16; 2022 Nov 16. PMID: 36595959.
- Optimized protocol for quantifying 5' UTR-mediated translation initiation in S. cerevisiae using direct analysis of ribosome targeting.Lewis CJT, Niederer RO, Neupane R, Gilbert WV. STAR Protoc. 2022 Dec 16; 2022 Nov 17. PMID: 36595943.
- Epiregulin is a dendritic cell-derived EGFR ligand that maintains skin and lung fibrosis.Odell ID, Steach H, Gauld SB, Reinke-Breen L, Karman J, Carr TL, Wetter JB, Phillips L, Hinchcliff M, Flavell RA. Sci Immunol. 2022 Dec 16; 2022 Dec 9. PMID: 36490328.
- Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates.Wei Y, Ho YC. Mol Cell. 2022 Dec 15. PMID: 36525953.
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- DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations.Chen Z, King WC, Hwang A, Gerstein M, Zhang J. Sci Adv. 2022 Dec 2; 2022 Nov 30. PMID: 36449617.
- Polymer nanocarriers for targeted local delivery of agents in treating brain tumors.Josowitz AD, Bindra RS, Saltzman WM. Nanotechnology. 2022 Dec 2; 2022 Dec 2. PMID: 36179653.
- Manifold Interpolating Optimal-Transport Flows for Trajectory Inference.Huguet G, Magruder DS, Tong A, Fasina O, Kuchroo M, Wolf G, Krishnaswamy S. Adv Neural Inf Process Syst. 2022 Dec. PMID: 37397786.
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- Association between primary or booster COVID-19 mRNA vaccination and Omicron lineage BA.1 SARS-CoV-2 infection in people with a prior SARS-CoV-2 infection: A test-negative case-control analysis.Lind ML, Robertson AJ, Silva J, Warner F, Coppi AC, Price N, Duckwall C, Sosensky P, Di Giuseppe EC, Borg R, Fofana MO, Ranzani OT, Dean NE, Andrews JR, Croda J, Iwasaki A, Cummings DAT, Ko AI, Hitchings MDT, Schulz WL. PLoS Med. 2022 Dec; 2022 Dec 1. PMID: 36454733.
- Structure-function analysis of the role of megakaryoblastic leukemia 1 in megakaryocyte polyploidization.Reed FE, Eskow NM, Min E, Carlino M, Mancuso R, Kwon N, Smith EC, Larsuel ST, Wang L, Scanlon V, Krause DS. Haematologica. 2022 Dec 1; 2022 Dec 1. PMID: 36453520.
- GATTACA is still pertinent 25 years later.Greenbaum D, Gerstein M. Nat Genet. 2022 Dec. PMID: 36424501.
- Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function.Lyon SE, Harris KA, Odzer NB, Wilkins SG, Breaker RR. J Biol Chem. 2022 Dec; 2022 Nov 3. PMID: 36336078.
- Finding consistency in classifications of myeloid neoplasms: a perspective on behalf of the International Workshop for Myelodysplastic Syndromes.Zeidan AM, Bewersdorf JP, Buckstein R, Sekeres MA, Steensma DP, Platzbecker U, Loghavi S, Boultwood J, Bejar R, Bennett JM, Borate U, Brunner AM, Carraway H, Churpek JE, Daver NG, Della Porta M, DeZern AE, Efficace F, Fenaux P, Figueroa ME, Greenberg P, Griffiths EA, Halene S, Hasserjian RP, Hourigan CS, Kim N, Kim TK, Komrokji RS, Kutchroo V, List AF, Little RF, Majeti R, Nazha A, Nimer SD, Odenike O, Padron E, Patnaik MM, Roboz GJ, Sallman DA, Sanz G, Stahl M, Starczynowski DT, Taylor J, Xie Z, Xu M, Savona MR, Wei AH, Abdel-Wahab O, Santini V. Leukemia. 2022 Dec; 2022 Oct 20. PMID: 36266326.
- mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay.van den Elzen AMG, Watson MJ, Thoreen CC. PLoS Genet. 2022 Nov; 2022 Nov 28. PMID: 36441824.
- circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment.Piras R, Ko EY, Barrett C, De Simone M, Lin X, Broz MT, Tessaro FHG, Castillo-Martin M, Cordon-Cardo C, Goodridge HS, Di Vizio D, Batish M, Lawrenson K, Chen YG, Chan KS, Guarnerio J. Nat Commun. 2022 Nov 25; 2022 Nov 25. PMID: 36433954.
- Cellular Stress-Induced Metabolites in Escherichia coli.Gatsios A, Kim CS, York AG, Flavell RA, Crawford JM. J Nat Prod. 2022 Nov 25; 2022 Nov 8. PMID: 36346625.
- Unadjuvanted intranasal spike vaccine elicits protective mucosal immunity against sarbecoviruses.Mao T, Israelow B, Peña-Hernández MA, Suberi A, Zhou L, Luyten S, Reschke M, Dong H, Homer RJ, Saltzman WM, Iwasaki A. Science. 2022 Nov 25; 2022 Nov 25. PMID: 36302057.
- Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex.Liu S, Won H, Clarke D, Matoba N, Khullar S, Mu Y, Wang D, Gerstein M. Genome Med. 2022 Nov 24; 2022 Nov 24. PMID: 36424644.
- Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins.Tsai PL, Cameron CJF, Forni MF, Wasko RR, Naughton BS, Horsley V, Gerstein MB, Schlieker C. Cell Rep. 2022 Nov 22. PMID: 36417855.
- Cells Adapt to Resist Fluoride through Metabolic Deactivation and Intracellular Acidification.Johnston NR, Cline G, Strobel SA. Chem Res Toxicol. 2022 Nov 21; 2022 Oct 25. PMID: 36282204.
- N-Acyl Amides from Neisseria meningitidis and Their Role in Sphingosine Receptor Signaling.Cho W, York AG, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Chembiochem. 2022 Nov 18; 2022 Oct 13. PMID: 36112057.
- Serological fingerprints link antiviral activity of therapeutic antibodies to affinity and concentration.Fiedler S, Devenish SRA, Morgunov AS, Ilsley A, Ricci F, Emmenegger M, Kosmoliaptsis V, Theel ES, Mills JR, Sholukh AM, Aguzzi A, Iwasaki A, Lynn AK, Knowles TPJ. Sci Rep. 2022 Nov 17; 2022 Nov 17. PMID: 36396691.
- Global disparities in SARS-CoV-2 genomic surveillance.Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. Nat Commun. 2022 Nov 16; 2022 Nov 16. PMID: 36385137.
- Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study.Hay JA, Kissler SM, Fauver JR, Mack C, Tai CG, Samant RM, Connolly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley JT, Mason CE, Nair M, Huang Y, DiFiori J, Ho DD, Grubaugh ND, Grad YH. Elife. 2022 Nov 16; 2022 Nov 16. PMID: 36383192.
- A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study.Würstle S, Hapfelmeier A, Karapetyan S, Studen F, Isaakidou A, Schneider T, Schmid RM, von Delius S, Gundling F, Triebelhorn J, Burgkart R, Obermeier A, Mayr U, Heller S, Rasch S, Lahmer T, Geisler F, Chan B, Turner PE, Rothe K, Spinner CD, Schneider J. Antibiotics (Basel). 2022 Nov 12; 2022 Nov 12. PMID: 36421254.
- Structures of a mobile intron retroelement poised to attack its structured DNA target.Chung K, Xu L, Chai P, Peng J, Devarkar SC, Pyle AM. Science. 2022 Nov 11; 2022 Nov 10. PMID: 36356138.
- Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes.White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Sci Rep. 2022 Nov 9; 2022 Nov 9. PMID: 36352003.
- Tuft-cell-intrinsic and -extrinsic mediators of norovirus tropism regulate viral immunity.Strine MS, Alfajaro MM, Graziano VR, Song J, Hsieh LL, Hill R, Guo J, VanDussen KL, Orchard RC, Baldridge MT, Lee S, Wilen CB. Cell Rep. 2022 Nov 8. PMID: 36351394.
- HIV-1 Vpu restricts Fc-mediated effector functions in vivo.Prévost J, Anand SP, Rajashekar JK, Zhu L, Richard J, Goyette G, Medjahed H, Gendron-Lepage G, Chen HC, Chen Y, Horwitz JA, Grunst MW, Zolla-Pazner S, Haynes BF, Burton DR, Flavell RA, Kirchhoff F, Hahn BH, Smith AB 3rd, Pazgier M, Nussenzweig MC, Kumar P, Finzi A. Cell Rep. 2022 Nov 8. PMID: 36351384.
- Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M. Genome Biol. 2022 Nov 8; 2022 Nov 8. PMID: 36348471.
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- The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands.Wang W, Pyle AM. Mol Cell. 2022 Nov 3; 2022 Oct 21. PMID: 36272408.
- Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing.McCool MA, Buhagiar AF, Bryant CJ, Ogawa LM, Abriola L, Surovtseva YV, Baserga SJ. RNA. 2022 Nov 2; 2022 Nov 2. PMID: 36323459.
- The neurobiology of long COVID.Monje M, Iwasaki A. Neuron. 2022 Nov 2; 2022 Oct 7. PMID: 36288726.
- Targeting the EIF2AK1 Signaling Pathway Rescues Red Blood Cell Production in SF3B1-Mutant Myelodysplastic Syndromes With Ringed Sideroblasts.Adema V, Ma F, Kanagal-Shamanna R, Thongon N, Montalban-Bravo G, Yang H, Peslak SA, Wang F, Acha P, Sole F, Lockyer P, Cassari M, Maciejewski JP, Visconte V, Gañán-Gómez I, Song Y, Bueso-Ramos C, Pellegrini M, Tan TM, Bejar R, Carew JS, Halene S, Santini V, Al-Atrash G, Clise-Dwyer K, Garcia-Manero G, Blobel GA, Colla S. Blood Cancer Discov. 2022 Nov 2. PMID: 35926182.
- Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD.Gandal MJ, Haney JR, Wamsley B, Yap CX, Parhami S, Emani PS, Chang N, Chen GT, Hoftman GD, de Alba D, Ramaswami G, Hartl CL, Bhattacharya A, Luo C, Jin T, Wang D, Kawaguchi R, Quintero D, Ou J, Wu YE, Parikshak NN, Swarup V, Belgard TG, Gerstein M, Pasaniuc B, Geschwind DH. Nature. 2022 Nov; 2022 Nov 2. PMID: 36323788.
- Spatiotemporal and genetic regulation of A-to-I editing throughout human brain development.Cuddleston WH, Fan X, Sloofman L, Liang L, Mossotto E, Moore K, Zipkowitz S, Wang M, Zhang B, Wang J, Sestan N, Devlin B, Roeder K, Sanders SJ, Buxbaum JD, Breen MS. Cell Rep. 2022 Nov 1. PMID: 36323256.
- Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial translocation and bacteremia.Bernard-Raichon L, Venzon M, Klein J, Axelrad JE, Zhang C, Sullivan AP, Hussey GA, Casanovas-Massana A, Noval MG, Valero-Jimenez AM, Gago J, Putzel G, Pironti A, Wilder E, Thorpe LE, Littman DR, Dittmann M, Stapleford KA, Shopsin B, Torres VJ, Ko AI, Iwasaki A, Cadwell K, Schluter J. Nat Commun. 2022 Nov 1; 2022 Nov 1. PMID: 36319618.
- A lung targeted miR-29 mimic as a therapy for pulmonary fibrosis.Chioccioli M, Roy S, Newell R, Pestano L, Dickinson B, Rigby K, Herazo-Maya J, Jenkins G, Ian S, Saini G, Johnson SR, Braybrooke R, Yu G, Sauler M, Ahangari F, Ding S, DeIuliis J, Aurelien N, Montgomery RL, Kaminski N. EBioMedicine. 2022 Nov; 2022 Oct 17. PMID: 36265417.
- Pneumococcal within-host diversity during colonization, transmission and treatment.Tonkin-Hill G, Ling C, Chaguza C, Salter SJ, Hinfonthong P, Nikolaou E, Tate N, Pastusiak A, Turner C, Chewapreecha C, Frost SDW, Corander J, Croucher NJ, Turner P, Bentley SD. Nat Microbiol. 2022 Nov; 2022 Oct 10. PMID: 36216891.
- MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression.Jaudal M, Mayo-Smith M, Poulet A, Whibley A, Peng Y, Zhang L, Thomson G, Trimborn L, Jacob Y, van Wolfswinkel JC, Goldstone DC, Wen J, Mysore KS, Putterill J. Plant J. 2022 Nov; 2022 Oct 17. PMID: 36178149.
- Arms race and fluctuating selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1.Kortright KE, Chan BK, Evans BR, Turner PE. J Evol Biol. 2022 Nov; 2022 Sep 27. PMID: 36168737.
- Ancestral archaea expanded the genetic code with pyrrolysine.Guo LT, Amikura K, Jiang HK, Mukai T, Fu X, Wang YS, O'Donoghue P, Söll D, Tharp JM. J Biol Chem. 2022 Nov; 2022 Sep 22. PMID: 36152750.
- Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry.Courvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD. Nucleic Acids Res. 2022 Oct 28. PMID: 36018791.
- Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.Lee CY, Chen Y, Duan Z, Xu M, Girgenti MJ, Xu K, Gerstein M, Zhang J. PLoS Comput Biol. 2022 Oct; 2022 Oct 27. PMID: 36301997.
- Human neutrophil development and functionality are enabled in a humanized mouse model.Zheng Y, Sefik E, Astle J, Karatepe K, Öz HH, Solis AG, Jackson R, Luo HR, Bruscia EM, Halene S, Shan L, Flavell RA. Proc Natl Acad Sci U S A. 2022 Oct 25; 2022 Oct 21. PMID: 36269862.
- A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.Zhang C, Pyle AM. iScience. 2022 Oct 21; 2022 Sep 28. PMID: 36248743.
- Building integrative functional maps of gene regulation.Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Hum Mol Genet. 2022 Oct 20. PMID: 36083269.
- Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence.Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Alex Perkins T, Cavany SM. R Soc Open Sci. 2022 Oct; 2022 Oct 19. PMID: 36277835.
- LINE-1 activation in the cerebellum drives ataxia.Takahashi T, Stoiljkovic M, Song E, Gao XB, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu ZW, Kristant A, Zhang Y, Sulkowski P, Glazer PM, Kaczmarek LK, Horvath TL, Iwasaki A. Neuron. 2022 Oct 19; 2022 Sep 6. PMID: 36070749.
- An in Vitro Cytomimetic of In-Cell RNA Folding.Yoo H, Davis CM. Chembiochem. 2022 Oct 19; 2022 Sep 14. PMID: 35999178.
- Uncovering translation roadblocks during the development of a synthetic tRNA.Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, Puglisi J. Nucleic Acids Res. 2022 Oct 14. PMID: 35882385.
- Efficient quantitative monitoring of translational initiation by RelE cleavage.Focht CM, Strobel SA. Nucleic Acids Res. 2022 Oct 14. PMID: 35871288.
- LRRC15 inhibits SARS-CoV-2 cellular entry in trans.Song J, Chow RD, Peña-Hernández MA, Zhang L, Loeb SA, So EY, Liang OD, Ren P, Chen S, Wilen CB, Lee S. PLoS Biol. 2022 Oct; 2022 Oct 13. PMID: 36228039.
- The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies.Courchaine E, Gelles-Watnick S, Machyna M, Straube K, Sauyet S, Enright J, Neugebauer KM. Nat Commun. 2022 Oct 12; 2022 Oct 12. PMID: 36224177.
- Predicting the locations of force-generating dyneins in beating cilia and flagella.Howard J, Chasteen A, Ouyang X, Geyer VF, Sartori P. Front Cell Dev Biol. 2022; 2022 Oct 11. PMID: 36303602.
- Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5.Fang Z, Monteiro VS, Hahn AM, Grubaugh ND, Lucas C, Chen S. Cell Discov. 2022 Oct 11; 2022 Oct 11. PMID: 36220819.
- In vivo correction of cystic fibrosis mediated by PNA nanoparticles.Piotrowski-Daspit AS, Barone C, Lin CY, Deng Y, Wu D, Binns TC, Xu E, Ricciardi AS, Putman R, Garrison A, Nguyen R, Gupta A, Fan R, Glazer PM, Saltzman WM, Egan ME. Sci Adv. 2022 Oct 7; 2022 Oct 5. PMID: 36197984.
- Degradation of gene silencer is essential for expression of foreign genes and bacterial colonization of the mammalian gut.Choi J, Schmukler M, Groisman EA. Proc Natl Acad Sci U S A. 2022 Oct 4; 2022 Sep 26. PMID: 36161931.
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Outbreak at a College With High Coronavirus Disease 2019 (COVID-19) Vaccination Coverage-Connecticut, August 2021-September 2021.Bart SM, Curtiss CC, Earnest R, Lobe-Costonis R, Peterson H, McWilliams C, Billig K, Hadler JL, Grubaugh ND, Arcelus VJ, Sosa LE. Clin Infect Dis. 2022 Oct 3. PMID: 35675696.
- Synthetic biodegradable polyesters for implantable controlled-release devices.Pothupitiya JU, Zheng C, Saltzman WM. Expert Opin Drug Deliv. 2022 Oct; 2022 Oct 25. PMID: 36197839.
- Developmental dynamics of RNA translation in the human brain.Duffy EE, Finander B, Choi G, Carter AC, Pritisanac I, Alam A, Luria V, Karger A, Phu W, Sherman MA, Assad EG, Pajarillo N, Khitun A, Crouch EE, Ganesh S, Chen J, Berger B, Sestan N, O'Donnell-Luria A, Huang EJ, Griffith EC, Forman-Kay JD, Moses AM, Kalish BT, Greenberg ME. Nat Neurosci. 2022 Oct; 2022 Sep 28. PMID: 36171426.
- Coronavirus Lung Infection Impairs Host Immunity against Secondary Bacterial Infection by Promoting Lysosomal Dysfunction.Peng X, Kim J, Gupta G, Agaronyan K, Mankowski MC, Korde A, Takyar SS, Shin HJ, Habet V, Voth S, Audia JP, Chang D, Liu X, Wang L, Cai Y, Tian X, Ishibe S, Kang MJ, Compton S, Wilen CB, Dela Cruz CS, Sharma L. J Immunol. 2022 Oct 1; 2022 Sep 2. PMID: 36165196.
- tRNA-m(1)A modification promotes T cell expansion via efficient MYC protein synthesis.Liu Y, Zhou J, Li X, Zhang X, Shi J, Wang X, Li H, Miao S, Chen H, He X, Dong L, Lee GR, Zheng J, Liu RJ, Su B, Ye Y, Flavell RA, Yi C, Wu Y, Li HB. Nat Immunol. 2022 Oct; 2022 Sep 22. PMID: 36138184.
- An ELISA-based platform for rapid identification of structure-dependent nucleic acid-protein interactions detects novel DNA triplex interactors.Economos NG, Thapar U, Balasubramanian N, Karras GI, Glazer PM. J Biol Chem. 2022 Oct; 2022 Aug 18. PMID: 35988651.
- AgRP neurons control structure and function of the medial prefrontal cortex.Stutz B, Waterson MJ, Šestan-Peša M, Dietrich MO, Škarica M, Sestan N, Racz B, Magyar A, Sotonyi P, Liu ZW, Gao XB, Matyas F, Stoiljkovic M, Horvath TL. Mol Psychiatry. 2022 Oct; 2022 Jul 29. PMID: 35906488.
- Molecular determinants of peri-apical targeting of inositol 1,4,5-trisphosphate receptor type 3 in cholangiocytes.Rodrigues MA, Gomes DA, Fiorotto R, Guerra MT, Weerachayaphorn J, Bo T, Sessa WC, Strazzabosco M, Nathanson MH. Hepatol Commun. 2022 Oct; 2022 Jul 19. PMID: 35852334.
- GSK3β mediates the spatiotemporal dynamics of NLRP3 inflammasome activation.Arumugam S, Qin Y, Liang Z, Han SN, Boodapati SLT, Li J, Lu Q, Flavell RA, Mehal WZ, Ouyang X. Cell Death Differ. 2022 Oct; 2022 Apr 27. PMID: 35477991.
- Molecular and cellular evolution of the primate dorsolateral prefrontal cortex.Ma S, Skarica M, Li Q, Xu C, Risgaard RD, Tebbenkamp ATN, Mato-Blanco X, Kovner R, Krsnik Ž, de Martin X, Luria V, Martí-Pérez X, Liang D, Karger A, Schmidt DK, Gomez-Sanchez Z, Qi C, Gobeske KT, Pochareddy S, Debnath A, Hottman CJ, Spurrier J, Teo L, Boghdadi AG, Homman-Ludiye J, Ely JJ, Daadi EW, Mi D, Daadi M, Marín O, Hof PR, Rasin MR, Bourne J, Sherwood CC, Santpere G, Girgenti MJ, Strittmatter SM, Sousa AMM, Sestan N. Science. 2022 Sep 30; 2022 Sep 30. PMID: 36007006.
- Systems Vaccinology in HIV Vaccine Development.Zhang J, Askenase P, Crumpacker CS. Vaccines (Basel). 2022 Sep 28; 2022 Sep 28. PMID: 36298489.
- Multiparameter analysis of timelapse imaging reveals kinetics of megakaryocytic erythroid progenitor clonal expansion and differentiation.Scanlon VM, Thompson EN, Lawton BR, Kochugaeva M, Ta K, Mayday MY, Xavier-Ferrucio J, Kang E, Eskow NM, Lu YC, Kwon N, Laumas A, Cenci M, Lawrence K, Barden K, Larsuel ST, Reed FE, Peña-Carmona G, Ubbelohde A, Lee JP, Boobalan S, Oppong Y, Anderson R, Maynard C, Sahirul K, Lajeune C, Ivathraya V, Addy T, Sanchez P, Holbrook C, Van Ho AT, Duncan JS, Blau HM, Levchenko A, Krause DS. Sci Rep. 2022 Sep 28; 2022 Sep 28. PMID: 36171423.
- Airway basal cells show a dedifferentiated KRT17(high)Phenotype and promote fibrosis in idiopathic pulmonary fibrosis.Jaeger B, Schupp JC, Plappert L, Terwolbeck O, Artysh N, Kayser G, Engelhard P, Adams TS, Zweigerdt R, Kempf H, Lienenklaus S, Garrels W, Nazarenko I, Jonigk D, Wygrecka M, Klatt D, Schambach A, Kaminski N, Prasse A. Nat Commun. 2022 Sep 26; 2022 Sep 26. PMID: 36163190.
- Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction.Griffin KN, Walters BW, Li H, Wang H, Biancon G, Tebaldi T, Kaya CB, Kanyo J, Lam TT, Cox AL, Halene S, Chung JJ, Lesch BJ. Genome Res. 2022 Sep 15; 2022 Sep 15. PMID: 36109149.
- The matricellular protein SPARC induces inflammatory interferon-response in macrophages during aging.Ryu S, Sidorov S, Ravussin E, Artyomov M, Iwasaki A, Wang A, Dixit VD. Immunity. 2022 Sep 13; 2022 Aug 12. PMID: 35963236.
- CINS: Cell Interaction Network inference from Single cell expression data.Yuan Y, Cosme C Jr, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. PLoS Comput Biol. 2022 Sep; 2022 Sep 12. PMID: 36095011.
- Single-cell multi-modal GAN reveals spatial patterns in single-cell data from triple-negative breast cancer.Amodio M, Youlten SE, Venkat A, San Juan BP, Chaffer CL, Krishnaswamy S. Patterns (N Y). 2022 Sep 9; 2022 Sep 1. PMID: 36124302.
- Unconventional genetic code systems in archaea.Meng K, Chung CZ, Söll D, Krahn N. Front Microbiol. 2022; 2022 Sep 8. PMID: 36160229.
- Immune cells and their inflammatory mediators modify β cells and cause checkpoint inhibitor-induced diabetes.Perdigoto AL, Deng S, Du KC, Kuchroo M, Burkhardt DB, Tong A, Israel G, Robert ME, Weisberg SP, Kirkiles-Smith N, Stamatouli AM, Kluger HM, Quandt Z, Young A, Yang ML, Mamula MJ, Pober JS, Anderson MS, Krishnaswamy S, Herold KC. JCI Insight. 2022 Sep 8; 2022 Sep 8. PMID: 35925682.
- Managing food allergy: GA(2)LEN guideline 2022.Muraro A, de Silva D, Halken S, Worm M, Khaleva E, Arasi S, Dunn-Galvin A, Nwaru BI, De Jong NW, Rodríguez Del Río P, Turner PJ, Smith P, Begin P, Angier E, Arshad H, Ballmer-Weber B, Beyer K, Bindslev-Jensen C, Cianferoni A, Demoulin C, Deschildre A, Ebisawa M, Fernandez-Rivas MM, Fiocchi A, Flokstra-de Blok B, Gerdts J, Gradman J, Grimshaw K, Jones C, Lau S, Loh R, Alvaro Lozano M, Makela M, Marchisotto MJ, Meyer R, Mills C, Nilsson C, Nowak-Wegrzyn A, Nurmatov U, Pajno G, Podestà M, Poulsen LK, Sampson HA, Sanchez A, Schnadt S, Szajewska H, Van Ree R, Venter C, Vlieg-Boerstra B, Warner A, Wong G, Wood R, Zuberbier T, Roberts G. World Allergy Organ J. 2022 Sep; 2022 Sep 7. PMID: 36119657.
- Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity.Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. bioRxiv. 2022 Sep 2; 2022 Sep 2. PMID: 36093346.
- An RNA link for METTL16 and DNA repair in PDAC.Perez-Pepe M, Alarcón CR. Nat Cancer. 2022 Sep. PMID: 36138137.
- Antagonism of miR-148a attenuates atherosclerosis progression in APOB(TG)Apobec(-/-)Ldlr(+/-) mice: A brief report.Rotllan N, Zhang X, Canfrán-Duque A, Goedeke L, Griñán R, Ramírez CM, Suárez Y, Fernández-Hernando C. Biomed Pharmacother. 2022 Sep; 2022 Jul 19. PMID: 36076541.
- US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Zhang C, Shine M, Pyle AM, Zhang Y. Nat Methods. 2022 Sep; 2022 Aug 29. PMID: 36038728.
- LACC1 bridges NOS2 and polyamine metabolism in inflammatory macrophages.Wei Z, Oh J, Flavell RA, Crawford JM. Nature. 2022 Sep; 2022 Aug 17. PMID: 35978195.
- Spatial profiling of chromatin accessibility in mouse and human tissues.Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Nature. 2022 Sep; 2022 Aug 17. PMID: 35978191.
- Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study.Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. EBioMedicine. 2022 Sep; 2022 Aug 8. PMID: 35952496.
- Topical formulation based on disease-specific nanoparticles for single-dose cure of psoriasis.Mai Y, Ouyang Y, Yu M, Qin Y, Girardi M, Saltzman WM, Cocco E, Zhao C, Yu L, Jia Y, Xiao L, Dou L, Deng W, Liu Y, Xie J, Deng Y. J Control Release. 2022 Sep; 2022 Jul 12. PMID: 35817278.
- Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations.Choudhary GS, Pellagatti A, Agianian B, Smith MA, Bhagat TD, Gordon-Mitchell S, Sahu S, Pandey S, Shah N, Aluri S, Aggarwal R, Aminov S, Schwartz L, Steeples V, Booher RN, Ramachandra M, Samson M, Carbajal M, Pradhan K, Bowman TV, Pillai MM, Will B, Wickrema A, Shastri A, Bradley RK, Martell RE, Steidl UG, Gavathiotis E, Boultwood J, Starczynowski DT, Verma A. Elife. 2022 Aug 30; 2022 Aug 30. PMID: 36040792.
- Structure-function analysis of the role of megakaryoblastic leukemia 1 in megakaryocyte polyploidization.Reed FE, Eskow NM, Min E, Carlino M, Mancuso R, Kwon N, Smith EC, Larsuel ST, Wang L, Scanlon V, Krause DS. Haematologica. 2022 Aug 25; 2022 Aug 25. PMID: 36005559.
- Diversification of aminoacyl-tRNA synthetase activities via genomic duplication.Krahn N, Söll D, Vargas-Rodriguez O. Front Physiol. 2022; 2022 Aug 19. PMID: 36060688.
- Genomic research data and the justice system.Greenbaum D, Gerstein M. Science. 2022 Aug 19; 2022 Aug 18. PMID: 35981024.
- Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research.Mateescu B, Jones JC, Alexander RP, Alsop E, An JY, Asghari M, Boomgarden A, Bouchareychas L, Cayota A, Chang HC, Charest A, Chiu DT, Coffey RJ, Das S, De Hoff P, deMello A, D'Souza-Schorey C, Elashoff D, Eliato KR, Franklin JL, Galas DJ, Gerstein MB, Ghiran IH, Go DB, Gould S, Grogan TR, Higginbotham JN, Hladik F, Huang TJ, Huo X, Hutchins E, Jeppesen DK, Jovanovic-Talisman T, Kim BYS, Kim S, Kim KM, Kim Y, Kitchen RR, Knouse V, LaPlante EL, Lebrilla CB, Lee LJ, Lennon KM, Li G, Li F, Li T, Liu T, Liu Z, Maddox AL, McCarthy K, Meechoovet B, Maniya N, Meng Y, Milosavljevic A, Min BH, Morey A, Ng M, Nolan J, De Oliveira Junior GP, Paulaitis ME, Phu TA, Raffai RL, Reátegui E, Roth ME, Routenberg DA, Rozowsky J, Rufo J, Senapati S, Shachar S, Sharma H, Sood AK, Stavrakis S, Stürchler A, Tewari M, Tosar JP, Tucker-Schwartz AK, Turchinovich A, Valkov N, Van Keuren-Jensen K, Vickers KC, Vojtech L, Vreeland WN, Wang C, Wang K, Wang Z, Welsh JA, Witwer KW, Wong DTW, Xia J, Xie YH, Yang K, Zaborowski MP, Zhang C, Zhang Q, Zivkovic AM, Laurent LC. iScience. 2022 Aug 19; 2022 Jun 23. PMID: 35958027.
- RNA m(6)A demethylase ALKBH5 regulates the development of γδ T cells.Ding C, Xu H, Yu Z, Roulis M, Qu R, Zhou J, Oh J, Crawford J, Gao Y, Jackson R, Sefik E, Li S, Wei Z, Skadow M, Yin Z, Ouyang X, Wang L, Zou Q, Su B, Hu W, Flavell RA, Li HB. Proc Natl Acad Sci U S A. 2022 Aug 16; 2022 Aug 8. PMID: 35939687.
- CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging.Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. Am J Respir Crit Care Med. 2022 Aug 15. PMID: 35687485.
- Annexin A2: The diversity of pathological effects in tumorigenesis and immune response.Huang Y, Jia M, Yang X, Han H, Hou G, Bi L, Yang Y, Zhang R, Zhao X, Peng C, Ouyang X. Int J Cancer. 2022 Aug 15; 2022 May 6. PMID: 35474212.
- Deep learning for quality assessment of optical coherence tomography angiography images.Dhodapkar RM, Li E, Nwanyanwu K, Adelman R, Krishnaswamy S, Wang JC. Sci Rep. 2022 Aug 12; 2022 Aug 12. PMID: 35962007.
- Inflammatory stress signaling via NF-kB alters accessible cholesterol to upregulate SREBP2 transcriptional activity in endothelial cells.Fowler JWM, Zhang R, Tao B, Boutagy NE, Sessa WC. Elife. 2022 Aug 12; 2022 Aug 12. PMID: 35959888.
- Operation Nasal Vaccine-Lightning speed to counter COVID-19.Topol EJ, Iwasaki A. Sci Immunol. 2022 Aug 12; 2022 Aug 19. PMID: 35862488.
- Global collaboration: The spirit of the ISSCR.Lin H. Stem Cell Reports. 2022 Aug 9. PMID: 35947960.
- Microenvironmental sensing by fibroblasts controls macrophage population size.Zhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Proc Natl Acad Sci U S A. 2022 Aug 9; 2022 Aug 5. PMID: 35930670.
- SEMA7AR148W mutation promotes lipid accumulation and NAFLD progression via increased localization on the hepatocyte surface.Zhao N, Zhang X, Ding J, Pan Q, Zheng MH, Liu WY, Luo G, Qu J, Li M, Li L, Cheng Y, Peng Y, Xie Q, Wei Q, Li Q, Zou L, Ouyang X, Cai SY, Boyer JL, Chai J. JCI Insight. 2022 Aug 8; 2022 Aug 8. PMID: 35938531.
- Neurexin and frizzled intercept axonal transport at microtubule minus ends to control synapse formation.Balseiro-Gómez S, Park J, Yue Y, Ding C, Shao L, Ҫetinkaya S, Kuzoian C, Hammarlund M, Verhey KJ, Yogev S. Dev Cell. 2022 Aug 8; 2022 Jul 8. PMID: 35809561.
- Mapping Phenotypic Plasticity upon the Cancer Cell State Landscape Using Manifold Learning.Burkhardt DB, San Juan BP, Lock JG, Krishnaswamy S, Chaffer CL. Cancer Discov. 2022 Aug 5. PMID: 35736000.
- Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID.Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mol Cell. 2022 Aug 4; 2022 Jul 28. PMID: 35905735.
- Multiplexed LNP-mRNA vaccination against pathogenic coronavirus species.Peng L, Fang Z, Renauer PA, McNamara A, Park JJ, Lin Q, Zhou X, Dong MB, Zhu B, Zhao H, Wilen CB, Chen S. Cell Rep. 2022 Aug 2; 2022 Jul 19. PMID: 35921835.
- Cellular recovery after prolonged warm ischaemia of the whole body.Andrijevic D, Vrselja Z, Lysyy T, Zhang S, Skarica M, Spajic A, Dellal D, Thorn SL, Duckrow RB, Ma S, Duy PQ, Isiktas AU, Liang D, Li M, Kim SK, Daniele SG, Banu K, Perincheri S, Menon MC, Huttner A, Sheth KN, Gobeske KT, Tietjen GT, Zaveri HP, Latham SR, Sinusas AJ, Sestan N. Nature. 2022 Aug; 2022 Aug 3. PMID: 35922506.
- Na(+) riboswitches regulate genes for diverse physiological processes in bacteria.White N, Sadeeshkumar H, Sun A, Sudarsan N, Breaker RR. Nat Chem Biol. 2022 Aug; 2022 Jul 25. PMID: 35879547.
- Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection.Biering SB, Sarnik SA, Wang E, Zengel JR, Leist SR, Schäfer A, Sathyan V, Hawkins P, Okuda K, Tau C, Jangid AR, Duffy CV, Wei J, Gilmore RC, Alfajaro MM, Strine MS, Nguyenla X, Van Dis E, Catamura C, Yamashiro LH, Belk JA, Begeman A, Stark JC, Shon DJ, Fox DM, Ezzatpour S, Huang E, Olegario N, Rustagi A, Volmer AS, Livraghi-Butrico A, Wehri E, Behringer RR, Cheon DJ, Schaletzky J, Aguilar HC, Puschnik AS, Button B, Pinsky BA, Blish CA, Baric RS, O'Neal WK, Bertozzi CR, Wilen CB, Boucher RC, Carette JE, Stanley SA, Harris E, Konermann S, Hsu PD. Nat Genet. 2022 Aug; 2022 Jul 25. PMID: 35879412.
- Author Correction: Unexplained post-acute infection syndromes.Choutka J, Jansari V, Hornig M, Iwasaki A. Nat Med. 2022 Aug. PMID: 35859204.
- Polyglycerol and Poly(ethylene glycol) exhibit different effects on pharmacokinetics and antibody generation when grafted to nanoparticle surfaces.Shin K, Suh HW, Grundler J, Lynn AY, Pothupitiya JU, Moscato ZM, Reschke M, Bracaglia LG, Piotrowski-Daspit AS, Saltzman WM. Biomaterials. 2022 Aug; 2022 Jul 11. PMID: 35849999.
- Pneumococcal genetic variability in age-dependent bacterial carriage.Kremer PHC, Ferwerda B, Bootsma HJ, Rots NY, Wijmenga-Monsuur AJ, Sanders EAM, Trzciński K, Wyllie AL, Turner P, van der Ende A, Brouwer MC, Bentley SD, van de Beek D, Lees JA. Elife. 2022 Jul 26; 2022 Jul 26. PMID: 35881438.
- Enzymes flying under the radar: Cryptic METTL3 can persist in knockout cells.Nachtergaele S. PLoS Biol. 2022 Jul; 2022 Jul 20. PMID: 35857761.
- Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2.Fang Z, Peng L, Lucas C, Lin Q, Zhou L, Yang L, Feng Y, Ren P, Renauer PA, Monteiro VS, Hahn AM, Park JJ, Zhou X, Grubaugh ND, Wilen CB, Chen S. Cell Discov. 2022 Jul 19; 2022 Jul 19. PMID: 35853867.
- Development of an efficient reproducible cell-cell transmission assay for rapid quantification of SARS-CoV-2 spike interaction with hACE2.Ssenyange G, Kerfoot M, Zhao M, Farhadian S, Chen S, Peng L, Ren P, Dela Cruz CS, Gupta S, Sutton RE. Cell Rep Methods. 2022 Jul 18; 2022 Jun 20. PMID: 35757815.
- Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine.Zomorrodi AR, Hemez C, Arranz-Gibert P, Wu T, Isaacs FJ, Segrè D. iScience. 2022 Jul 15; 2022 Jun 9. PMID: 35789833.
- Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC.Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. ACS Chem Biol. 2022 Jul 15; 2022 Jun 24. PMID: 35749470.
- Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen.Pedersen SF, Collora JA, Kim RN, Yang K, Razmi A, Catalano AA, Yeh YJ, Mounzer K, Tebas P, Montaner LJ, Ho YC. J Virol. 2022 Jul 13; 2022 Jun 22. PMID: 35730977.
- Interspecies commensal interactions have nonlinear impacts on host immunity.Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW. Cell Host Microbe. 2022 Jul 13; 2022 May 30. PMID: 35640610.
- Cancer Relevance of Human Genes.Qing T, Mohsen H, Cannataro VL, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend JP, Kluger Y, Gerstein M, Pusztai L. J Natl Cancer Inst. 2022 Jul 11. PMID: 35417011.
- Direct tracking of reverse-transcriptase speed and template sensitivity: implications for sequencing and analysis of long RNA molecules.Guo LT, Olson S, Patel S, Graveley BR, Pyle AM. Nucleic Acids Res. 2022 Jul 8. PMID: 35713547.
- Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation.Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, O'Dea MR, Dutton S, Shamardani K, Nwangwu K, Mancusi R, Yalçın B, Taylor KR, Acosta-Alvarez L, Malacon K, Keough MB, Ni L, Woo PJ, Contreras-Esquivel D, Toland AMS, Gehlhausen JR, Klein J, Takahashi T, Silva J, Israelow B, Lucas C, Mao T, Peña-Hernández MA, Tabachnikova A, Homer RJ, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Vogel H, Hefti MM, Perl DP, Liddelow S, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M. Cell. 2022 Jul 7; 2022 Jun 13. PMID: 35768006.
- Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. medRxiv. 2022 Jul 2; 2022 Jul 2. PMID: 35794895.
- The Manifold Scattering Transform for High-Dimensional Point Cloud Data.Chew J, Steach HR, Viswanath S, Wu HT, Hirn M, Needell D, Krishnaswamy S, Perlmutter M. Proc Mach Learn Res. 2022 Jul. PMID: 37159759.
- Standardized annotation of translated open reading frames.Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Nat Biotechnol. 2022 Jul. PMID: 35831657.
- Mouse pulmonary interstitial macrophages mediate the pro-tumorigenic effects of IL-9.Fu Y, Pajulas A, Wang J, Zhou B, Cannon A, Cheung CCL, Zhang J, Zhou H, Fisher AJ, Omstead DT, Khan S, Han L, Renauld JC, Paczesny S, Gao H, Liu Y, Yang L, Tighe RM, Licona-Limón P, Flavell RA, Takatsuka S, Kitamura D, Sun J, Bilgicer B, Sears CR, Yang K, Kaplan MH. Nat Commun. 2022 Jul 1; 2022 Jul 1. PMID: 35778404.
- Using social media to promote science.Iwasaki A. Nat Immunol. 2022 Jul. PMID: 35726062.
- Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.Rajan KS, Adler K, Doniger T, Cohen-Chalamish S, Aharon-Hefetz N, Aryal S, Pilpel Y, Tschudi C, Unger R, Michaeli S. J Biol Chem. 2022 Jul; 2022 Jun 14. PMID: 35714765.
- Storing and analyzing a genome on a blockchain.Gürsoy G, Brannon CM, Ni E, Wagner S, Khanna A, Gerstein M. Genome Biol. 2022 Jun 29; 2022 Jun 29. PMID: 35765079.
- Targeted Suppression of miRNA-33 Using pHLIP Improves Atherosclerosis Regression.Zhang X, Rotllan N, Canfrán-Duque A, Sun J, Toczek J, Moshnikova A, Malik S, Price NL, Araldi E, Zhong W, Sadeghi MM, Andreev OA, Bahal R, Reshetnyak YK, Suárez Y, Fernández-Hernando C. Circ Res. 2022 Jun 24; 2022 May 9. PMID: 35534923.
- Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations.Chen Z, Goldwasser J, Tuckman P, Liu J, Zhang J, Gerstein M. Nat Commun. 2022 Jun 20; 2022 Jun 20. PMID: 35725981.
- IL18 signaling causes islet β cell development and insulin secretion via different receptors on acinar and β cells.Zhang X, Luo S, Wang M, Huang Q, Fang W, Li J, Liu T, Zhang Y, Deng Z, Liu CL, Guan S, Ayala JE, Flavell RA, Kulkarni RN, Libby P, Guo J, Liu Z, Shi GP. Dev Cell. 2022 Jun 20; 2022 Jun 7. PMID: 35675813.
- Chemoselective restoration of para-azido-phenylalanine at multiple sites in proteins.Arranz-Gibert P, Vanderschuren K, Haimovich A, Halder A, Gupta K, Rinehart J, Isaacs FJ. Cell Chem Biol. 2022 Jun 16; 2021 Dec 28. PMID: 34965380.
- Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. J Clin Microbiol. 2022 Jun 15; 2022 May 18. PMID: 35582905.
- Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones.Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Immunity. 2022 Jun 14; 2022 Mar 22. PMID: 35320704.
- From COVID to fibrosis: lessons from single-cell analyses of the human lung.Justet A, Zhao AY, Kaminski N. Hum Genomics. 2022 Jun 13; 2022 Jun 13. PMID: 35698166.
- Antispacer peptide nucleic acids for sequence-specific CRISPR-Cas9 modulation.Economos NG, Quijano E, Carufe KEW, Perera JDR, Glazer PM. Nucleic Acids Res. 2022 Jun 10. PMID: 35235944.
- Histone Acetyltransferases p300 and CBP Coordinate Distinct Chromatin Remodeling Programs in Vascular Smooth Muscle Plasticity.Chakraborty R, Ostriker AC, Xie Y, Dave JM, Gamez-Mendez A, Chatterjee P, Abu Y, Valentine J, Lezon-Geyda K, Greif DM, Schulz VP, Gallagher PG, Sessa WC, Hwa J, Martin KA. Circulation. 2022 Jun 7; 2022 May 3. PMID: 35502657.
- Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis.Bogoch Y, Jamieson-Lucy A, Vejnar CE, Levy K, Giraldez AJ, Mullins MC, Elkouby YM. Front Cell Dev Biol. 2022; 2022 Jun 6. PMID: 35733854.
- A group approach to growing as a principal investigator.Greco V, Politi K, Eisenbarth S, Colón-Ramos D, Giraldez AJ, Bewersdorf J, Berg DN. Curr Biol. 2022 Jun 6. PMID: 35671717.
- NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects.Dubos T, Poulet A, Thomson G, Péry E, Chausse F, Tatout C, Desset S, van Wolfswinkel JC, Jacob Y. BMC Bioinformatics. 2022 Jun 6; 2022 Jun 6. PMID: 35668354.
- Inhibition of type 1 immunity with tofacitinib is associated with marked improvement in longstanding sarcoidosis.Damsky W, Wang A, Kim DJ, Young BD, Singh K, Murphy MJ, Daccache J, Clark A, Ayasun R, Ryu C, McGeary MK, Odell ID, Fazzone-Chettiar R, Pucar D, Homer R, Gulati M, Miller EJ, Bosenberg M, Flavell RA, King B. Nat Commun. 2022 Jun 6; 2022 Jun 6. PMID: 35668129.
- Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2.Fang Z, Peng L, Filler R, Suzuki K, McNamara A, Lin Q, Renauer PA, Yang L, Menasche B, Sanchez A, Ren P, Xiong Q, Strine M, Clark P, Lin C, Ko AI, Grubaugh ND, Wilen CB, Chen S. Nat Commun. 2022 Jun 6; 2022 Jun 6. PMID: 35668119.
- SHIP164 is a chorein motif lipid transfer protein that controls endosome-Golgi membrane traffic.Hanna MG, Suen PH, Wu Y, Reinisch KM, De Camilli P. J Cell Biol. 2022 Jun 6; 2022 May 2. PMID: 35499567.
- Structural and biochemical insights into lipid transport by VPS13 proteins.Adlakha J, Hong Z, Li P, Reinisch KM. J Cell Biol. 2022 Jun 6; 2022 Mar 31. PMID: 35357422.
- Mission, Organization, and Future Direction of the Serological Sciences Network for COVID-19 (SeroNet) Epidemiologic Cohort Studies.Figueiredo JC, Hirsch FR, Kushi LH, Nembhard WN, Crawford JM, Mantis N, Finster L, Merin NM, Merchant A, Reckamp KL, Melmed GY, Braun J, McGovern D, Parekh S, Corley DA, Zohoori N, Amick BC, Du R, Gregersen PK, Diamond B, Taioli E, Sariol C, Espino A, Weiskopf D, Gifoni A, Brien J, Hanege W, Lipsitch M, Zidar DA, Scheck McAlearney A, Wajnberg A, LaBaer J, Yvonne Lewis E, Binder RA, Moormann AM, Forconi C, Forrester S, Batista J, Schieffelin J, Kim D, Biancon G, VanOudenhove J, Halene S, Fan R, Barouch DH, Alter G, Pinninti S, Boppana SB, Pati SK, Latting M, Karaba AH, Roback J, Sekaly R, Neish A, Brincks AM, Granger DA, Karger AB, Thyagarajan B, Thomas SN, Klein SL, Cox AL, Lucas T, Furr-Holden D, Key K, Jones N, Wrammerr J, Suthar M, Yu Wong S, Bowman NM, Simon V, Richardson LD, McBride R, Krammer F, Rana M, Kennedy J, Boehme K, Forrest C, Granger SW, Heaney CD, Knight Lapinski M, Wallet S, Baric RS, Schifanella L, Lopez M, Fernández S, Kenah E, Panchal AR, Britt WJ, Sanz I, Dhodapkar M, Ahmed R, Bartelt LA, Markmann AJ, Lin JT, Hagan RS, Wolfgang MC, Skarbinski J. Open Forum Infect Dis. 2022 Jun; 2022 Apr 27. PMID: 35765315.
- Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2).Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de Los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, Pillai MM. NAR Cancer. 2022 Jun; 2022 May 2. PMID: 35528200.
- Inflammasome activation in infected macrophages drives COVID-19 pathology.Sefik E, Qu R, Junqueira C, Kaffe E, Mirza H, Zhao J, Brewer JR, Han A, Steach HR, Israelow B, Blackburn HN, Velazquez SE, Chen YG, Halene S, Iwasaki A, Meffre E, Nussenzweig M, Lieberman J, Wilen CB, Kluger Y, Flavell RA. Nature. 2022 Jun; 2022 Apr 28. PMID: 35483404.
- Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro.Uthaya Kumar DB, Motakis E, Yurieva M, Kohar V, Martinek J, Wu TC, Khoury J, Grassmann J, Lu M, Palucka K, Kaminski N, Koff JL, Williams A. Am J Physiol Lung Cell Mol Physiol. 2022 Jun 1; 2022 Apr 19. PMID: 35438006.
- Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor.Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nat Chem Biol. 2022 Jun; 2022 Apr 7. PMID: 35393574.
- BAL Transcriptomes Characterize Idiopathic Pulmonary Fibrosis Endotypes With Prognostic Impact.De Sadeleer LJ, Verleden SE, Schupp JC, McDonough JE, Goos T, Yserbyt J, Bargagli E, Rottoli P, Kaminski N, Prasse A, Wuyts WA. Chest. 2022 Jun; 2022 Jan 19. PMID: 35063449.
- A humanized mouse model of chronic COVID-19.Sefik E, Israelow B, Mirza H, Zhao J, Qu R, Kaffe E, Song E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. Nat Biotechnol. 2022 Jun; 2021 Dec 17. PMID: 34921308.
- Exosome Carrier Effects; Resistance to Digestion in Phagolysosomes May Assist Transfers to Targeted Cells; II Transfers of miRNAs Are Better Analyzed via Systems Approach as They Do Not Fit Conventional Reductionist Stoichiometric Concepts.Askenase PW. Int J Mol Sci. 2022 May 31; 2022 May 31. PMID: 35682875.
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine.Hamal Dhakal S, Panchapakesan SSS, Slattery P, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2022 May 31; 2022 May 27. PMID: 35622895.
- Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA.Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV. PLoS Biol. 2022 May; 2022 May 24. PMID: 35609439.
- No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination.Lu-Culligan A, Tabachnikova A, Pérez-Then E, Tokuyama M, Lee HJ, Lucas C, Silva Monteiro V, Miric M, Brache V, Cochon L, Muenker MC, Mohanty S, Huang J, Kang I, Dela Cruz C, Farhadian S, Campbell M, Yildirim I, Shaw AC, Ma S, Vermund SH, Ko AI, Omer SB, Iwasaki A. PLoS Biol. 2022 May; 2022 May 24. PMID: 35609110.
- Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.Glasser E, Maji D, Biancon G, Puthenpeedikakkal AMK, Cavender CE, Tebaldi T, Jenkins JL, Mathews DH, Halene S, Kielkopf CL. Nucleic Acids Res. 2022 May 20. PMID: 35524551.
- Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function.Martinek J, Lin J, Kim KI, Wang VG, Wu TC, Chiorazzi M, Boruchov H, Gulati A, Seeniraj S, Sun L, Marches F, Robson P, Rongvaux A, Flavell RA, George J, Chuang JH, Banchereau J, Palucka K. Cell Rep Med. 2022 May 17; 2022 Apr 27. PMID: 35584631.
- Variant-specific vaccination induces systems immune responses and potent in vivo protection against SARS-CoV-2.Peng L, Renauer PA, Ökten A, Fang Z, Park JJ, Zhou X, Lin Q, Dong MB, Filler R, Xiong Q, Clark P, Lin C, Wilen CB, Chen S. Cell Rep Med. 2022 May 17; 2022 Apr 26. PMID: 35561673.
- APOBEC3A regulates transcription from interferon-stimulated response elements.Taura M, Frank JA, Takahashi T, Kong Y, Kudo E, Song E, Tokuyama M, Iwasaki A. Proc Natl Acad Sci U S A. 2022 May 17; 2022 May 12. PMID: 35549556.
- Are We Moving the Needle for Patients with TP53-Mutated Acute Myeloid Leukemia?Shallis RM, Bewersdorf JP, Stahl MF, Halene S, Zeidan AM. Cancers (Basel). 2022 May 14; 2022 May 14. PMID: 35626039.
- AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.Shine M, Zhang C, Pyle AM. Bioinformatics. 2022 May 13. PMID: 35561202.
- Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons.Chaguza C, Coppi A, Earnest R, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JL, Weinberger DM, Landry ML, Peaper DR, Schulz W, Vogels CBF, Grubaugh ND. Med. 2022 May 13; 2022 Apr 6. PMID: 35399324.
- Sequence Determinants of TDP-43 Ribonucleoprotein Condensate Formation and Axonal Transport in Neurons.Vishal SS, Wijegunawardana D, Salaikumaran MR, Gopal PP. Front Cell Dev Biol. 2022; 2022 May 12. PMID: 35646935.
- Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes.Vicencio J, Sánchez-Bolaños C, Moreno-Sánchez I, Brena D, Vejnar CE, Kukhtar D, Ruiz-López M, Cots-Ponjoan M, Rubio A, Melero NR, Crespo-Cuadrado J, Carolis C, Pérez-Pulido AJ, Giráldez AJ, Kleinstiver BP, Cerón J, Moreno-Mateos MA. Nat Commun. 2022 May 12; 2022 May 12. PMID: 35552388.
- Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St George K, Adams MD, Grubaugh ND. Commun Biol. 2022 May 11; 2022 May 11. PMID: 35545661.
- UVB-mediated DNA damage induces matrix metalloproteinases to promote photoaging in an AhR- and SP1-dependent manner.Kim DJ, Iwasaki A, Chien AL, Kang S. JCI Insight. 2022 May 9; 2022 May 9. PMID: 35316219.
- Cancer Microbiology.DiMaio D, Emu B, Goodman AL, Mothes W, Justice A. J Natl Cancer Inst. 2022 May 9. PMID: 34850062.
- The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism.Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV, Shen Y, Söll D, Fu X. Nucleic Acids Res. 2022 May 6. PMID: 35466371.
- Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection: A Case Series From a 12-Month Longitudinal Occupational Cohort.Mack CD, Tai C, Sikka R, Grad YH, Maragakis LL, Grubaugh ND, Anderson DJ, Ho D, Merson M, Samant RM, Fauver JR, Barrett J, Sims L, DiFiori J. Clin Infect Dis. 2022 May 3. PMID: 34453431.
- EMBEDDING SIGNALS ON GRAPHS WITH UNBALANCED DIFFUSION EARTH MOVER'S DISTANCE.Tong A, Huguet G, Shung D, Natik A, Kuchroo M, Lajoie G, Wolf G, Krishnaswamy S. Proc IEEE Int Conf Acoust Speech Signal Process. 2022 May; 2022 Apr 27. PMID: 36628172.
- Unexplained post-acute infection syndromes.Choutka J, Jansari V, Hornig M, Iwasaki A. Nat Med. 2022 May; 2022 May 18. PMID: 35585196.
- Recruitment of monocytes primed to express heme oxygenase-1 ameliorates pathological lung inflammation in cystic fibrosis.Di Pietro C, Öz HH, Zhang PX, Cheng EC, Martis V, Bonfield TL, Kelley TJ, Jubin R, Abuchowski A, Krause DS, Egan ME, Murray TS, Bruscia EM. Exp Mol Med. 2022 May; 2022 May 17. PMID: 35581352.
- Author Correction: Perspectives on ENCODE.Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Nature. 2022 May. PMID: 35474002.
- Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Nature. 2022 May. PMID: 35474001.
- A new RNA performs old chemistry.Hiller DA, Strobel SA. Nat Chem Biol. 2022 May. PMID: 35301480.
- In vivo anti-tumor effect of PARP inhibition in IDH1/2 mutant MDS/AML resistant to targeted inhibitors of mutant IDH1/2.Gbyli R, Song Y, Liu W, Gao Y, Biancon G, Chandhok NS, Wang X, Fu X, Patel A, Sundaram R, Tebaldi T, Mamillapalli P, Zeidan AM, Flavell RA, Prebet T, Bindra RS, Halene S. Leukemia. 2022 May; 2022 Mar 10. PMID: 35273342.
- Multiscale PHATE identifies multimodal signatures of COVID-19.Kuchroo M, Huang J, Wong P, Grenier JC, Shung D, Tong A, Lucas C, Klein J, Burkhardt DB, Gigante S, Godavarthi A, Rieck B, Israelow B, Simonov M, Mao T, Oh JE, Silva J, Takahashi T, Odio CD, Casanovas-Massana A, Fournier J, Farhadian S, Dela Cruz CS, Ko AI, Hirn MJ, Wilson FP, Hussin JG, Wolf G, Iwasaki A, Krishnaswamy S. Nat Biotechnol. 2022 May; 2022 Feb 28. PMID: 35228707.
- A mechanistic view of long noncoding RNAs in cancer.Winkler L, Dimitrova N. Wiley Interdiscip Rev RNA. 2022 May; 2021 Oct 19. PMID: 34668345.
- Intein-based Design Expands Diversity of Selenocysteine Reporters.Chung CZ, Krahn N, Crnković A, Söll D. J Mol Biol. 2022 Apr 30; 2021 Aug 16. PMID: 34411545.
- Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome.Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cell. 2022 Apr 28; 2022 Apr 1. PMID: 35366417.
- The In Vivo and In Vitro Architecture of the Hepatitis C Virus RNA Genome Uncovers Functional RNA Secondary and Tertiary Structures.Wan H, Adams RL, Lindenbach BD, Pyle AM. J Virol. 2022 Apr 27; 2022 Mar 30. PMID: 35353000.
- ZNF117 regulates glioblastoma stem cell differentiation towards oligodendroglial lineage.Liu J, Wang X, Chen AT, Gao X, Himes BT, Zhang H, Chen Z, Wang J, Sheu WC, Deng G, Xiao Y, Zou P, Zhang S, Liu F, Zhu Y, Fan R, Patel TR, Saltzman WM, Zhou J. Nat Commun. 2022 Apr 22; 2022 Apr 22. PMID: 35459228.
- Th17 cell plasticity towards a T-bet-dependent Th1 phenotype is required for bacterial control in Staphylococcus aureus infection.Bartsch P, Kilian C, Hellmig M, Paust HJ, Borchers A, Sivayoganathan A, Enk L, Zhao Y, Shaikh N, Büttner H, Wong MN, Puelles VG, Wiech T, Flavell R, Huber TB, Turner JE, Bonn S, Huber S, Gagliani N, Mittrücker HW, Rohde H, Panzer U, Krebs CF. PLoS Pathog. 2022 Apr; 2022 Apr 21. PMID: 35446923.
- Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Cell Rep Med. 2022 Apr 19; 2022 Mar 11. PMID: 35480627.
- Functional elements of the cis-regulatory lincRNA-p21.Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Cell Rep. 2022 Apr 19. PMID: 35443176.
- FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis.Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. Cells. 2022 Apr 14; 2022 Apr 14. PMID: 35456020.
- Human Papillomavirus L2 Capsid Protein Stabilizes γ-Secretase during Viral Infection.Crite M, DiMaio D. Viruses. 2022 Apr 13; 2022 Apr 13. PMID: 35458534.
- Translating virus evolution into epidemiology.Grubaugh ND. Cell Host Microbe. 2022 Apr 13. PMID: 35421340.
- TCR-mimic bispecific antibodies to target the HIV-1 reservoir.Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EH, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. Proc Natl Acad Sci U S A. 2022 Apr 12; 2022 Apr 8. PMID: 35394875.
- Surface conjugation of antibodies improves nanoparticle uptake in bronchial epithelial cells.Luks VL, Mandl H, DiRito J, Barone C, Freedman-Weiss MR, Ricciardi AS, Tietjen GG, Egan ME, Saltzman WM, Stitelman DH. PLoS One. 2022; 2022 Apr 6. PMID: 35385514.
- A genome-scale gain-of-function CRISPR screen in CD8 T cells identifies proline metabolism as a means to enhance CAR-T therapy.Ye L, Park JJ, Peng L, Yang Q, Chow RD, Dong MB, Lam SZ, Guo J, Tang E, Zhang Y, Wang G, Dai X, Du Y, Kim HR, Cao H, Errami Y, Clark P, Bersenev A, Montgomery RR, Chen S. Cell Metab. 2022 Apr 5; 2022 Mar 10. PMID: 35276062.
- Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus.Duy PQ, Weise SC, Marini C, Li XJ, Liang D, Dahl PJ, Ma S, Spajic A, Dong W, Juusola J, Kiziltug E, Kundishora AJ, Koundal S, Pedram MZ, Torres-Fernández LA, Händler K, De Domenico E, Becker M, Ulas T, Juranek SA, Cuevas E, Hao LT, Jux B, Sousa AMM, Liu F, Kim SK, Li M, Yang Y, Takeo Y, Duque A, Nelson-Williams C, Ha Y, Selvaganesan K, Robert SM, Singh AK, Allington G, Furey CG, Timberlake AT, Reeves BC, Smith H, Dunbar A, DeSpenza T Jr, Goto J, Marlier A, Moreno-De-Luca A, Yu X, Butler WE, Carter BS, Lake EMR, Constable RT, Rakic P, Lin H, Deniz E, Benveniste H, Malvankar NS, Estrada-Veras JI, Walsh CA, Alper SL, Schultze JL, Paeschke K, Doetzlhofer A, Wulczyn FG, Jin SC, Lifton RP, Sestan N, Kolanus W, Kahle KT. Nat Neurosci. 2022 Apr; 2022 Apr 4. PMID: 35379995.
- CSSR: assignment of secondary structure to coarse-grained RNA tertiary structures.Zhang C, Pyle AM. Acta Crystallogr D Struct Biol. 2022 Apr 1; 2022 Mar 11. PMID: 35362469.
- Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells.Sumida TS, Dulberg S, Schupp JC, Lincoln MR, Stillwell HA, Axisa PP, Comi M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Nat Immunol. 2022 Apr; 2022 Mar 17. PMID: 35301508.
- Mitigation of evolved bacterial resistance to phage therapy.Torres-Barceló C, Turner PE, Buckling A. Curr Opin Virol. 2022 Apr; 2022 Feb 15. PMID: 35180532.
- Centers for Mendelian Genomics: A decade of facilitating gene discovery.Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Genet Med. 2022 Apr; 2022 Feb 9. PMID: 35148959.
- A proteomics approach identifies novel resident zebrafish Balbiani body proteins Cirbpa and Cirbpb.Jamieson-Lucy AH, Kobayashi M, James Aykit Y, Elkouby YM, Escobar-Aguirre M, Vejnar CE, Giraldez AJ, Mullins MC. Dev Biol. 2022 Apr; 2022 Jan 20. PMID: 35065906.
- An outbreak of SARS-CoV-2 on a transplant unit in the early vaccination era.Roberts SC, Foppiano Palacios C, Grubaugh ND, Alpert T, Ott IM, Breban MI, Martinello RA, Smith C, Davis MW, Mcmanus D, Tirmizi S, Topal JE, Azar MM, Malinis M. Transpl Infect Dis. 2022 Apr; 2022 Jan 25. PMID: 34969164.
- Dissecting the Oncogenic Roles of Keratin 17 in the Hallmarks of Cancer.Baraks G, Tseng R, Pan CH, Kasliwal S, Leiton CV, Shroyer KR, Escobar-Hoyos LF. Cancer Res. 2022 Apr 1. PMID: 34921015.
- Cellular origins of dsRNA, their recognition and consequences.Chen YG, Hur S. Nat Rev Mol Cell Biol. 2022 Apr; 2021 Nov 23. PMID: 34815573.
- Author Correction: Functional genomics data: privacy risk assessment and technological mitigation.Gürsoy G, Li T, Liu S, Ni E, Brannon CM, Gerstein MB. Nat Rev Genet. 2022 Apr. PMID: 34811555.
- Functional genomics data: privacy risk assessment and technological mitigation.Gürsoy G, Li T, Liu S, Ni E, Brannon CM, Gerstein MB. Nat Rev Genet. 2022 Apr; 2021 Nov 10. PMID: 34759381.
- Aberrant H19 Expression Disrupts Ovarian Cyp17 and Testosterone Production and Is Associated with Polycystic Ovary Syndrome in Women.Chen Z, Liu L, Xi X, Burn M, Karakaya C, Kallen AN. Reprod Sci. 2022 Apr; 2021 Oct 15. PMID: 34655046.
- Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu.Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Ko AI, Grubaugh ND, Iwasak A, Wilen CB, Vogels CBF, Fauver JR. medRxiv. 2022 Mar 30; 2022 Mar 30. PMID: 35378749.
- Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping.Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. Res Sq. 2022 Mar 30; 2022 Mar 30. PMID: 35378748.
- CD4(+) T-cell-derived IL-10 promotes CNS inflammation in mice by sustaining effector T cell survival.Yogev N, Bedke T, Kobayashi Y, Brockmann L, Lukas D, Regen T, Croxford AL, Nikolav A, Hövelmeyer N, von Stebut E, Prinz M, Ubeda C, Maloy KJ, Gagliani N, Flavell RA, Waisman A, Huber S. Cell Rep. 2022 Mar 29. PMID: 35354043.
- De novo DHDDS variants cause a neurodevelopmental and neurodegenerative disorder with myoclonus.Galosi S, Edani BH, Martinelli S, Hansikova H, Eklund EA, Caputi C, Masuelli L, Corsten-Janssen N, Srour M, Oegema R, Bosch DGM, Ellis CA, Amlie-Wolf L, Accogli A, Atallah I, Averdunk L, Barañano KW, Bei R, Bagnasco I, Brusco A, Demarest S, Alaix AS, Di Bonaventura C, Distelmaier F, Elmslie F, Gan-Or Z, Good JM, Gripp K, Kamsteeg EJ, Macnamara E, Marcelis C, Mercier N, Peeden J, Pizzi S, Pannone L, Shinawi M, Toro C, Verbeek NE, Venkateswaran S, Wheeler PG, Zdrazilova L, Zhang R, Zorzi G, Guerrini R, Sessa WC, Lefeber DJ, Tartaglia M, Hamdan FF, Grabińska KA, Leuzzi V. Brain. 2022 Mar 29. PMID: 34382076.
- Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.Peng L, Hu Y, Mankowski MC, Ren P, Chen RE, Wei J, Zhao M, Li T, Tripler T, Ye L, Chow RD, Fang Z, Wu C, Dong MB, Cook M, Wang G, Clark P, Nelson B, Klein D, Sutton R, Diamond MS, Wilen CB, Xiong Y, Chen S. Nat Commun. 2022 Mar 28; 2022 Mar 28. PMID: 35347138.
- Revisiting the Principles of Preservation in an Era of Pandemic Obesity.Langford JT, DiRito JR, Doilicho N, Chickering GR, Stern DA, Ouyang X, Mehal W, Tietjen GT. Front Immunol. 2022; 2022 Mar 25. PMID: 35432296.
- PUMILIO proteins promote colorectal cancer growth via suppressing p21.Gong Y, Liu Z, Yuan Y, Yang Z, Zhang J, Lu Q, Wang W, Fang C, Lin H, Liu S. Nat Commun. 2022 Mar 25; 2022 Mar 25. PMID: 35338151.
- Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics.Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. BMC Infect Dis. 2022 Mar 25; 2022 Mar 25. PMID: 35337266.
- m(6)A mRNA modification maintains colonic epithelial cell homeostasis via NF-κB-mediated antiapoptotic pathway.Zhang T, Ding C, Chen H, Zhao J, Chen Z, Chen B, Mao K, Hao Y, Roulis M, Xu H, Kluger Y, Zou Q, Ye Y, Zhan M, Flavell RA, Li HB. Sci Adv. 2022 Mar 25; 2022 Mar 25. PMID: 35333576.
- Restriction of Viral Replication, Rather than T Cell Immunopathology, Drives Lethality in Murine Norovirus CR6-Infected STAT1-Deficient Mice.Sharon AJ, Filyk HA, Fonseca NM, Simister RL, Filler RB, Yuen W, Hardman BK, Robinson HG, Seo JH, Rocha-Pereira J, Welch I, Neyts J, Wilen CB, Crowe SA, Osborne LC. J Virol. 2022 Mar 23; 2022 Feb 2. PMID: 35107369.
- Allergic airway recall responses require IL-9 from resident memory CD4(+) T cells.Ulrich BJ, Kharwadkar R, Chu M, Pajulas A, Muralidharan C, Koh B, Fu Y, Gao H, Hayes TA, Zhou HM, Goplen NP, Nelson AS, Liu Y, Linnemann AK, Turner MJ, Licona-Limón P, Flavell RA, Sun J, Kaplan MH. Sci Immunol. 2022 Mar 18; 2022 Mar 18. PMID: 35302861.
- Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies.Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Mol Cell. 2022 Mar 17. PMID: 35303483.
- De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report.Gandhi S, Klein J, Robertson AJ, Peña-Hernández MA, Lin MJ, Roychoudhury P, Lu P, Fournier J, Ferguson D, Mohamed Bakhash SAK, Catherine Muenker M, Srivathsan A, Wunder EA Jr, Kerantzas N, Wang W, Lindenbach B, Pyle A, Wilen CB, Ogbuagu O, Greninger AL, Iwasaki A, Schulz WL, Ko AI. Nat Commun. 2022 Mar 17; 2022 Mar 17. PMID: 35301314.
- The Coming of Age of Preclinical Models of MDS.Liu W, Teodorescu P, Halene S, Ghiaur G. Front Oncol. 2022; 2022 Mar 16. PMID: 35372085.
- Measuring the tolerance of the genetic code to altered codon size.DeBenedictis EA, Söll D, Esvelt KM. Elife. 2022 Mar 16; 2022 Mar 16. PMID: 35293861.
- Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation.Niederer RO, Rojas-Duran MF, Zinshteyn B, Gilbert WV. Cell Syst. 2022 Mar 16; 2022 Jan 17. PMID: 35041803.
- A phase 2 evaluation of pembrolizumab for recurrent Lynch-like versus sporadic endometrial cancers with microsatellite instability.Bellone S, Roque DM, Siegel ER, Buza N, Hui P, Bonazzoli E, Guglielmi A, Zammataro L, Nagarkatti N, Zaidi S, Lee J, Silasi DA, Huang GS, Andikyan V, Damast S, Clark M, Azodi M, Schwartz PE, Tymon-Rosario JR, Harold JA, Mauricio D, Zeybek B, Menderes G, Altwerger G, Ratner E, Alexandrov LB, Iwasaki A, Kong Y, Song E, Dong W, Elvin JA, Choi J, Santin AD. Cancer. 2022 Mar 15; 2021 Dec 7. PMID: 34875107.
- Activation of the CaMKII-Sarm1-ASK1-p38 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria.Ding C, Wu Y, Dabas H, Hammarlund M. Elife. 2022 Mar 14; 2022 Mar 14. PMID: 35285800.
- The immunology and immunopathology of COVID-19.Merad M, Blish CA, Sallusto F, Iwasaki A. Science. 2022 Mar 11; 2022 Mar 10. PMID: 35271343.
- Tuft cells are key mediators of interkingdom interactions at mucosal barrier surfaces.Strine MS, Wilen CB. PLoS Pathog. 2022 Mar; 2022 Mar 10. PMID: 35271673.
- Directed Evolution of Methanomethylophilus alvus Pyrrolysyl-tRNA Synthetase Generates a Hyperactive and Highly Selective Variant.Fischer JT, Söll D, Tharp JM. Front Mol Biosci. 2022; 2022 Mar 9. PMID: 35372501.
- Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome.Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Sci Rep. 2022 Mar 9; 2022 Mar 9. PMID: 35264704.
- Reovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis.Ortega-Gonzalez P, Taylor G, Jangra RK, Tenorio R, Fernandez de Castro I, Mainou BA, Orchard RC, Wilen CB, Brigleb PH, Sojati J, Chandran K, Sachse M, Risco C, Dermody TS. PLoS Pathog. 2022 Mar; 2022 Mar 9. PMID: 35263388.
- Differential synthesis of novel small protein times Salmonella virulence program.Salvail H, Choi J, Groisman EA. PLoS Genet. 2022 Mar; 2022 Mar 4. PMID: 35245279.
- The lasting legacy of John von NeumannThe Man from the Future: The Visionary Life of John von Neumann Ananyo Bhattacharya Norton, 2022. 368 pp.Greenbaum D, Gerstein M. Science. 2022 Mar 4; 2022 Mar 3. PMID: 35239371.
- The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation.Miao L, Tang Y, Bonneau AR, Chan SH, Kojima ML, Pownall ME, Vejnar CE, Gao F, Krishnaswamy S, Hendry CE, Giraldez AJ. Mol Cell. 2022 Mar 3; 2022 Feb 18. PMID: 35182480.
- Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation.Venzon M, Bernard-Raichon L, Klein J, Axelrad JE, Zhang C, Hussey GA, Sullivan AP, Casanovas-Massana A, Noval MG, Valero-Jimenez AM, Gago J, Putzel G, Pironti A, Wilder E, Thorpe LE, Littman DR, Dittmann M, Stapleford KA, Shopsin B, Torres VJ, Ko AI, Iwasaki A, Cadwell K, Schluter J. bioRxiv. 2022 Mar 2; 2022 Mar 2. PMID: 35262080.
- Call for Special Issue Papers: Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defense: Deadline for Manuscript Submission: July 1, 2022.Hinton DM, Turner PE. Phage (New Rochelle). 2022 Mar 1; 2022 Mar 18. PMID: 36161192.
- A possible role for VPS13-family proteins in bulk lipid transfer, membrane expansion and organelle biogenesis.Melia TJ, Reinisch KM. J Cell Sci. 2022 Mar 1; 2022 Mar 10. PMID: 35267021.
- Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents.Oliveira CR, Niccolai LM, Sheikha H, Elmansy L, Kalinich CC, Grubaugh ND, Shapiro ED. JAMA Netw Open. 2022 Mar 1; 2022 Mar 1. PMID: 35238933.
- Lack of association between pandemic chilblains and SARS-CoV-2 infection.Gehlhausen JR, Little AJ, Ko CJ, Emmenegger M, Lucas C, Wong P, Klein J, Lu P, Mao T, Jaycox J, Wang E, Ugwu N, Muenker C, Mekael D, Klein RQ, Patrignelli R, Antaya R, McNiff J, Damsky W, Kamath K, Shon J, Ring AM, Yildirim I, Omer S, Ko AI, Aguzzi A, Iwasaki A. Proc Natl Acad Sci U S A. 2022 Mar 1. PMID: 35217624.
- Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion.Vora SM, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman J, Gehrke L, Shi M, Wang L, Iwasaki A, Wu H. Proc Natl Acad Sci U S A. 2022 Mar 1. PMID: 35149555.
- Equity, diversity, and inclusion in academia: lessons from the Canadian Society of Immunology.Tejeira YV, Iwasaki A, Tye C. Trends Immunol. 2022 Mar; 2022 Jan 31. PMID: 35093304.
- Clinical effectiveness of additional primary SARS-CoV-2 vaccine doses for solid organ transplant recipients.Radcliffe C, Azar MM, Cohen E, Tucker M, Grubaugh ND, Malinis M. Clin Transplant. 2022 Mar; 2022 Jan 28. PMID: 35064939.
- Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination.Pérez-Then E, Lucas C, Monteiro VS, Miric M, Brache V, Cochon L, Vogels CBF, Malik AA, De la Cruz E, Jorge A, De Los Santos M, Leon P, Breban MI, Billig K, Yildirim I, Pearson C, Downing R, Gagnon E, Muyombwe A, Razeq J, Campbell M, Ko AI, Omer SB, Grubaugh ND, Vermund SH, Iwasaki A. Nat Med. 2022 Mar; 2022 Jan 20. PMID: 35051990.
- The METTL5-TRMT112 N(6)-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation.Sepich-Poore C, Zheng Z, Schmitt E, Wen K, Zhang ZS, Cui XL, Dai Q, Zhu AC, Zhang L, Sanchez Castillo A, Tan H, Peng J, Zhuang X, He C, Nachtergaele S. J Biol Chem. 2022 Mar; 2022 Jan 14. PMID: 35033535.
- Tumor immunology CRISPR screening: present, past, and future.Dong MB, Tang K, Zhou X, Zhou JJ, Chen S. Trends Cancer. 2022 Mar; 2021 Dec 15. PMID: 34920978.
- Direct targeting of amplified gene loci for proapoptotic anticancer therapy.Kaushik Tiwari M, Colon-Rios DA, Tumu HCR, Liu Y, Quijano E, Krysztofiak A, Chan C, Song E, Braddock DT, Suh HW, Saltzman WM, Rogers FA. Nat Biotechnol. 2022 Mar; 2021 Oct 28. PMID: 34711990.
- Who let the DoGs out? - biogenesis of stress-induced readthrough transcripts.Rosa-Mercado NA, Steitz JA. Trends Biochem Sci. 2022 Mar; 2021 Sep 3. PMID: 34489151.
- Engineering alginate microparticles for optimized accumulation in fetal rat myelomeningocele.Freedman-Weiss MR, Wu D, Maassel N, Ullrich SJ, Ahle SL, Roberts K, Farrelly JS, Buzzelli G, Saltzman WM, Stitelman DH. J Pediatr Surg. 2022 Mar; 2021 Apr 15. PMID: 33933264.
- DNMT3A R882 Mutations Confer Unique Clinicopathologic Features in MDS Including a High Risk of AML Transformation.Jawad M, Afkhami M, Ding Y, Zhang X, Li P, Young K, Xu ML, Cui W, Zhao Y, Halene S, Al-Kali A, Viswanatha D, Chen D, He R, Zheng G. Front Oncol. 2022; 2022 Feb 28. PMID: 35296003.
- Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2.Fang Z, Peng L, Filler R, Suzuki K, McNamara A, Lin Q, Renauer PA, Yang L, Menasche B, Sanchez A, Ren P, Xiong Q, Strine M, Clark P, Lin C, Ko AI, Grubaugh ND, Wilen CB, Chen S. bioRxiv. 2022 Feb 28; 2022 Feb 28. PMID: 35194606.
- Decay and damage of therapeutic phage OMKO1 by environmental stressors.Blazanin M, Lam WT, Vasen E, Chan BK, Turner PE. PLoS One. 2022; 2022 Feb 23. PMID: 35196336.
- Population Genomics Approaches for Genetic Characterization of SARS-CoV-2 Lineages.Mostefai F, Gamache I, N'Guessan A, Pelletier J, Huang J, Murall CL, Pesaranghader A, Gaonac'h-Lovejoy V, Hamelin DJ, Poujol R, Grenier JC, Smith M, Caron E, Craig M, Wolf G, Krishnaswamy S, Shapiro BJ, Hussin JG. Front Med (Lausanne). 2022; 2022 Feb 21. PMID: 35265640.
- Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis.Brereton CJ, Yao L, Davies ER, Zhou Y, Vukmirovic M, Bell JA, Wang S, Ridley RA, Dean LSN, Andriotis OG, Conforti F, Brewitz L, Mohammed S, Wallis T, Tavassoli A, Ewing RM, Alzetani A, Marshall BG, Fletcher SV, Thurner PJ, Fabre A, Kaminski N, Richeldi L, Bhaskar A, Schofield CJ, Loxham M, Davies DE, Wang Y, Jones MG. Elife. 2022 Feb 21; 2022 Feb 21. PMID: 35188460.
- An IL-9-pulmonary macrophage axis defines the allergic lung inflammatory environment.Fu Y, Wang J, Zhou B, Pajulas A, Gao H, Ramdas B, Koh B, Ulrich BJ, Yang S, Kapur R, Renauld JC, Paczesny S, Liu Y, Tighe RM, Licona-Limón P, Flavell RA, Takatsuka S, Kitamura D, Tepper RS, Sun J, Kaplan MH. Sci Immunol. 2022 Feb 18; 2022 Feb 18. PMID: 35179949.
- Making Security Viral: Shifting Engineering Biology Culture and Publishing.Mackelprang R, Adamala KP, Aurand ER, Diggans JC, Ellington AD, Evans SW, Fortman JLC, Hillson NJ, Hinman AW, Isaacs FJ, Medford JI, Mamaghani S, Moon TS, Palmer MJ, Peccoud J, Vitalis EA, Hook-Barnard I, Friedman DC. ACS Synth Biol. 2022 Feb 18. PMID: 35176864.
- Assembly and Annotation of Escherichia coli Bacteriophage U115.An W, Emsbo C, Frey E, Hu V, Jones A, Latif N, Perrilli M, Reillo K, Schwarz JC, Strasner S, Theroux A, Vargas LD, Turner PE, Burmeister AR. Microbiol Resour Announc. 2022 Feb 17; 2022 Feb 17. PMID: 35175109.
- Privacy-preserving genotype imputation with fully homomorphic encryption.Gürsoy G, Chielle E, Brannon CM, Maniatakos M, Gerstein M. Cell Syst. 2022 Feb 16; 2021 Nov 9. PMID: 34758288.
- Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis.Shapiro DM, Mandava G, Yalcin SE, Arranz-Gibert P, Dahl PJ, Shipps C, Gu Y, Srikanth V, Salazar-Morales AI, O'Brien JP, Vanderschuren K, Vu D, Batista VS, Malvankar NS, Isaacs FJ. Nat Commun. 2022 Feb 11; 2022 Feb 11. PMID: 35149672.
- Metaviromic identification of discriminative genomic features in SARS-CoV-2 using machine learning.Park JJ, Chen S. Patterns (N Y). 2022 Feb 11; 2021 Nov 18. PMID: 34812427.
- Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells.Vijayakumar A, Park A, Steitz JA. Front Immunol. 2022; 2022 Feb 10. PMID: 35222412.
- CD116+ fetal precursors migrate to the perinatal lung and give rise to human alveolar macrophages.Evren E, Ringqvist E, Doisne JM, Thaller A, Sleiers N, Flavell RA, Di Santo JP, Willinger T. J Exp Med. 2022 Feb 7; 2022 Jan 12. PMID: 35019940.
- High-affinity, neutralizing antibodies to SARS-CoV-2 can be made without T follicular helper cells.Chen JS, Chow RD, Song E, Mao T, Israelow B, Kamath K, Bozekowski J, Haynes WA, Filler RB, Menasche BL, Wei J, Alfajaro MM, Song W, Peng L, Carter L, Weinstein JS, Gowthaman U, Chen S, Craft J, Shon JC, Iwasaki A, Wilen CB, Eisenbarth SC. Sci Immunol. 2022 Feb 4; 2022 Feb 4. PMID: 34914544.
- Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing.Martinez NM, Su A, Burns MC, Nussbacher JK, Schaening C, Sathe S, Yeo GW, Gilbert WV. Mol Cell. 2022 Feb 3; 2022 Jan 19. PMID: 35051350.
- Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells.Franjic D, Skarica M, Ma S, Arellano JI, Tebbenkamp ATN, Choi J, Xu C, Li Q, Morozov YM, Andrijevic D, Vrselja Z, Spajic A, Santpere G, Li M, Zhang S, Liu Y, Spurrier J, Zhang L, Gudelj I, Rapan L, Takahashi H, Huttner A, Fan R, Strittmatter SM, Sousa AMM, Rakic P, Sestan N. Neuron. 2022 Feb 2; 2021 Nov 18. PMID: 34798047.
- The Biochemical Landscape of Riboswitch Ligands.Breaker RR. Biochemistry. 2022 Feb 1; 2022 Jan 24. PMID: 35068140.
- Impact of Chronic HIV Infection on SARS-CoV-2 Infection, COVID-19 Disease and Vaccines.Yang Y, Iwasaki A. Curr HIV/AIDS Rep. 2022 Feb; 2021 Nov 29. PMID: 34843064.
- Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient.Klein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM. J Infect Dis. 2022 Feb 1. PMID: 34718647.
- Prognostic Significance of Urinary Biomarkers in Patients Hospitalized With COVID-19.Menez S, Moledina DG, Thiessen-Philbrook H, Wilson FP, Obeid W, Simonov M, Yamamoto Y, Corona-Villalobos CP, Chang C, Garibaldi BT, Clarke W, Farhadian S, Dela Cruz C, Coca SG, Parikh CR. Am J Kidney Dis. 2022 Feb; 2021 Oct 25. PMID: 34710516.
- Prevention of host-to-host transmission by SARS-CoV-2 vaccines.Mostaghimi D, Valdez CN, Larson HT, Kalinich CC, Iwasaki A. Lancet Infect Dis. 2022 Feb; 2021 Sep 14. PMID: 34534512.
- A Phase 2 Randomized, Double-Blind, Placebo-controlled Trial of Oral Camostat Mesylate for Early Treatment of COVID-19 Outpatients Showed Shorter Illness Course and Attenuation of Loss of Smell and Taste.Chupp G, Spichler-Moffarah A, Søgaard OS, Esserman D, Dziura J, Danzig L, Chaurasia R, Patra KP, Salovey A, Nunez A, May J, Astorino L, Patel A, Halene S, Wang J, Hui P, Patel P, Lu J, Li F, Gan G, Parziale S, Katsovich L, Desir GV, Vinetz JM. medRxiv. 2022 Jan 31; 2022 Jan 31. PMID: 35132421.
- m6A modifications regulate intestinal immunity and rotavirus infection.Wang A, Tao W, Tong J, Gao J, Wang J, Hou G, Qian C, Zhang G, Li R, Wang D, Ren X, Zhang K, Ding S, Flavell RA, Li H, Pan W, Zhu S. Elife. 2022 Jan 31; 2022 Jan 31. PMID: 35098923.
- Distinct Roles of Type I and Type III Interferons during a Native Murine β Coronavirus Lung Infection.Sharma L, Peng X, Qing H, Hilliard BK, Kim J, Swaminathan A, Tian J, Israni-Winger K, Zhang C, Habet V, Wang L, Gupta G, Tian X, Ma Y, Shin HJ, Kim SH, Kang MJ, Ishibe S, Young LH, Kotenko S, Compton S, Wilen CB, Wang A, Dela Cruz CS. J Virol. 2022 Jan 26; 2021 Oct 27. PMID: 34705554.
- Characterization of the COPD alveolar niche using single-cell RNA sequencing.Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C Jr, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Nat Commun. 2022 Jan 25; 2022 Jan 25. PMID: 35078977.
- Tuning protein half-life in mouse using sequence-defined biopolymers functionalized with lipids.Vanderschuren K, Arranz-Gibert P, Khang M, Hadar D, Gaudin A, Yang F, Folta-Stogniew E, Saltzman WM, Amiram M, Isaacs FJ. Proc Natl Acad Sci U S A. 2022 Jan 25. PMID: 35046019.
- Selection for Phage Resistance Reduces Virulence of Shigella flexneri.Kortright KE, Done RE, Chan BK, Souza V, Turner PE. Appl Environ Microbiol. 2022 Jan 25; 2021 Nov 17. PMID: 34788068.
- Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19.Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C Jr, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Nat Commun. 2022 Jan 21; 2022 Jan 21. PMID: 35064122.
- The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist.Collora JA, Ho YC. Cell. 2022 Jan 20. PMID: 35063069.
- Development and utilization of a surrogate SARS-CoV-2 viral neutralization assay to assess mRNA vaccine responses.Wisnewski AV, Liu J, Lucas C, Klein J, Iwasaki A, Cantley L, Fazen L, Campillo Luna J, Slade M, Redlich CA. PLoS One. 2022; 2022 Jan 18. PMID: 35041700.
- Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome.Dutrow EV, Emera D, Yim K, Uebbing S, Kocher AA, Krenzer M, Nottoli T, Burkhardt DB, Krishnaswamy S, Louvi A, Noonan JP. Nat Commun. 2022 Jan 13; 2022 Jan 13. PMID: 35027568.
- Zero-preserving imputation of single-cell RNA-seq data.Linderman GC, Zhao J, Roulis M, Bielecki P, Flavell RA, Nadler B, Kluger Y. Nat Commun. 2022 Jan 11; 2022 Jan 11. PMID: 35017482.
- Phenotyping Zebrafish Mutant Models to Assess Candidate Genes Associated with Aortic Aneurysm.Prendergast A, Ziganshin BA, Papanikolaou D, Zafar MA, Nicoli S, Mukherjee S, Elefteriades JA. Genes (Basel). 2022 Jan 10; 2022 Jan 10. PMID: 35052463.
- Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain.Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, Yalçın B, Taylor KR, Dutton S, Acosta-Alvarez L, Ni L, Contreras-Esquivel D, Gehlhausen JR, Klein J, Lucas C, Mao T, Silva J, Peña-Hernández MA, Tabachnikova A, Takahashi T, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Hefti M, Perl D, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M. bioRxiv. 2022 Jan 10; 2022 Jan 10. PMID: 35043113.
- Targeted editing and evolution of engineered ribosomes in vivo by filtered editing.Radford F, Elliott SD, Schepartz A, Isaacs FJ. Nat Commun. 2022 Jan 10; 2022 Jan 10. PMID: 35013328.
- An assembly of nuclear bodies associates with the active VSG expression site in African trypanosomes.Budzak J, Jones R, Tschudi C, Kolev NG, Rudenko G. Nat Commun. 2022 Jan 10; 2022 Jan 10. PMID: 35013170.
- Brain ventricles as windows into brain development and disease.Duy PQ, Rakic P, Alper SL, Butler WE, Walsh CA, Sestan N, Geschwind DH, Jin SC, Kahle KT. Neuron. 2022 Jan 5. PMID: 34990576.
- Author Correction: Visualizing group II intron dynamics between the first and second steps of splicing.Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Nat Commun. 2022 Jan 4; 2022 Jan 4. PMID: 34983933.
- Sequencing SARS-CoV-2 genomes from saliva.Alpert T, Vogels CBF, Breban MI, Petrone ME, Wyllie AL, Grubaugh ND, Fauver JR. Virus Evol. 2022; 2022 Jan 3. PMID: 35542310.
- A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice.Mao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. J Exp Med. 2022 Jan 3; 2021 Nov 10. PMID: 34757384.
- DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.Brewer KI, Gaffield GJ, Puri M, Breaker RR. Bioinformatics. 2022 Jan 3. PMID: 34524415.
- High-content CRISPR screening.Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X. Nat Rev Methods Primers. 2022; 2022 Feb 10. PMID: 37214176.
- Harnessing selenocysteine to enhance microbial cell factories for hydrogen production.Patel A, Mulder DW, Söll D, Krahn N. Front Catal. 2022; 2022 Dec 22. PMID: 36844461.
- RNA methylation in immune cells.Chen Y, Oh MH, Flavell R, Li HB. Adv Immunol. 2022; 2022 Sep 13. PMID: 36357012.
- Architectures and complex functions of tandem riboswitches.Sherlock ME, Higgs G, Yu D, Widner DL, White NA, Sudarsan N, Sadeeshkumar H, Perkins KR, Mirihana Arachchilage G, Malkowski SN, King CG, Harris KA, Gaffield G, Atilho RM, Breaker RR. RNA Biol. 2022 Jan. PMID: 36093908.
- Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study.Guo R, Pyle AM. Methods Enzymol. 2022; 2022 Jul 21. PMID: 35965013.
- Reinventing positive-strand RNA virus reverse genetics.Lindenbach BD. Adv Virus Res. 2022; 2022 Mar 29. PMID: 35840179.
- Fermented Soy Drink (Q-CAN® PLUS) Induces Apoptosis and Reduces Viability of Cancer Cells.Ouyang X, Chen Y, Tejaswi BS, Arumugam S, Secor E, Weiss TR, Leapman M, Ali A. Nutr Cancer. 2022; 2022 May 23. PMID: 35603899.
- U8 variants on the brain: a small nucleolar RNA and human disease.McFadden EJ, Baserga SJ. RNA Biol. 2022; 2021 Dec 31. PMID: 35389826.
- Development of Humanized Mouse Models for Studying Human NK Cells in Health and Disease.Shan L, Flavell RA, Herndler-Brandstetter D. Methods Mol Biol. 2022. PMID: 35344167.
- A digital pathology tool for quantification of color features in histologic specimens.Reschke M, DiRito JR, Stern D, Day W, Plebanek N, Harris M, Hosgood SA, Nicholson ML, Haakinson DJ, Zhang X, Mehal WZ, Ouyang X, Pober JS, Saltzman WM, Tietjen GT. Bioeng Transl Med. 2022 Jan; 2021 Aug 24. PMID: 35111944.
- Using selenocysteine-specific reporters to screen for efficient tRNA(Sec) variants.Chung CZ, Söll D, Krahn N. Methods Enzymol. 2022; 2021 Nov 14. PMID: 35101219.
- CD4 T cell-intrinsic STING signaling controls the differentiation and effector functions of T(H)1 and T(H)9 cells.Benoit-Lizon I, Jacquin E, Rivera Vargas T, Richard C, Roussey A, Dal Zuffo L, Martin T, Melis A, Vinokurova D, Shahoei SH, Baeza Garcia A, Pignol C, Giorgiutti S, Carapito R, Boidot R, Végran F, Flavell RA, Ryffel B, Nelson ER, Soulas-Sprauel P, Lawrence T, Apetoh L. J Immunother Cancer. 2022 Jan. PMID: 35091453.
- Long-acting and extended-release implant and nanoformulations with a synergistic antiretroviral two-drug combination controls HIV-1 infection in a humanized mouse model.Beloor J, Kudalkar SN, Buzzelli G, Yang F, Mandl HK, Rajashekar JK, Spasov KA, Jorgensen WL, Saltzman WM, Anderson KS, Kumar P. Bioeng Transl Med. 2022 Jan; 2021 Jun 26. PMID: 35079625.
- A high-throughput assay for directly monitoring nucleolar rRNA biogenesis.Bryant CJ, McCool MA, Abriola L, Surovtseva YV, Baserga SJ. Open Biol. 2022 Jan; 2022 Jan 26. PMID: 35078352.
- Measuring mRNA Decay with Roadblock-qPCR.Watson MJ, Thoreen CC. Curr Protoc. 2022 Jan. PMID: 35041257.
- Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Nat Microbiol. 2022 Jan; 2021 Dec 14. PMID: 34907347.
- Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis.De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Am J Respir Crit Care Med. 2022 Jan 1. PMID: 34724391.
- Traptamer screening: a new functional genomics approach to study virus entry and other cellular processes.Xie J, DiMaio D. FEBS J. 2022 Jan; 2021 May 8. PMID: 33604985.
2021
- Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA.Schärfen L, Zigackova D, Reimer KA, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD. Front Genet. 2021; 2022 Jan 28. PMID: 35154260.
- Endogenous Retroviruses Provide Protection Against Vaginal HSV-2 Disease.Jayewickreme R, Mao T, Philbrick W, Kong Y, Treger RS, Lu P, Rakib T, Dong H, Dang-Lawson M, Guild WA, Lau TJ, Iwasaki A, Tokuyama M. Front Immunol. 2021; 2022 Jan 4. PMID: 35058919.
- Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems.Mukai T, Amikura K, Fu X, Söll D, Crnković A. Front Genet. 2021; 2022 Jan 3. PMID: 35047015.
- SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes.Pawlica P, Yario TA, White S, Wang J, Moss WN, Hui P, Vinetz JM, Steitz JA. Proc Natl Acad Sci U S A. 2021 Dec 28; 2021 Dec 13. PMID: 34903581.
- Monospecific and bispecific monoclonal SARS-CoV-2 neutralizing antibodies that maintain potency against B.1.617.Peng L, Hu Y, Mankowski MC, Ren P, Chen RE, Wei J, Zhao M, Li T, Tripler T, Ye L, Chow RD, Fang Z, Wu C, Dong MB, Cook M, Wang G, Clark P, Nelson B, Klein D, Sutton R, Diamond MS, Wilen CB, Xiong Y, Chen S. bioRxiv. 2021 Dec 24; 2021 Dec 24. PMID: 34981065.
- Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons.Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. N Engl J Med. 2021 Dec 23; 2021 Dec 1. PMID: 34941024.
- Fibroblasts positive for meflin have anti-fibrotic properties in pulmonary fibrosis.Nakahara Y, Hashimoto N, Sakamoto K, Enomoto A, Adams TS, Yokoi T, Omote N, Poli S, Ando A, Wakahara K, Suzuki A, Inoue M, Hara A, Mizutani Y, Imaizumi K, Kawabe T, Rosas IO, Takahashi M, Kaminski N, Hasegawa Y. Eur Respir J. 2021 Dec; 2021 Dec 23. PMID: 34049947.
- Of variants and vaccines.Grubaugh ND, Cobey S. Cell. 2021 Dec 22. PMID: 34942096.
- A multidimensional HIV-1 persistence model for clonal expansion and viral rebound in vitro.Eshetu A, Ho YC. Cell Rep Methods. 2021 Dec 20; 2021 Dec 20. PMID: 35475216.
- COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis.Lee M, Sallah YH, Petrone M, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert TD, Grubaugh ND, Gupta S. JMIRx Med. 2021 Oct-Dec; 2021 Dec 17. PMID: 35014989.
- Natural circularly permuted group II introns in bacteria produce RNA circles.Roth A, Weinberg Z, Vanderschuren K, Murdock MH, Breaker RR. iScience. 2021 Dec 17; 2021 Nov 13. PMID: 34901790.
- Distinct roles of KLF4 in mesenchymal cell subtypes during lung fibrogenesis.Chandran RR, Xie Y, Gallardo-Vara E, Adams T, Garcia-Milian R, Kabir I, Sheikh AQ, Kaminski N, Martin KA, Herzog EL, Greif DM. Nat Commun. 2021 Dec 10; 2021 Dec 10. PMID: 34893592.
- Intranasal priming induces local lung-resident B cell populations that secrete protective mucosal antiviral IgA.Oh JE, Song E, Moriyama M, Wong P, Zhang S, Jiang R, Strohmeier S, Kleinstein SH, Krammer F, Iwasaki A. Sci Immunol. 2021 Dec 10; 2021 Dec 10. PMID: 34890255.
- Global disparities in SARS-CoV-2 genomic surveillance.Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR. medRxiv. 2021 Dec 9; 2021 Dec 9. PMID: 34462754.
- The zinc-finger protein OEF-1 stabilizes histone modification patterns and promotes efficient splicing in the Caenorhabditis elegans germline.McManus CE, Mazzetto M, Wei G, Han M, Reinke V. G3 (Bethesda). 2021 Dec 8. PMID: 34519784.
- Correction to 'Tumor-selective, antigen-independent delivery of a pH sensitive peptide-topoisomerase inhibitor conjugate suppresses tumor growth without systemic toxicity'.Gayle S, Aiello R, Leelatian N, Beckta JM, Bechtold J, Bourassa P, Csengery J, Maguire RJ, Marshall D, Sundaram RK, Van Doorn J, Jones K, Moore H, Lopresti-Morrow L, Paradis T, Tylaska L, Zhang Q, Visca H, Reshetnyak YK, Andreev OA, Engelman DM, Glazer PM, Bindra RS, Paralkar VM. NAR Cancer. 2021 Dec; 2021 Dec 7. PMID: 34888524.
- Transcriptomics of bronchoalveolar lavage cells identifies new molecular endotypes of sarcoidosis.Vukmirovic M, Yan X, Gibson KF, Gulati M, Schupp JC, DeIuliis G, Adams TS, Hu B, Mihaljinec A, Woolard TN, Lynn H, Emeagwali N, Herzog EL, Chen ES, Morris A, Leader JK, Zhang Y, Garcia JGN, Maier LA, Collman RG, Drake WP, Becich MJ, Hochheiser H, Wisniewski SR, Benos PV, Moller DR, Prasse A, Koth LL, Kaminski N. Eur Respir J. 2021 Dec; 2021 Dec 2. PMID: 34083402.
- IL-17 Receptor C Signaling Controls CD4(+) T(H)17 Immune Responses and Tissue Injury in Immune-Mediated Kidney Diseases.Schmidt T, Luebbe J, Kilian C, Riedel JH, Hiekmann S, Asada N, Ginsberg P, Robben L, Song N, Kaffke A, Peters A, Borchers A, Flavell RA, Gagliani N, Pelzcar P, Huber S, Huber TB, Turner JE, Paust HJ, Krebs CF, Panzer U. J Am Soc Nephrol. 2021 Dec. PMID: 35167487.
- Building skill-sets, confidence, and interest for diverse scientific careers in the biological and biomedical sciences.Claydon J, Farley-Barnes K, Baserga S. FASEB Bioadv. 2021 Dec; 2021 Sep 15. PMID: 34938961.
- Comprehensive Genomic Characterization of A Case of Granular Cell Tumor of the Posterior Pituitary Gland: A Case Report.Hong CS, Elsamadicy AA, Fisayo A, Inzucchi SE, Gopal PP, Vining EM, Erson-Omay EZ, Bulent Omay S. Front Endocrinol (Lausanne). 2021; 2021 Dec 1. PMID: 34925233.
- Can we eradicate viral pathogens?Alizon S, Turner PE. J Evol Biol. 2021 Dec; 2021 Dec 14. PMID: 34907625.
- PPIL4 is essential for brain angiogenesis and implicated in intracranial aneurysms in humans.Barak T, Ristori E, Ercan-Sencicek AG, Miyagishima DF, Nelson-Williams C, Dong W, Jin SC, Prendergast A, Armero W, Henegariu O, Erson-Omay EZ, Harmancı AS, Guy M, Gültekin B, Kilic D, Rai DK, Goc N, Aguilera SM, Gülez B, Altinok S, Ozcan K, Yarman Y, Coskun S, Sempou E, Deniz E, Hintzen J, Cox A, Fomchenko E, Jung SW, Ozturk AK, Louvi A, Bilgüvar K, Connolly ES Jr, Khokha MK, Kahle KT, Yasuno K, Lifton RP, Mishra-Gorur K, Nicoli S, Günel M. Nat Med. 2021 Dec; 2021 Dec 9. PMID: 34887573.
- Design and implementation of a cohort study of persons living with HIV infection who are initiating medication treatment for opioid use disorder to evaluate HIV-1 persistence.Schultheis A, Sanchez M, Pedersen S, Kyriakides T, Ho YC, Kluger Y, Springer SA. Contemp Clin Trials Commun. 2021 Dec; 2021 Nov 11. PMID: 34825103.
- IL-27 signalling promotes adipocyte thermogenesis and energy expenditure.Wang Q, Li D, Cao G, Shi Q, Zhu J, Zhang M, Cheng H, Wen Q, Xu H, Zhu L, Zhang H, Perry RJ, Spadaro O, Yang Y, He S, Chen Y, Wang B, Li G, Liu Z, Yang C, Wu X, Zhou L, Zhou Q, Ju Z, Lu H, Xin Y, Yang X, Wang C, Liu Y, Shulman GI, Dixit VD, Lu L, Yang H, Flavell RA, Yin Z. Nature. 2021 Dec; 2021 Nov 24. PMID: 34819664.
- Noncoding RNAs: biology and applications-a Keystone Symposia report.Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Ann N Y Acad Sci. 2021 Dec; 2021 Nov 17. PMID: 34791665.
- Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity.Lucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, Gehlhausen JR, Campbell M, Silva J, Tabachnikova A, Peña-Hernandez MA, Muenker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Shaw AC, Ko AI, Omer SB, Grubaugh ND, Iwasaki A. Nature. 2021 Dec; 2021 Oct 11. PMID: 34634791.
- Vulnerability of IDH1-Mutant Cancers to Histone Deacetylase Inhibition via Orthogonal Suppression of DNA Repair.Dow J, Krysztofiak A, Liu Y, Colon-Rios DA, Rogers FA, Glazer PM. Mol Cancer Res. 2021 Dec; 2021 Sep 17. PMID: 34535560.
- Correction: Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons.Runge K, Mathieu R, Bugeon S, Lafi S, Beurrier C, Sahu S, Schaller F, Loubat A, Herault L, Gaillard S, Pallesi-Pocachard E, Montheil A, Bosio A, Rosenfeld JA, Hudson E, Lindstrom K, Mercimek-Andrews S, Jeffries L, van Haeringen A, Vanakker O, Van Hecke A, Amrom D, Küry S, Ratner C, Jethva R, Gamble C, Jacq B, Fasano L, Santpere G, Lorente-Galdos B, Sestan N, Gelot A, Giacuzz S, Goebbels S, Represa A, Cardoso C, Cremer H, de Chevigny A. Mol Psychiatry. 2021 Dec. PMID: 34282265.
- Peptide nucleic acids and their role in gene regulation and editing.Perera JDR, Carufe KEW, Glazer PM. Biopolymers. 2021 Dec; 2021 Jun 15. PMID: 34129732.
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.Brewer KI, Greenlee EB, Higgs G, Yu D, Mirihana Arachchilage G, Chen X, King N, White N, Breaker RR. RNA Biol. 2021 Dec; 2021 May 10. PMID: 33970790.
- The design and synthesis of circular RNAs.Obi P, Chen YG. Methods. 2021 Dec; 2021 Mar 2. PMID: 33662562.
- Regulation of the Cell-Intrinsic DNA Damage Response by the Innate Immune Machinery.Hayman TJ, Glazer PM. Int J Mol Sci. 2021 Nov 25; 2021 Nov 25. PMID: 34884568.
- NogoA-expressing astrocytes limit peripheral macrophage infiltration after ischemic brain injury in primates.Boghdadi AG, Spurrier J, Teo L, Li M, Skarica M, Cao B, Kwan WC, Merson TD, Nilsson SK, Sestan N, Strittmatter SM, Bourne JA. Nat Commun. 2021 Nov 25; 2021 Nov 25. PMID: 34824275.
- LRRC15 is an inhibitory receptor blocking SARS-CoV-2 spike-mediated entry in trans.Song J, Chow RD, Pena-Hernandez M, Zhang L, Loeb SA, So EY, Liang OD, Wilen CB, Lee S. bioRxiv. 2021 Nov 24; 2021 Nov 24. PMID: 34845449.
- rab-27 acts in an intestinal pathway to inhibit axon regeneration in C. elegans.Lin-Moore AT, Oyeyemi MJ, Hammarlund M. PLoS Genet. 2021 Nov; 2021 Nov 24. PMID: 34818334.
- Desmosterol suppresses macrophage inflammasome activation and protects against vascular inflammation and atherosclerosis.Zhang X, McDonald JG, Aryal B, Canfrán-Duque A, Goldberg EL, Araldi E, Ding W, Fan Y, Thompson BM, Singh AK, Li Q, Tellides G, Ordovás-Montanes J, García Milian R, Dixit VD, Ikonen E, Suárez Y, Fernández-Hernando C. Proc Natl Acad Sci U S A. 2021 Nov 23. PMID: 34782454.
- High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19.Haynes WA, Kamath K, Bozekowski J, Baum-Jones E, Campbell M, Casanovas-Massana A, Daugherty PS, Dela Cruz CS, Dhal A, Farhadian SF, Fitzgibbons L, Fournier J, Jhatro M, Jordan G, Klein J, Lucas C, Kessler D, Luchsinger LL, Martinez B, Catherine Muenker M, Pischel L, Reifert J, Sawyer JR, Waitz R, Wunder EA Jr, Zhang M, Iwasaki A, Ko A, Shon JC. Commun Biol. 2021 Nov 22; 2021 Nov 22. PMID: 34811480.
- 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development.Wang T, Wang Z, de Fabritus L, Tao J, Saied EM, Lee HJ, Ramazanov BR, Jackson B, Burkhardt D, Parker M, Gleinich AS, Wang Z, Seo DE, Zhou T, Xu S, Alecu I, Azadi P, Arenz C, Hornemann T, Krishnaswamy S, van de Pavert SA, Kaech SM, Ivanova NB, Santori FR. Dev Cell. 2021 Nov 22; 2021 Nov 10. PMID: 34762852.
- A Pulmonary Vascular Model From Endothelialized Whole Organ Scaffolds.Yuan Y, Leiby KL, Greaney AM, Raredon MSB, Qian H, Schupp JC, Engler AJ, Baevova P, Adams TS, Kural MH, Wang J, Obata T, Yoder MC, Kaminski N, Niklason LE. Front Bioeng Biotechnol. 2021; 2021 Nov 19. PMID: 34869270.
- RNA chaperone activates Salmonella virulence program during infection.Choi J, Salvail H, Groisman EA. Nucleic Acids Res. 2021 Nov 18. PMID: 34751407.
- Interleukin-10 improves stroke outcome by controlling the detrimental Interleukin-17A response.Piepke M, Clausen BH, Ludewig P, Vienhues JH, Bedke T, Javidi E, Rissiek B, Jank L, Brockmann L, Sandrock I, Degenhardt K, Jander A, Roth V, Schädlich IS, Prinz I, Flavell RA, Kobayashi Y, Renné T, Gerloff C, Huber S, Magnus T, Gelderblom M. J Neuroinflammation. 2021 Nov 13; 2021 Nov 13. PMID: 34772416.
- Phase separation drives RNA virus-induced activation of the NLRP6 inflammasome.Shen C, Li R, Negro R, Cheng J, Vora SM, Fu TM, Wang A, He K, Andreeva L, Gao P, Tian Z, Flavell RA, Zhu S, Wu H. Cell. 2021 Nov 11; 2021 Oct 21. PMID: 34678144.
- m(6)A mRNA methylation-directed myeloid cell activation controls progression of NAFLD and obesity.Qin Y, Li B, Arumugam S, Lu Q, Mankash SM, Li J, Sun B, Li J, Flavell RA, Li HB, Ouyang X. Cell Rep. 2021 Nov 9. PMID: 34758326.
- Giving translation a hand.Strayer EC, Tornini VA, Giraldez AJ. Dev Cell. 2021 Nov 8. PMID: 34752744.
- MMAB promotes negative feedback control of cholesterol homeostasis.Goedeke L, Canfrán-Duque A, Rotllan N, Chaube B, Thompson BM, Lee RG, Cline GW, McDonald JG, Shulman GI, Lasunción MA, Suárez Y, Fernández-Hernando C. Nat Commun. 2021 Nov 8; 2021 Nov 8. PMID: 34750386.
- Machine learning implicates the IL-18 signaling axis in severe asthma.Camiolo MJ, Zhou X, Wei Q, Trejo Bittar HE, Kaminski N, Ray A, Wenzel SE. JCI Insight. 2021 Nov 8; 2021 Nov 8. PMID: 34591794.
- Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses.Xiong K, Gerstein M, Masel J. Genetics. 2021 Nov 5. PMID: 34740240.
- Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin.Wang G, Kitaoka T, Crawford A, Mao Q, Hesketh A, Guppy FM, Ash GI, Liu J, Gerstein MB, Pitsiladis YP. Sci Rep. 2021 Nov 4; 2021 Nov 4. PMID: 34737331.
- STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. Mol Cell. 2021 Nov 4; 2021 Sep 13. PMID: 34520723.
- Clinical Efficacy of Olaparib in IDH1/IDH2-Mutant Mesenchymal Sarcomas.Eder JP, Doroshow DB, Do KT, Keedy VL, Sklar JS, Glazer P, Bindra R, Shapiro GI. JCO Precis Oncol. 2021 Nov. PMID: 34994649.
- The molecular mechanism of RIG-I activation and signaling.Thoresen D, Wang W, Galls D, Guo R, Xu L, Pyle AM. Immunol Rev. 2021 Nov; 2021 Sep 12. PMID: 34514601.
- Establishing a Global Standard for Wearable Devices in Sport and Exercise Medicine: Perspectives from Academic and Industry Stakeholders.Ash GI, Stults-Kolehmainen M, Busa MA, Gaffey AE, Angeloudis K, Muniz-Pardos B, Gregory R, Huggins RA, Redeker NS, Weinzimer SA, Grieco LA, Lyden K, Megally E, Vogiatzis I, Scher L, Zhu X, Baker JS, Brandt C, Businelle MS, Fucito LM, Griggs S, Jarrin R, Mortazavi BJ, Prioleau T, Roberts W, Spanakis EK, Nally LM, Debruyne A, Bachl N, Pigozzi F, Halabchi F, Ramagole DA, Janse van Rensburg DC, Wolfarth B, Fossati C, Rozenstoka S, Tanisawa K, Börjesson M, Casajus JA, Gonzalez-Aguero A, Zelenkova I, Swart J, Gursoy G, Meyerson W, Liu J, Greenbaum D, Pitsiladis YP, Gerstein MB. Sports Med. 2021 Nov; 2021 Sep 1. PMID: 34468950.
- Disruption of NEUROD2 causes a neurodevelopmental syndrome with autistic features via cell-autonomous defects in forebrain glutamatergic neurons.Runge K, Mathieu R, Bugeon S, Lafi S, Beurrier C, Sahu S, Schaller F, Loubat A, Herault L, Gaillard S, Pallesi-Pocachard E, Montheil A, Bosio A, Rosenfeld JA, Hudson E, Lindstrom K, Mercimek-Andrews S, Jeffries L, van Haeringen A, Vanakker O, Van Hecke A, Amrom D, Küry S, Ratner C, Jethva R, Gamble C, Jacq B, Fasano L, Santpere G, Lorente-Galdos B, Sestan N, Gelot A, Giacuzz S, Goebbels S, Represa A, Cardoso C, Cremer H, de Chevigny A. Mol Psychiatry. 2021 Nov; 2021 Jun 29. PMID: 34188164.
- Community context matters for bacteria-phage ecology and evolution.Blazanin M, Turner PE. ISME J. 2021 Nov; 2021 Jun 14. PMID: 34127803.
- Keratin 17 testing in pancreatic cancer needle aspiration biopsies predicts survival.Roa-Peña L, Babu S, Leiton CV, Wu M, Taboada S, Akalin A, Buscaglia J, Escobar-Hoyos LF, Shroyer KR. Cancer Cytopathol. 2021 Nov; 2021 Jun 2. PMID: 34076963.
- Exosomes provide unappreciated carrier effects that assist transfers of their miRNAs to targeted cells; I. They are 'The Elephant in the Room'.Askenase PW. RNA Biol. 2021 Nov; 2021 May 4. PMID: 33944671.
- Role of MBD3-SOX2 axis in residual myeloma following pomalidomide.Verma R, Branagan AR, Xu ML, Flavell RA, Dhodapkar KM, Dhodapkar MV. Leukemia. 2021 Nov; 2021 Feb 18. PMID: 33603141.
- Rare Skin Reactions after mRNA Vaccination, Similar to Jones-Mote Basophil Responses.Askenase PW. N Engl J Med. 2021 Oct 28. PMID: 34706177.
- A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data.Li H, Zhu B, Xu Z, Adams T, Kaminski N, Zhao H. BMC Bioinformatics. 2021 Oct 26; 2021 Oct 26. PMID: 34702190.
- Model Systems to Study the Chronic, Polymicrobial Infections in Cystic Fibrosis: Current Approaches and Exploring Future Directions.O'Toole GA, Crabbé A, Kümmerli R, LiPuma JJ, Bomberger JM, Davies JC, Limoli D, Phelan VV, Bliska JB, DePas WH, Dietrich LE, Hampton TH, Hunter R, Khursigara CM, Price-Whelan A, Ashare A, Cramer RA, Goldberg JB, Harrison F, Hogan DA, Henson MA, Madden DR, Mayers JR, Nadell C, Newman D, Prince A, Rivett DW, Schwartzman JD, Schultz D, Sheppard DC, Smyth AR, Spero MA, Stanton BA, Turner PE, van der Gast C, Whelan FJ, Whitaker R, Whiteson K. mBio. 2021 Oct 26; 2021 Sep 21. PMID: 34544277.
- Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions.Girskis KM, Stergachis AB, DeGennaro EM, Doan RN, Qian X, Johnson MB, Wang PP, Sejourne GM, Nagy MA, Pollina EA, Sousa AMM, Shin T, Kenny CJ, Scotellaro JL, Debo BM, Gonzalez DM, Rento LM, Yeh RC, Song JHT, Beaudin M, Fan J, Kharchenko PV, Sestan N, Greenberg ME, Walsh CA. Neuron. 2021 Oct 20; 2021 Sep 2. PMID: 34478631.
- Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis.Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg CP, Galande S. Nat Commun. 2021 Oct 19; 2021 Oct 19. PMID: 34667153.
- The loss of DHX15 impairs endothelial energy metabolism, lymphatic drainage and tumor metastasis in mice.Ribera J, Portolés I, Córdoba-Jover B, Rodríguez-Vita J, Casals G, González-de la Presa B, Graupera M, Solsona-Vilarrasa E, Garcia-Ruiz C, Fernández-Checa JC, Soria G, Tudela R, Esteve-Codina A, Espadas G, Sabidó E, Jiménez W, Sessa WC, Morales-Ruiz M. Commun Biol. 2021 Oct 15; 2021 Oct 15. PMID: 34654883.
- Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2.Israelow B, Mao T, Klein J, Song E, Menasche B, Omer SB, Iwasaki A. Sci Immunol. 2021 Oct 15; 2021 Sep 2. PMID: 34623900.
- Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA.Ren X, Gelinas AD, Linehan M, Iwasaki A, Wang W, Janjic N, Pyle AM. J Mol Biol. 2021 Oct 15; 2021 Sep 3. PMID: 34487794.
- Activation of the PDGF β Receptor by a Persistent Artificial Signal Peptide.Petti LM, Koleske BN, DiMaio D. J Mol Biol. 2021 Oct 15; 2021 Aug 30. PMID: 34474086.
- Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase.Boddu PC, Gupta AK, Kim JS, Neugebauer KM, Waldman T, Pillai MM. Commun Biol. 2021 Oct 13; 2021 Oct 13. PMID: 34645977.
- Keratin 17 Is a Novel Cytologic Biomarker for Urothelial Carcinoma Diagnosis.Babu S, Kim NW, Wu M, Chan I, Escobar-Hoyos LF, Shroyer KR. Am J Clin Pathol. 2021 Oct 13. PMID: 34086841.
- Cellular Adaptations to Cytoplasmic Mg(2+) Limitation.Groisman EA, Chan C. Annu Rev Microbiol. 2021 Oct 8. PMID: 34623895.
- Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. medRxiv. 2021 Oct 7; 2021 Oct 7. PMID: 34642698.
- Network propagation-based prioritization of long tail genes in 17 cancer types.Mohsen H, Gunasekharan V, Qing T, Seay M, Surovtseva Y, Negahban S, Szallasi Z, Pusztai L, Gerstein MB. Genome Biol. 2021 Oct 7; 2021 Oct 7. PMID: 34620211.
- How COVID-19 has transformed my science.Iwasaki A. Neuron. 2021 Oct 6; 2021 Aug 6. PMID: 34363752.
- PIWI-mediated control of tissue-specific transposons is essential for somatic cell differentiation.Li D, Taylor DH, van Wolfswinkel JC. Cell Rep. 2021 Oct 5. PMID: 34610311.
- Placenta-derived interferon-stimulated gene 20 controls ZIKA virus infection.Ding J, Aldo P, Roberts CM, Stabach P, Liu H, You Y, Qiu X, Jeong J, Maxwell A, Lindenbach B, Braddock D, Liao A, Mor G. EMBO Rep. 2021 Oct 5; 2021 Aug 18. PMID: 34405956.
- DATA-DRIVEN LEARNING OF GEOMETRIC SCATTERING MODULES FOR GNNS.Tong A, Wenkel F, Macdonald K, Krishnaswamy S, Wolf G. IEEE Int Workshop Mach Learn Signal Process. 2021 Oct; 2021 Nov 15. PMID: 36945315.
- MULTIMODAL DATA VISUALIZATION AND DENOISING WITH INTEGRATED DIFFUSION.Kuchroo M, Godavarthi A, Tong A, Wolf G, Krishnaswamy S. IEEE Int Workshop Mach Learn Signal Process. 2021 Oct; 2021 Nov 15. PMID: 35340810.
- KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements.Zhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, McGeary MK, Song E, Blenman KRM, Micevic G, Jessel S, Zhang Y, Yin M, Booth CJ, Jilaveanu LB, Damsky W, Sznol M, Kluger HM, Iwasaki A, Bosenberg MW, Yan Q. Nature. 2021 Oct; 2021 Oct 20. PMID: 34671158.
- Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis.Shibata M, Pattabiraman K, Muchnik SK, Kaur N, Morozov YM, Cheng X, Waxman SG, Sestan N. Nature. 2021 Oct; 2021 Oct 1. PMID: 34599306.
- Regulation of prefrontal patterning and connectivity by retinoic acid.Shibata M, Pattabiraman K, Lorente-Galdos B, Andrijevic D, Kim SK, Kaur N, Muchnik SK, Xing X, Santpere G, Sousa AMM, Sestan N. Nature. 2021 Oct; 2021 Oct 1. PMID: 34599305.
- A reservoir of stem-like CD8(+) T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response.Connolly KA, Kuchroo M, Venkat A, Khatun A, Wang J, William I, Hornick NI, Fitzgerald BL, Damo M, Kasmani MY, Cui C, Fagerberg E, Monroy I, Hutchins A, Cheung JF, Foster GG, Mariuzza DL, Nader M, Zhao H, Cui W, Krishnaswamy S, Joshi NS. Sci Immunol. 2021 Oct; 2021 Sep 2. PMID: 34597124.
- The regulation of DNA supercoiling across evolution.Duprey A, Groisman EA. Protein Sci. 2021 Oct; 2021 Aug 23. PMID: 34398513.
- tRNA-like leader-trailer interaction promotes 3'-end maturation of MALAT1.Torabi SF, DeGregorio SJ, Steitz JA. RNA. 2021 Oct; 2021 Jul 12. PMID: 34253686.
- Insights into VPS13 properties and function reveal a new mechanism of eukaryotic lipid transport.Leonzino M, Reinisch KM, De Camilli P. Biochim Biophys Acta Mol Cell Biol Lipids. 2021 Oct; 2021 Jul 1. PMID: 34216812.
- Split-personality inhibitors.Thoreen CC. Nat Chem Biol. 2021 Oct. PMID: 34168366.
- COVID-19 vaccines: Keeping pace with SARS-CoV-2 variants.Cevik M, Grubaugh ND, Iwasaki A, Openshaw P. Cell. 2021 Sep 30; 2021 Sep 17. PMID: 34534444.
- Multiplex suppression of four quadruplet codons via tRNA directed evolution.DeBenedictis EA, Carver GD, Chung CZ, Söll D, Badran AH. Nat Commun. 2021 Sep 29; 2021 Sep 29. PMID: 34588441.
- Recurring Revolutions in Virology.Enquist LW, DiMaio D, Dermody TS. Annu Rev Virol. 2021 Sep 29. PMID: 33826854.
- Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization.Lou S, Li T, Liu J, Gerstein M. Bioinformatics. 2021 Sep 29. PMID: 33792640.
- Vaccine Safety, Efficacy, and Trust Take Time.Dermody TS, DiMaio D, Enquist LW. Annu Rev Virol. 2021 Sep 29. PMID: 33186082.
- The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence.Yeh YJ, Yang K, Razmi A, Ho YC. Viruses. 2021 Sep 17; 2021 Sep 17. PMID: 34578439.
- METTL3-mediated m(6)A RNA methylation promotes the anti-tumour immunity of natural killer cells.Song H, Song J, Cheng M, Zheng M, Wang T, Tian S, Flavell RA, Zhu S, Li HB, Ding C, Wei H, Sun R, Peng H, Tian Z. Nat Commun. 2021 Sep 17; 2021 Sep 17. PMID: 34535671.
- Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5.Maerker M, Getwan M, Dowdle ME, McSheene JC, Gonzalez V, Pelliccia JL, Hamilton DS, Yartseva V, Vejnar C, Tingler M, Minegishi K, Vick P, Giraldez AJ, Hamada H, Burdine RD, Sheets MD, Blum M, Schweickert A. Nat Commun. 2021 Sep 16; 2021 Sep 16. PMID: 34531379.
- Emergence of an early SARS-CoV-2 epidemic in the United States.Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G Jr, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Cell. 2021 Sep 16; 2021 Jul 27. PMID: 34508652.
- Mechanisms of Hypoxia-Induced Pulmonary Arterial Stiffening in Mice Revealed by a Functional Genetics Assay of Structural, Functional, and Transcriptomic Data.Manning EP, Ramachandra AB, Schupp JC, Cavinato C, Raredon MSB, Bärnthaler T, Cosme C Jr, Singh I, Tellides G, Kaminski N, Humphrey JD. Front Physiol. 2021; 2021 Sep 14. PMID: 34594238.
- Live imaging of SARS-CoV-2 infection in mice reveals that neutralizing antibodies require Fc function for optimal efficacy.Ullah I, Prévost J, Ladinsky MS, Stone H, Lu M, Anand SP, Beaudoin-Bussières G, Symmes K, Benlarbi M, Ding S, Gasser R, Fink C, Chen Y, Tauzin A, Goyette G, Bourassa C, Medjahed H, Mack M, Chung K, Wilen CB, Dekaban GA, Dikeakos JD, Bruce EA, Kaufmann DE, Stamatatos L, McGuire AT, Richard J, Pazgier M, Bjorkman PJ, Mothes W, Finzi A, Kumar P, Uchil PD. Immunity. 2021 Sep 14; 2021 Aug 18. PMID: 34453881.
- Comprehensive Clinicopathologic and Molecular Analysis of Mast Cell Leukemia With Associated Hematologic Neoplasm: A Report and In-Depth Study of 5 Cases.Li P, Biancon G, Patel T, Pan Z, Kothari S, Halene S, Prebet T, Xu ML. Front Oncol. 2021; 2021 Sep 13. PMID: 34589432.
- Witnessing the structural evolution of an RNA enzyme.Portillo X, Huang YT, Breaker RR, Horning DP, Joyce GF. Elife. 2021 Sep 9; 2021 Sep 9. PMID: 34498588.
- Recovering genotypes and phenotypes using allele-specific genes.Gürsoy G, Lu N, Wagner S, Gerstein M. Genome Biol. 2021 Sep 7; 2021 Sep 7. PMID: 34493313.
- Defective Flow-Migration Coupling Causes Arteriovenous Malformations in Hereditary Hemorrhagic Telangiectasia.Park H, Furtado J, Poulet M, Chung M, Yun S, Lee S, Sessa WC, Franco CA, Schwartz MA, Eichmann A. Circulation. 2021 Sep 7; 2021 Jun 29. PMID: 34182767.
- Extracellular vesicles mediated exocytosis of antisense peptide nucleic acids.Malik S, Saltzman WM, Bahal R. Mol Ther Nucleic Acids. 2021 Sep 3; 2021 Aug 8. PMID: 34458012.
- Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Hanage WP, Grubaugh ND, Peccia J, Baym M. medRxiv. 2021 Sep 2; 2021 Sep 2. PMID: 34494031.
- Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes.Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Nature. 2021 Sep. PMID: 34552250.
- Small extracellular vesicles released by infused mesenchymal stromal cells target M2 macrophages and promote TGF-β upregulation, microvascular stabilization and functional recovery in a rodent model of severe spinal cord injury.Nakazaki M, Morita T, Lankford KL, Askenase PW, Kocsis JD. J Extracell Vesicles. 2021 Sep. PMID: 34478241.
- Reply to: Rectally shed SARS-CoV-2 lacks infectivity: time to rethink faecal-oral transmission?Guo M, Tao W, Flavell RA, Zhu S. Nat Rev Gastroenterol Hepatol. 2021 Sep. PMID: 34312525.
- Brain vulnerability and viability after ischaemia.Daniele SG, Trummer G, Hossmann KA, Vrselja Z, Benk C, Gobeske KT, Damjanovic D, Andrijevic D, Pooth JS, Dellal D, Beyersdorf F, Sestan N. Nat Rev Neurosci. 2021 Sep; 2021 Jul 21. PMID: 34290397.
- Pseudouridines on Trypanosoma brucei mRNAs are developmentally regulated: Implications to mRNA stability and protein binding.Rajan KS, Adler K, Madmoni H, Peleg-Chen D, Cohen-Chalamish S, Doniger T, Galili B, Gerber D, Unger R, Tschudi C, Michaeli S. Mol Microbiol. 2021 Sep; 2021 Jul 7. PMID: 34165831.
- BBIT20 inhibits homologous DNA repair with disruption of the BRCA1-BARD1 interaction in breast and ovarian cancer.Raimundo L, Paterna A, Calheiros J, Ribeiro J, Cardoso DSP, Piga I, Neto SJ, Hegan D, Glazer PM, Indraccolo S, Mulhovo S, Costa JL, Ferreira MU, Saraiva L. Br J Pharmacol. 2021 Sep; 2021 Jun 11. PMID: 33899955.
- Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer.Armstrong AJ, Li X, Tucker M, Li S, Mu XJ, Eng KW, Sboner A, Rubin M, Gerstein M. Prostate Cancer Prostatic Dis. 2021 Sep; 2021 Feb 10. PMID: 33568750.
- Vibrational optical coherence tomography detects unique skin fibrotic states: Preliminary results of animal and human studies.Odell ID, Flavell RA, Silver FH. J Am Acad Dermatol. 2021 Sep; 2020 Aug 26. PMID: 32860914.
- Bacterial translation machinery for deliberate mistranslation of the genetic code.Vargas-Rodriguez O, Badran AH, Hoffman KS, Chen M, Crnković A, Ding Y, Krieger JR, Westhof E, Söll D, Melnikov S. Proc Natl Acad Sci U S A. 2021 Aug 31. PMID: 34413202.
- Associations of SARS-CoV-2 serum IgG with occupation and demographics of military personnel.Zell J, Wisnewski AV, Liu J, Klein J, Lucas C, Slade M, Iwasaki A, Redlich CA. PLoS One. 2021; 2021 Aug 30. PMID: 34460832.
- Influenza Antigens NP and M2 Confer Cross Protection to BALB/c Mice against Lethal Challenge with H1N1, Pandemic H1N1 or H5N1 Influenza A Viruses.Mytle N, Leyrer S, Inglefield JR, Harris AM, Hickey TE, Minang J, Lu H, Ma Z, Andersen H, Grubaugh ND, Guina T, Skiadopoulos MH, Lacy MJ. Viruses. 2021 Aug 27; 2021 Aug 27. PMID: 34578289.
- Maternal Piwi regulates primordial germ cell development to ensure the fertility of female progeny in Drosophila.Gonzalez LE, Tang X, Lin H. Genetics. 2021 Aug 26. PMID: 34142134.
- Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain.Liang L, Fazel Darbandi S, Pochareddy S, Gulden FO, Gilson MC, Sheppard BK, Sahagun A, An JY, Werling DM, Rubenstein JLR, Sestan N, Bender KJ, Sanders SJ. Genome Med. 2021 Aug 23; 2021 Aug 23. PMID: 34425903.
- Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions.Liu J, Spakowicz DJ, Ash GI, Hoyd R, Ahluwalia R, Zhang A, Lou S, Lee D, Zhang J, Presley C, Greene A, Stults-Kolehmainen M, Nally LM, Baker JS, Fucito LM, Weinzimer SA, Papachristos AV, Gerstein M. PLoS Comput Biol. 2021 Aug; 2021 Aug 23. PMID: 34424894.
- Phosphorylation of a Human Microprotein Promotes Dissociation of Biomolecular Condensates.Na Z, Luo Y, Cui DS, Khitun A, Smelyansky S, Loria JP, Slavoff SA. J Am Chem Soc. 2021 Aug 18; 2021 Aug 4. PMID: 34346674.
- How the PhoP/PhoQ System Controls Virulence and Mg(2+) Homeostasis: Lessons in Signal Transduction, Pathogenesis, Physiology, and Evolution.Groisman EA, Duprey A, Choi J. Microbiol Mol Biol Rev. 2021 Aug 18; 2021 Jun 30. PMID: 34191587.
- STK11/LKB1 Loss of Function Is Associated with Global DNA Hypomethylation and S-Adenosyl-Methionine Depletion in Human Lung Adenocarcinoma.Koenig MJ, Agana BA, Kaufman JM, Sharpnack MF, Wang WZ, Weigel C, Navarro FCP, Amann JM, Cacciato N, Arasada RR, Gerstein MB, Wysocki VH, Oakes C, Carbone DP. Cancer Res. 2021 Aug 15; 2021 May 27. PMID: 34045189.
- Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency.Zhang CH, Spasov KA, Reilly RA, Hollander K, Stone EA, Ippolito JA, Liosi ME, Deshmukh MG, Tirado-Rives J, Zhang S, Liang Z, Miller SJ, Isaacs F, Lindenbach BD, Anderson KS, Jorgensen WL. ACS Med Chem Lett. 2021 Aug 12; 2021 Jul 14. PMID: 34408808.
- New Vistas for Cell-Surface GlycoRNAs.Nachtergaele S, Krishnan Y. N Engl J Med. 2021 Aug 12. PMID: 34379930.
- Challenges in interpreting cytokine data in COVID-19 affect patient care and management.Wang SY, Takahashi T, Pine AB, Damsky WE, Simonov M, Zhang Y, Kieras E, Price CC, King BA, Siegel MD, Desir GV, Lee AI, Iwasaki A, Chun HJ. PLoS Biol. 2021 Aug; 2021 Aug 6. PMID: 34358229.
- Molecular topography of an entire nervous system.Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM 3rd. Cell. 2021 Aug 5; 2021 Jul 7. PMID: 34237253.
- The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs.Tesfaye E, Martinez-Terroba E, Bendor J, Winkler L, Olivero C, Chen K, Feldser DM, Zamudio JR, Dimitrova N. Proc Natl Acad Sci U S A. 2021 Aug 3. PMID: 34326251.
- TMEM41B acts as an ER scramblase required for lipoprotein biogenesis and lipid homeostasis.Huang D, Xu B, Liu L, Wu L, Zhu Y, Ghanbarpour A, Wang Y, Chen FJ, Lyu J, Hu Y, Kang Y, Zhou W, Wang X, Ding W, Li X, Jiang Z, Chen J, Zhang X, Zhou H, Li JZ, Guo C, Zheng W, Zhang X, Li P, Melia T, Reinisch K, Chen XW. Cell Metab. 2021 Aug 3; 2021 May 19. PMID: 34015269.
- Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets.Reichmann MT, Tezera LB, Vallejo AF, Vukmirovic M, Xiao R, Reynolds J, Jogai S, Wilson S, Marshall B, Jones MG, Leslie A, D'Armiento JM, Kaminski N, Polak ME, Elkington P. J Clin Invest. 2021 Aug 2. PMID: 34128839.
- Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology.Amaya C, Cameron CJF, Devarkar SC, Seager SJH, Gerstein MB, Xiong Y, Schlieker C. J Biol Chem. 2021 Aug; 2021 Jul 3. PMID: 34224731.
- Spatial and cell type transcriptional landscape of human cerebellar development.Aldinger KA, Thomson Z, Phelps IG, Haldipur P, Deng M, Timms AE, Hirano M, Santpere G, Roco C, Rosenberg AB, Lorente-Galdos B, Gulden FO, O'Day D, Overman LM, Lisgo SN, Alexandre P, Sestan N, Doherty D, Dobyns WB, Seelig G, Glass IA, Millen KJ. Nat Neurosci. 2021 Aug; 2021 Jun 17. PMID: 34140698.
- Alcohol-induced Hsp90 acetylation is a novel driver of liver sinusoidal endothelial dysfunction and alcohol-related liver disease.Yang Y, Sangwung P, Kondo R, Jung Y, McConnell MJ, Jeong J, Utsumi T, Sessa WC, Iwakiri Y. J Hepatol. 2021 Aug; 2021 Mar 3. PMID: 33675874.
- CFTR is a negative regulator of γδ T cell IFN-γ production and antitumor immunity.Duan Y, Li G, Xu M, Qi X, Deng M, Lin X, Lei Z, Hu Y, Jia Z, Yang Q, Cao G, Liu Z, Wen Q, Li Z, Tang J, Zhang WK, Huang P, Zheng L, Flavell RA, Hao J, Yin Z. Cell Mol Immunol. 2021 Aug; 2020 Jul 15. PMID: 32669666.
- Antibodies Enhance the Suppressive Activity of Extracellular Vesicles in Mouse Delayed-Type Hypersensitivity.Nazimek K, Bustos-Morán E, Blas-Rus N, Nowak B, Totoń-Żurańska J, Seweryn MT, Wołkow P, Woźnicka O, Szatanek R, Siedlar M, Askenase PW, Sánchez-Madrid F, Bryniarski K. Pharmaceuticals (Basel). 2021 Jul 27; 2021 Jul 27. PMID: 34451831.
- Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation.Venzon M, Bernard-Raichon L, Klein J, Axelrad JE, Hussey GA, Sullivan AP, Casanovas-Massana A, Noval MG, Valero-Jimenez AM, Gago J, Wilder E, Thorpe LE, Littman DR, Dittmann M, Stapleford KA, Shopsin B, Torres VJ, Ko AI, Iwasaki A, Cadwell K, Schluter J. Res Sq. 2021 Jul 27; 2021 Jul 27. PMID: 34341786.
- Methylation of dual-specificity phosphatase 4 controls cell differentiation.Su H, Jiang M, Senevirathne C, Aluri S, Zhang T, Guo H, Xavier-Ferrucio J, Jin S, Tran NT, Liu SM, Sun CW, Zhu Y, Zhao Q, Chen Y, Cable L, Shen Y, Liu J, Qu CK, Han X, Klug CA, Bhatia R, Chen Y, Nimer SD, Zheng YG, Iancu-Rubin C, Jin J, Deng H, Krause DS, Xiang J, Verma A, Luo M, Zhao X. Cell Rep. 2021 Jul 27. PMID: 34320342.
- Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung.Schupp JC, Adams TS, Cosme C Jr, Raredon MSB, Yuan Y, Omote N, Poli S, Chioccioli M, Rose KA, Manning EP, Sauler M, DeIuliis G, Ahangari F, Neumark N, Habermann AC, Gutierrez AJ, Bui LT, Lafyatis R, Pierce RW, Meyer KB, Nawijn MC, Teichmann SA, Banovich NE, Kropski JA, Niklason LE, Pe'er D, Yan X, Homer RJ, Rosas IO, Kaminski N. Circulation. 2021 Jul 27; 2021 May 25. PMID: 34030460.
- Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function.Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Cell Rep. 2021 Jul 20. PMID: 34289367.
- SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments.Chen Z, Zhang J, Liu J, Zhang Z, Zhu J, Lee D, Xu M, Gerstein M. Bioinformatics. 2021 Jul 19. PMID: 33471102.
- Blood Transcriptomics Predicts Progression of Pulmonary Fibrosis and Associated Natural Killer Cells.Huang Y, Oldham JM, Ma SF, Unterman A, Liao SY, Barros AJ, Bonham CA, Kim JS, Vij R, Adegunsoye A, Strek ME, Molyneaux PL, Maher TM, Herazo-Maya JD, Kaminski N, Moore BB, Martinez FJ, Noth I. Am J Respir Crit Care Med. 2021 Jul 15. PMID: 33689671.
- Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity.Bui LT, Winters NI, Chung MI, Joseph C, Gutierrez AJ, Habermann AC, Adams TS, Schupp JC, Poli S, Peter LM, Taylor CJ, Blackburn JB, Richmond BW, Nicholson AG, Rassl D, Wallace WA, Rosas IO, Jenkins RG, Kaminski N, Kropski JA, Banovich NE. Nat Commun. 2021 Jul 14; 2021 Jul 14. PMID: 34262047.
- A head-to-head comparison of ribodepletion and polyA selection approaches for Caenorhabditis elegans low input RNA-sequencing libraries.Barrett A, McWhirter R, Taylor SR, Weinreb A, Miller DM, Hammarlund M. G3 (Bethesda). 2021 Jul 14. PMID: 33856427.
- Hepatocyte-specific suppression of ANGPTL4 improves obesity-associated diabetes and mitigates atherosclerosis in mice.Singh AK, Chaube B, Zhang X, Sun J, Citrin KM, Canfrán-Duque A, Aryal B, Rotllan N, Varela L, Lee RG, Horvath TL, Price N, Suárez Y, Fernandez-Hernando C. J Clin Invest. 2021 Jul 13; 2021 Jul 13. PMID: 34255741.
- DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.Chen Z, Zhang J, Liu J, Dai Y, Lee D, Min MR, Xu M, Gerstein M. Bioinformatics. 2021 Jul 12. PMID: 34252960.
- Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies.Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. PLoS Biol. 2021 Jul; 2021 Jul 12. PMID: 34252080.
- Escaping the endosome: assessing cellular trafficking mechanisms of non-viral vehicles.Xu E, Saltzman WM, Piotrowski-Daspit AS. J Control Release. 2021 Jul 10; 2021 May 30. PMID: 34077782.
- Generating hard-to-obtain information from easy-to-obtain information: Applications in drug discovery and clinical inference.Amodio M, Shung D, Burkhardt DB, Wong P, Simonov M, Yamamoto Y, van Dijk D, Wilson FP, Iwasaki A, Krishnaswamy S. Patterns (N Y). 2021 Jul 9; 2021 Jun 17. PMID: 34286302.
- Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development.Xia S, VanKuren NW, Chen C, Zhang L, Kemkemer C, Shao Y, Jia H, Lee U, Advani AS, Gschwend A, Vibranovski MD, Chen S, Zhang YE, Long M. PLoS Genet. 2021 Jul; 2021 Jul 9. PMID: 34242211.
- Transcription Regulation Through Nascent RNA Folding.Schärfen L, Neugebauer KM. J Mol Biol. 2021 Jul 9; 2021 Apr 1. PMID: 33811916.
- DMA-tudor interaction modules control the specificity of in vivo condensates.Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM. Cell. 2021 Jul 8; 2021 Jun 10. PMID: 34115980.
- Do Epigenetic Timers Control Petal Development?Huang R, Huang T, Irish VF. Front Plant Sci. 2021; 2021 Jul 6. PMID: 34295349.
- Kynurenic acid may underlie sex-specific immune responses to COVID-19.Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Yan H, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh JE, Silva J, Wong P, Ko AI, Khan SA, Iwasaki A, Johnson CH. Sci Signal. 2021 Jul 6; 2021 Jul 6. PMID: 34230210.
- Diagnosis and Management of Infertility: A Review.Carson SA, Kallen AN. JAMA. 2021 Jul 6. PMID: 34228062.
- Antibodies against human endogenous retrovirus K102 envelope activate neutrophils in systemic lupus erythematosus.Tokuyama M, Gunn BM, Venkataraman A, Kong Y, Kang I, Rakib T, Townsend MJ, Costenbader KH, Alter G, Iwasaki A. J Exp Med. 2021 Jul 5; 2021 May 21. PMID: 34019642.
- Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics.Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. medRxiv. 2021 Jul 3; 2021 Jul 3. PMID: 33564787.
- Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, St George K, Adams MD, Grubaugh ND. medRxiv. 2021 Jul 2; 2021 Jul 2. PMID: 34230938.
- Retromer stabilizes transient membrane insertion of L2 capsid protein during retrograde entry of human papillomavirus.Xie J, Zhang P, Crite M, Lindsay CV, DiMaio D. Sci Adv. 2021 Jul; 2021 Jun 30. PMID: 34193420.
- Author Correction: Delayed production of neutralizing antibodies correlates with fatal COVID-19.Lucas C, Klein J, Sundaram ME, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Vogels CBF, Muenker MC, Chang CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie AL, Campbell M, Lee AI, Chun HJ, Grubaugh ND, Schulz WL, Farhadian S, Dela Cruz C, Ring AM, Shaw AC, Wisnewski AV, Yildirim I, Ko AI, Omer SB, Iwasaki A. Nat Med. 2021 Jul. PMID: 34145437.
- Author Correction: Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes.Wang YT, Zaitsev K, Lu Q, Li S, Schaiff WT, Kim KW, Droit L, Wilen CB, Desai C, Balce DR, Orchard RC, Orvedahl A, Park S, Kreamalmeyer D, Handley SA, Pfeifer JD, Baldridge MT, Artyomov MN, Stallings CL, Virgin HW. Nat Microbiol. 2021 Jul. PMID: 34035496.
- Diverse functional autoantibodies in patients with COVID-19.Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian SF, Schulz WL, Ma S, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Nature. 2021 Jul; 2021 May 19. PMID: 34010947.
- Effects of historical co-infection on host shift abilities of exploitative and competitive viruses.Singhal S, Turner PE. Evolution. 2021 Jul; 2021 Jun 2. PMID: 33969482.
- Delayed production of neutralizing antibodies correlates with fatal COVID-19.Lucas C, Klein J, Sundaram ME, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Vogels CBF, Muenker MC, Chang CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie AL, Campbell M, Lee AI, Chun HJ, Grubaugh ND, Schulz WL, Farhadian S, Dela Cruz C, Ring AM, Shaw AC, Wisnewski AV, Yildirim I, Ko AI, Omer SB, Iwasaki A. Nat Med. 2021 Jul; 2021 May 5. PMID: 33953384.
- Clinical Activity and Safety of Cediranib and Olaparib Combination in Patients with Metastatic Pancreatic Ductal Adenocarcinoma without BRCA Mutation.Kim JW, Cardin DB, Vaishampayan UN, Kato S, Grossman SR, Glazer PM, Shyr Y, Ivy SP, LoRusso PM. Oncologist. 2021 Jul; 2021 May 5. PMID: 33742489.
- A new tool for technical standardization of the Ki67 immunohistochemical assay.Aung TN, Acs B, Warrell J, Bai Y, Gaule P, Martinez-Morilla S, Vathiotis I, Shafi S, Moutafi M, Gerstein M, Freiberg B, Fulton R, Rimm DL. Mod Pathol. 2021 Jul; 2021 Feb 3. PMID: 33536573.
- MicroRNA regulation of cholesterol metabolism.Citrin KM, Fernández-Hernando C, Suárez Y. Ann N Y Acad Sci. 2021 Jul; 2021 Jan 31. PMID: 33521946.
- Quantum computing at the frontiers of biological sciences.Emani PS, Warrell J, Anticevic A, Bekiranov S, Gandal M, McConnell MJ, Sapiro G, Aspuru-Guzik A, Baker JT, Bastiani M, Murray JD, Sotiropoulos SN, Taylor J, Senthil G, Lehner T, Gerstein MB, Harrow AW. Nat Methods. 2021 Jul. PMID: 33398186.
- RNA-binding proteins in neurological development and disease.Prashad S, Gopal PP. RNA Biol. 2021 Jul; 2020 Aug 30. PMID: 32865115.
- The Practice of Science as the Pursuit of Knowledge.Groisman EA. Yale J Biol Med. 2021 Jun; 2021 Jun 30. PMID: 34211357.
- Sequencing SARS-CoV-2 Genomes from Saliva.Alpert T, Vogels CBF, Breban MI, Petrone ME, Wyllie AL, Grubaugh ND, Fauver JR. medRxiv. 2021 Jun 29; 2021 Jun 29. PMID: 34230934.
- Restriction of SARS-CoV-2 replication by targeting programmed -1 ribosomal frameshifting.Sun Y, Abriola L, Niederer RO, Pedersen SF, Alfajaro MM, Silva Monteiro V, Wilen CB, Ho YC, Gilbert WV, Surovtseva YV, Lindenbach BD, Guo JU. Proc Natl Acad Sci U S A. 2021 Jun 29. PMID: 34185680.
- Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders.Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH. Nat Commun. 2021 Jun 25; 2021 Jun 25. PMID: 34172755.
- Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients.George S, Pal AC, Gagnon J, Timalsina S, Singh P, Vydyam P, Munshi M, Chiu JE, Renard I, Harden CA, Ott IM, Watkins AE, Vogels CBF, Lu P, Tokuyama M, Venkataraman A, Casanovas-Massana A, Wyllie AL, Rao V, Campbell M, Farhadian SF, Grubaugh ND, Dela Cruz CS, Ko AI, Berna Perez AZ, Akaho EH, Moledina DG, Testani J, John AR, Ledizet M, Mamoun CB. Kidney360. 2021 Jun 24; 2021 Apr 14. PMID: 35373072.
- In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system.Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM 3rd, Hobert O. Elife. 2021 Jun 24; 2021 Jun 24. PMID: 34165430.
- Bone Marrow-Derived VSELs Engraft as Lung Epithelial Progenitor Cells after Bleomycin-Induced Lung Injury.Ciechanowicz AK, Sielatycka K, Cymer M, Skoda M, Suszyńska M, Bujko K, Ratajczak MZ, Krause DS, Kucia M. Cells. 2021 Jun 22; 2021 Jun 22. PMID: 34206516.
- Transcriptional repression by FEZF2 restricts alternative identities of cortical projection neurons.Tsyporin J, Tastad D, Ma X, Nehme A, Finn T, Huebner L, Liu G, Gallardo D, Makhamreh A, Roberts JM, Katzman S, Sestan N, McConnell SK, Yang Z, Qiu S, Chen B. Cell Rep. 2021 Jun 22. PMID: 34161768.
- Deficiency of histone lysine methyltransferase SETDB2 in hematopoietic cells promotes vascular inflammation and accelerates atherosclerosis.Zhang X, Sun J, Canfrán-Duque A, Aryal B, Tellides G, Chang YJ, Suárez Y, Osborne TF, Fernández-Hernando C. JCI Insight. 2021 Jun 22; 2021 Jun 22. PMID: 34003795.
- Low Cytoplasmic Magnesium Increases the Specificity of the Lon and ClpAP Proteases.Yeom J, Groisman EA. J Bacteriol. 2021 Jun 22; 2021 Jun 22. PMID: 33941609.
- Ketogenic diet restrains aging-induced exacerbation of coronavirus infection in mice.Ryu S, Shchukina I, Youm YH, Qing H, Hilliard B, Dlugos T, Zhang X, Yasumoto Y, Booth CJ, Fernández-Hernando C, Suárez Y, Khanna K, Horvath TL, Dietrich MO, Artyomov M, Wang A, Dixit VD. Elife. 2021 Jun 21; 2021 Jun 21. PMID: 34151773.
- Evolution of Bacterial Cross-Resistance to Lytic Phages and Albicidin Antibiotic.Kortright KE, Doss-Gollin S, Chan BK, Turner PE. Front Microbiol. 2021; 2021 Jun 17. PMID: 34220747.
- A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice.Mao T, Israelow B, Lucas C, Vogels CBF, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. bioRxiv. 2021 Jun 17; 2021 Jun 17. PMID: 34159330.
- m(6)A demethylase ALKBH5 controls CD4(+) T cell pathogenicity and promotes autoimmunity.Zhou J, Zhang X, Hu J, Qu R, Yu Z, Xu H, Chen H, Yan L, Ding C, Zou Q, Ye Y, Wang Z, Flavell RA, Li HB. Sci Adv. 2021 Jun; 2021 Jun 16. PMID: 34134995.
- Eruptive xanthoma model reveals endothelial cells internalize and metabolize chylomicrons, leading to extravascular triglyceride accumulation.Cabodevilla AG, Tang S, Lee S, Mullick AE, Aleman JO, Hussain MM, Sessa WC, Abumrad NA, Goldberg IJ. J Clin Invest. 2021 Jun 15. PMID: 34128469.
- Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. J Immunol. 2021 Jun 15; 2021 May 28. PMID: 34049971.
- Translational shutdown and evasion of the innate immune response by SARS-CoV-2 NSP14 protein.Hsu JC, Laurent-Rolle M, Pawlak JB, Wilen CB, Cresswell P. Proc Natl Acad Sci U S A. 2021 Jun 15. PMID: 34045361.
- Modulating HIV-1 envelope glycoprotein conformation to decrease the HIV-1 reservoir.Rajashekar JK, Richard J, Beloor J, Prévost J, Anand SP, Beaudoin-Bussières G, Shan L, Herndler-Brandstetter D, Gendron-Lepage G, Medjahed H, Bourassa C, Gaudette F, Ullah I, Symmes K, Peric A, Lindemuth E, Bibollet-Ruche F, Park J, Chen HC, Kaufmann DE, Hahn BH, Sodroski J, Pazgier M, Flavell RA, Smith AB 3rd, Finzi A, Kumar P. Cell Host Microbe. 2021 Jun 9; 2021 May 20. PMID: 34019804.
- Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Hafler D, Sumida T, Dulberg S, Schupp J, Stillwell H, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo V. Res Sq. 2021 Jun 8; 2021 Jun 8. PMID: 34127967.
- Mitochondrial apoptotic priming is a key determinant of cell fate upon p53 restoration.Sánchez-Rivera FJ, Ryan J, Soto-Feliciano YM, Clare Beytagh M, Xuan L, Feldser DM, Hemann MT, Zamudio J, Dimitrova N, Letai A, Jacks T. Proc Natl Acad Sci U S A. 2021 Jun 8. PMID: 34074758.
- Tumor-selective, antigen-independent delivery of a pH sensitive peptide-topoisomerase inhibitor conjugate suppresses tumor growth without systemic toxicity.Gayle S, Aiello R, Leelatian N, Beckta JM, Bechtold J, Bourassa P, Csengery J, Maguire RJ, Marshall D, Sundaram RK, Van Doorn J, Jones K, Moore H, Lopresti-Morrow L, Paradis T, Tylaska L, Zhang Q, Visca H, Reshetnyak YK, Andreev OA, Engelman DM, Glazer PM, Bindra RS, Paralkar VM. NAR Cancer. 2021 Jun; 2021 Jun 4. PMID: 34316708.
- Detection of differentially abundant cell subpopulations in scRNA-seq data.Zhao J, Jaffe A, Li H, Lindenbaum O, Sefik E, Jackson R, Cheng X, Flavell RA, Kluger Y. Proc Natl Acad Sci U S A. 2021 Jun 1. PMID: 34001664.
- Elevated IL-15 concentrations in the sarcoidosis lung are independent of granuloma burden and disease phenotypes.Minasyan M, Sharma L, Pivarnik T, Liu W, Adams T, Bermejo S, Peng X, Liu A, Ishikawa G, Perry C, Kaminski N, Gulati M, Herzog EL, Dela Cruz CS, Ryu C. Am J Physiol Lung Cell Mol Physiol. 2021 Jun 1; 2021 Apr 14. PMID: 33851886.
- PINK1 mediates the protective effects of thyroid hormone T3 in hyperoxia-induced lung injury.Zhang Y, Yu G, Kaminski N, Lee PJ. Am J Physiol Lung Cell Mol Physiol. 2021 Jun 1; 2021 Apr 14. PMID: 33851544.
- Hydrogel-based biocontainment of bacteria for continuous sensing and computation.Tang TC, Tham E, Liu X, Yehl K, Rovner AJ, Yuk H, de la Fuente-Nunez C, Isaacs FJ, Zhao X, Lu TK. Nat Chem Biol. 2021 Jun; 2021 Apr 5. PMID: 33820990.
- Corrigendum to: TCP5 controls leaf margin development by regulating KNOX and BEL-like transcription factors in Arabidopsis.Yu H, Zhang L, Wang W, Tian P, Wang W, Wang K, Gao Z, Liu S, Zhang Y, Irish VF, Huang T. J Exp Bot. 2021 May 28. PMID: 33877291.
- CENTRORADIALIS maintains shoot meristem indeterminacy by antagonizing THORN IDENTITY1 in Citrus.Zhang F, Wang Y, Irish VF. Curr Biol. 2021 May 24; 2021 Mar 23. PMID: 33761317.
- Guiding Ethical Principles in Engineering Biology Research.Mackelprang R, Aurand ER, Bovenberg RAL, Brink KR, Charo RA, Delborne JA, Diggans J, Ellington AD, Fortman JLC, Isaacs FJ, Medford JI, Murray RM, Noireaux V, Palmer MJ, Zoloth L, Friedman DC. ACS Synth Biol. 2021 May 21; 2021 May 12. PMID: 33977723.
- Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms.Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. Cell Rep Med. 2021 May 18; 2021 May 3. PMID: 33969321.
- Investigate the origins of COVID-19.Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA. Science. 2021 May 14. PMID: 33986172.
- A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements.Fish L, Khoroshkin M, Navickas A, Garcia K, Culbertson B, Hänisch B, Zhang S, Nguyen HCB, Soto LM, Dermit M, Mardakheh FK, Molina H, Alarcón C, Najafabadi HS, Goodarzi H. Science. 2021 May 14. PMID: 33986153.
- Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface.Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. Med. 2021 May 14; 2021 Apr 30. PMID: 33969332.
- Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States.Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Cong L, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, St George K, MacCannell DR, Grubaugh ND. Cell. 2021 May 13; 2021 Apr 3. PMID: 33891875.
- Cathepsin B promotes collagen biosynthesis, which drives bronchiolitis obliterans syndrome.Morrone C, Smirnova NF, Jeridi A, Kneidinger N, Hollauer C, Schupp JC, Kaminski N, Jenne D, Eickelberg O, Yildirim AÖ. Eur Respir J. 2021 May; 2021 May 13. PMID: 33303550.
- Plasmodium infection induces cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein.Lapidus S, Liu F, Casanovas-Massana A, Dai Y, Huck JD, Lucas C, Klein J, Filler RB, Strine MS, Sy M, Deme AB, Badiane AS, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Diagne CT, Vigan-Womas I, Mbengue A, Sadio BD, Diagne MM, Moore AJ, Mangou K, Diallo F, Sene SD, Pouye MN, Faye R, Diouf B, Nery N Jr, Costa F, Reis M, Muenker MC, Hodson DZ, Mbarga Y, Katz BZ, Andrews JR, Campbell M, Srivathsan A, Kamath K, Baum-Jones E, Faye O, Sall AA, Quintero Vélez JC, Cappello M, Wilson M, Ben-Mamoun C, Somé FA, Dabiré RK, Moukoko CEE, Ouédraogo JB, Boum Y 2nd, Shon J, Ndiaye D, Wisnewski A, Parikh S, Iwasaki A, Wilen CB, Ko AI, Ring AM, Bei AK. medRxiv. 2021 May 12; 2021 May 12. PMID: 34013301.
- Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil.Brito AF, Machado LC, Oidtman RJ, Siconelli MJL, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, de Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, España GC, Huang AT, Cummings DAT, Baele G, Franca RFO, da Fonseca BAL, Perkins TA, Wallau GL, Grubaugh ND. Nat Commun. 2021 May 11; 2021 May 11. PMID: 33976183.
- Biallelic splicing variants in the nucleolar 60S assembly factor RBM28 cause the ribosomopathy ANE syndrome.Bryant CJ, Lorea CF, de Almeida HL Jr, Weinert L, Vedolin L, Pinto E Vairo F, Baserga SJ. Proc Natl Acad Sci U S A. 2021 May 11. PMID: 33941690.
- Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children.Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immunity. 2021 May 11; 2021 Apr 13. PMID: 33891889.
- COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy.Novelli G, Biancolella M, Mehrian-Shai R, Colona VL, Brito AF, Grubaugh ND, Vasiliou V, Luzzatto L, Reichardt JKV. Hum Genomics. 2021 May 10; 2021 May 10. PMID: 33966626.
- Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. PLoS Biol. 2021 May; 2021 May 7. PMID: 33961632.
- miR-33 in cardiometabolic diseases: lessons learned from novel animal models and approaches.Price NL, Goedeke L, Suárez Y, Fernández-Hernando C. EMBO Mol Med. 2021 May 7; 2021 May 3. PMID: 33938628.
- Single cell epigenetic visualization assay.Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, Denisenko O. Nucleic Acids Res. 2021 May 7. PMID: 33511400.
- Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME. Am J Hum Genet. 2021 May 6; 2021 Mar 30. PMID: 33789087.
- Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient.Klein J, Brito A, Trubin P, Lu P, Wong P, Alpert T, Pena-Hernandez M, Haynes W, Kamath K, Liu F, Vogels C, Fauver J, Lucas C, Oh JE, Mao T, Silva J, Wyllie A, Muenker MC, Casanovas-Massana A, Moore A, Petrone M, Kalinich C, Cruz CD, Farhadian S, Ring A, Shon J, Ko A, Grubaugh N, Goldman-Israelow B, Iwasaki A, Azar M. Res Sq. 2021 May 5; 2021 May 5. PMID: 34013255.
- Characterization of a Novel Caveolin Modulator That Reduces Vascular Permeability and Ocular Inflammation.Bernatchez PN, Tao B, Bradshaw RA, Eveleth D, Sessa WC. Transl Vis Sci Technol. 2021 May 3. PMID: 34111267.
- B cells join T cell clusters in the host response to recurrent herpes simplex virus 2 infection.Gehlhausen JR, Iwasaki A. J Clin Invest. 2021 May 3. PMID: 33938452.
- Response.Price CC, Altice FL, Azar MM, McManus D, Gleeson SE, Britto CJ, Azmy V, Kaman K, Davis M, Chupp G, Bucala R, Kaminski N, Topal JE, Dela Cruz C, Malinis M. Chest. 2021 May. PMID: 33965143.
- PEGylation of poly(amine-co-ester) polyplexes for tunable gene delivery.Grun MK, Suberi A, Shin K, Lee T, Gomerdinger V, Moscato ZM, Piotrowski-Daspit AS, Saltzman WM. Biomaterials. 2021 May; 2021 Mar 24. PMID: 33813260.
- MOG-associated encephalitis following SARS-COV-2 infection.Peters J, Alhasan S, Vogels CBF, Grubaugh ND, Farhadian S, Longbrake EE. Mult Scler Relat Disord. 2021 May; 2021 Feb 23. PMID: 33647592.
- JUN Amino-Terminal Kinase 1 Signaling in the Proximal Tubule Causes Cell Death and Acute Renal Failure in Rat and Mouse Models of Renal Ischemia/Reperfusion Injury.Grynberg K, Ozols E, Mulley WR, Davis RJ, Flavell RA, Nikolic-Paterson DJ, Ma FY. Am J Pathol. 2021 May; 2021 Feb 16. PMID: 33607044.
- Quantifying the effect of experimental perturbations at single-cell resolution.Burkhardt DB, Stanley JS 3rd, Tong A, Perdigoto AL, Gigante SA, Herold KC, Wolf G, Giraldez AJ, van Dijk D, Krishnaswamy S. Nat Biotechnol. 2021 May; 2021 Feb 8. PMID: 33558698.
- Challenges in the Evaluation and Management of Toxicities Arising From Immune Checkpoint Inhibitor Therapy for Patients With Myeloid Malignancies.Shallis RM, Bewersdorf JP, Swoboda DM, Wei W, Gowda L, Prebet T, Halene S, Pillai MM, Parker T, Neparidze N, Podoltsev NA, Seropian S, Sallman DA, Gore SD, Zeidan AM. Clin Lymphoma Myeloma Leuk. 2021 May; 2021 Jan 12. PMID: 33551344.
- Treatment of granuloma annulare and suppression of proinflammatory cytokine activity with tofacitinib.Wang A, Rahman NT, McGeary MK, Murphy M, McHenry A, Peterson D, Bosenberg M, Flavell RA, King B, Damsky W. J Allergy Clin Immunol. 2021 May; 2020 Dec 11. PMID: 33317858.
- ZTCG: Viruses expand the genetic alphabet.Grome MW, Isaacs FJ. Science. 2021 Apr 30. PMID: 33926938.
- Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB, Satpathy AT. Cell. 2021 Apr 29; 2021 Mar 11. PMID: 33743211.
- Pazopanib ameliorates acute lung injuries via inhibition of MAP3K2 and MAP3K3.Yuan Q, Basit A, Liang W, Qu R, Luan Y, Ren C, Li A, Xu X, Liu X, Yang C, Kuo A, Pierce R, Zhang L, Turk B, Hu X, Li F, Cui W, Li R, Huang D, Mo L, Sessa WC, Lee PJ, Kluger Y, Su B, Tang W, He J, Wu D. Sci Transl Med. 2021 Apr 28. PMID: 33910977.
- Pooled CRISPR screening identifies m(6)A as a positive regulator of macrophage activation.Tong J, Wang X, Liu Y, Ren X, Wang A, Chen Z, Yao J, Mao K, Liu T, Meng FL, Pan W, Zou Q, Liu J, Zhou Y, Xia Q, Flavell RA, Zhu S, Li HB. Sci Adv. 2021 Apr; 2021 Apr 28. PMID: 33910903.
- eNOS-induced vascular barrier disruption in retinopathy by c-Src activation and tyrosine phosphorylation of VE-cadherin.Ninchoji T, Love DT, Smith RO, Hedlund M, Vestweber D, Sessa WC, Claesson-Welsh L. Elife. 2021 Apr 28; 2021 Apr 28. PMID: 33908348.
- Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers.Li X, Kumar S, Harmanci A, Li S, Kitchen RR, Zhang Y, Wali VB, Reddy SM, Woodward WA, Reuben JM, Rozowsky J, Hatzis C, Ueno NT, Krishnamurthy S, Pusztai L, Gerstein M. Genome Med. 2021 Apr 26; 2021 Apr 26. PMID: 33902690.
- Neural network predicts need for red blood cell transfusion for patients with acute gastrointestinal bleeding admitted to the intensive care unit.Shung D, Huang J, Castro E, Tay JK, Simonov M, Laine L, Batra R, Krishnaswamy S. Sci Rep. 2021 Apr 23; 2021 Apr 23. PMID: 33893364.
- Measuring the size and decay dynamics of the HIV-1 latent reservoir.Liu R, Catalano AA, Ho YC. Cell Rep Med. 2021 Apr 20; 2021 Apr 20. PMID: 33948579.
- A model for a partnership of lipid transfer proteins and scramblases in membrane expansion and organelle biogenesis.Ghanbarpour A, Valverde DP, Melia TJ, Reinisch KM. Proc Natl Acad Sci U S A. 2021 Apr 20. PMID: 33850023.
- Shock-and-kill versus block-and-lock: Targeting the fluctuating and heterogeneous HIV-1 gene expression.Yeh YJ, Ho YC. Proc Natl Acad Sci U S A. 2021 Apr 20. PMID: 33758027.
- CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini.Wang H, Huang R, Li L, Zhu J, Li Z, Peng C, Zhuang X, Lin H, Shi S, Huang P. Cell Discov. 2021 Apr 19; 2021 Apr 19. PMID: 33867522.
- Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription.Ogawa LM, Buhagiar AF, Abriola L, Leland BA, Surovtseva YV, Baserga SJ. Mol Biol Cell. 2021 Apr 19; 2021 Mar 10. PMID: 33689394.
- Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor.Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Cell Chem Biol. 2021 Apr 15; 2020 Dec 22. PMID: 33357462.
- Mitochondrial antiviral signaling protein is crucial for the development of pulmonary fibrosis.Kim SH, Lee JY, Yoon CM, Shin HJ, Lee SW, Rosas I, Herzog E, Dela Cruz CS, Kaminski N, Kang MJ. Eur Respir J. 2021 Apr; 2021 Apr 15. PMID: 33093124.
- Structural analyses of an RNA stability element interacting with poly(A).Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Proc Natl Acad Sci U S A. 2021 Apr 6. PMID: 33785601.
- Haplotype-resolved diverse human genomes and integrated analysis of structural variation.Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Science. 2021 Apr 2; 2021 Feb 25. PMID: 33632895.
- The NIH Somatic Cell Genome Editing program.Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, Bursac N, Campbell JM, Carlson DF, Chaikof EL, Chen ZY, Cheng RH, Clark KJ, Curiel DT, Dahlman JE, Deverman BE, Dickinson ME, Doudna JA, Ekker SC, Emborg ME, Feng G, Freedman BS, Gamm DM, Gao G, Ghiran IC, Glazer PM, Gong S, Heaney JD, Hennebold JD, Hinson JT, Khvorova A, Kiani S, Lagor WR, Lam KS, Leong KW, Levine JE, Lewis JA, Lutz CM, Ly DH, Maragh S, McCray PB Jr, McDevitt TC, Mirochnitchenko O, Morizane R, Murthy N, Prather RS, Ronald JA, Roy S, Roy S, Sabbisetti V, Saltzman WM, Santangelo PJ, Segal DJ, Shimoyama M, Skala MC, Tarantal AF, Tilton JC, Truskey GA, Vandsburger M, Watts JK, Wells KD, Wolfe SA, Xu Q, Xue W, Yi G, Zhou J. Nature. 2021 Apr; 2021 Apr 7. PMID: 33828315.
- Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes.Courage C, Oliver KL, Park EJ, Cameron JM, Grabińska KA, Muona M, Canafoglia L, Gambardella A, Said E, Afawi Z, Baykan B, Brandt C, di Bonaventura C, Chew HB, Criscuolo C, Dibbens LM, Castellotti B, Riguzzi P, Labate A, Filla A, Giallonardo AT, Berecki G, Jackson CB, Joensuu T, Damiano JA, Kivity S, Korczyn A, Palotie A, Striano P, Uccellini D, Giuliano L, Andermann E, Scheffer IE, Michelucci R, Bahlo M, Franceschetti S, Sessa WC, Berkovic SF, Lehesjoki AE. Am J Hum Genet. 2021 Apr 1. PMID: 33798445.
- Complete Genome Sequence of Escherichia coli Bacteriophage U136B.Burmeister AR, Piya D, Turner PE. Microbiol Resour Announc. 2021 Apr 1; 2021 Apr 1. PMID: 33795337.
- The first 12 months of COVID-19: a timeline of immunological insights.Carvalho T, Krammer F, Iwasaki A. Nat Rev Immunol. 2021 Apr; 2021 Mar 15. PMID: 33723416.
- MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche.Wu N, Sun H, Zhao X, Zhang Y, Tan J, Qi Y, Wang Q, Ng M, Liu Z, He L, Niu X, Chen L, Liu Z, Li HB, Zeng YA, Roulis M, Liu D, Cheng J, Zhou B, Ng LG, Zou D, Ye Y, Flavell RA, Ginhoux F, Su B. Nature. 2021 Apr; 2021 Mar 3. PMID: 33658717.
- Gene Expression Signature in Patients With Symptomatic Peripheral Artery Disease.Newman JD, Cornwell MG, Zhou H, Rockman C, Heguy A, Suarez Y, Cheng HS, Feinberg MW, Hochman JS, Ruggles KV, Berger JS. Arterioscler Thromb Vasc Biol. 2021 Apr; 2021 Mar 4. PMID: 33657880.
- Potential intestinal infection and faecal-oral transmission of SARS-CoV-2.Guo M, Tao W, Flavell RA, Zhu S. Nat Rev Gastroenterol Hepatol. 2021 Apr; 2021 Feb 15. PMID: 33589829.
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- Macrophage-derived PDGF-B induces muscularization in murine and human pulmonary hypertension.Ntokou A, Dave JM, Kauffman AC, Sauler M, Ryu C, Hwa J, Herzog EL, Singh I, Saltzman WM, Greif DM. JCI Insight. 2021 Mar 22; 2021 Mar 22. PMID: 33591958.
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- Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq.Gao Y, Chen S, Halene S, Tebaldi T. STAR Protoc. 2021 Mar 19; 2021 Mar 18. PMID: 33778776.
- Cooperation between oncogenic Ras and wild-type p53 stimulates STAT non-cell autonomously to promote tumor radioresistance.Dong YL, Vadla GP, Lu JJ, Ahmad V, Klein TJ, Liu LF, Glazer PM, Xu T, Chabu CY. Commun Biol. 2021 Mar 19; 2021 Mar 19. PMID: 33742110.
- Cerebellar Kv3.3 potassium channels activate TANK-binding kinase 1 to regulate trafficking of the cell survival protein Hax-1.Zhang Y, Varela L, Szigeti-Buck K, Williams A, Stoiljkovic M, Šestan-Peša M, Henao-Mejia J, D'Acunzo P, Levy E, Flavell RA, Horvath TL, Kaczmarek LK. Nat Commun. 2021 Mar 19; 2021 Mar 19. PMID: 33741962.
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- A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options.Sefik E, Israelow B, Zhao J, Qu R, Song E, Mirza H, Kaffe E, Halene S, Meffre E, Kluger Y, Nussenzweig M, Wilen CB, Iwasaki A, Flavell RA. Res Sq. 2021 Mar 17; 2021 Mar 17. PMID: 33758831.
- Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. PLoS Biol. 2021 Mar; 2021 Mar 17. PMID: 33730024.
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- Pancreatic cancer driver mutations are targetable through distant alternative RNA splicing dependencies.Kawalerski RR, Leach SD, Escobar-Hoyos LF. Oncotarget. 2021 Mar 16; 2021 Mar 16. PMID: 33796221.
- Limitation of phosphate assimilation maintains cytoplasmic magnesium homeostasis.Bruna RE, Kendra CG, Groisman EA, Pontes MH. Proc Natl Acad Sci U S A. 2021 Mar 16. PMID: 33707210.
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- Identification of positive and negative regulators in the stepwise developmental progression towards infectivity in Trypanosoma brucei.Toh JY, Nkouawa A, Sánchez SR, Shi H, Kolev NG, Tschudi C. Sci Rep. 2021 Mar 11; 2021 Mar 11. PMID: 33707699.
- Norovirus evolution in immunodeficient mice reveals potentiated pathogenicity via a single nucleotide change in the viral capsid.Walker FC, Hassan E, Peterson ST, Rodgers R, Schriefer LA, Thompson CE, Li Y, Kalugotla G, Blum-Johnston C, Lawrence D, McCune BT, Graziano VR, Lushniak L, Lee S, Roth AN, Karst SM, Nice TJ, Miner JJ, Wilen CB, Baldridge MT. PLoS Pathog. 2021 Mar; 2021 Mar 11. PMID: 33705489.
- Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States.Alpert T, Brito AF, Lasek-Nesselquist E, Rothman J, Valesano AL, MacKay MJ, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Fauntleroy KA, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, George KS, MacCannell DR, Grubaugh ND. medRxiv. 2021 Mar 11; 2021 Mar 11. PMID: 33594373.
- Non-steroidal anti-inflammatory drugs dampen the cytokine and antibody response to SARS-CoV-2 infection.Chen JS, Alfajaro MM, Chow RD, Wei J, Filler RB, Eisenbarth SC, Wilen CB. J Virol. 2021 Mar 10; 2021 Jan 13. PMID: 33441348.
- A neutrophil activation signature predicts critical illness and mortality in COVID-19.Meizlish ML, Pine AB, Bishai JD, Goshua G, Nadelmann ER, Simonov M, Chang CH, Zhang H, Shallow M, Bahel P, Owusu K, Yamamoto Y, Arora T, Atri DS, Patel A, Gbyli R, Kwan J, Won CH, Dela Cruz C, Price C, Koff J, King BA, Rinder HM, Wilson FP, Hwa J, Halene S, Damsky W, van Dijk D, Lee AI, Chun HJ. Blood Adv. 2021 Mar 9. PMID: 33635335.
- Combined liver-cytokine humanization comes to the rescue of circulating human red blood cells.Song Y, Shan L, Gbyli R, Liu W, Strowig T, Patel A, Fu X, Wang X, Xu ML, Gao Y, Qin A, Bruscia EM, Tebaldi T, Biancon G, Mamillapalli P, Urbonas D, Eynon E, Gonzalez DG, Chen J, Krause DS, Alderman J, Halene S, Flavell RA. Science. 2021 Mar 5. PMID: 33674488.
- Targeting the Hypoxic and Acidic Tumor Microenvironment with pH-Sensitive Peptides.Dharmaratne NU, Kaplan AR, Glazer PM. Cells. 2021 Mar 4; 2021 Mar 4. PMID: 33806273.
- The fermented soy beverage Q-CAN® plus induces beneficial changes in the oral and intestinal microbiome.Dioletis E, Paiva RS, Kaffe E, Secor ER, Weiss TR, Fields MR, Ouyang X, Ali A. BMC Nutr. 2021 Mar 4; 2021 Mar 4. PMID: 33658080.
- Public health actions to control new SARS-CoV-2 variants.Grubaugh ND, Hodcroft EB, Fauver JR, Phelan AL, Cevik M. Cell. 2021 Mar 4; 2021 Jan 29. PMID: 33581746.
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- Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis.Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Mol Cell. 2021 Mar 4; 2021 Jan 12. PMID: 33440169.
- Tracking smell loss to identify healthcare workers with SARS-CoV-2 infection.Weiss JJ, Attuquayefio TN, White EB, Li F, Herz RS, White TL, Campbell M, Geng B, Datta R, Wyllie AL, Grubaugh ND, Casanovas-Massana A, Muenker MC, Moore AJ, Handoko R, Iwasaki A, Martinello RA, Ko AI, Small DM, Farhadian SF. PLoS One. 2021; 2021 Mar 3. PMID: 33657167.
- Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex.Yang Y, Harris KA, Widner DL, Breaker RR. Proc Natl Acad Sci U S A. 2021 Mar 2. PMID: 33619097.
- Voices of biotech research.Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD Jr, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J. Nat Biotechnol. 2021 Mar. PMID: 33692517.
- Structural and developmental principles of neuropil assembly in C. elegans.Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA. Nature. 2021 Mar; 2021 Feb 24. PMID: 33627875.
- Mechanisms of nonvesicular lipid transport.Reinisch KM, Prinz WA. J Cell Biol. 2021 Mar 1. PMID: 33605998.
- Neuroinvasion of SARS-CoV-2 in human and mouse brain.Song E, Zhang C, Israelow B, Lu-Culligan A, Prado AV, Skriabine S, Lu P, Weizman OE, Liu F, Dai Y, Szigeti-Buck K, Yasumoto Y, Wang G, Castaldi C, Heltke J, Ng E, Wheeler J, Alfajaro MM, Levavasseur E, Fontes B, Ravindra NG, Van Dijk D, Mane S, Gunel M, Ring A, Kazmi SAJ, Zhang K, Wilen CB, Horvath TL, Plu I, Haik S, Thomas JL, Louvi A, Farhadian SF, Huttner A, Seilhean D, Renier N, Bilguvar K, Iwasaki A. J Exp Med. 2021 Mar 1. PMID: 33433624.
- Editorial: Do not lose focus on myeloid biology in the era of COVID-19.Halene S, Prebet T. Curr Opin Hematol. 2021 Mar 1. PMID: 33394725.
- Fighting microbial pathogens by integrating host ecosystem interactions and evolution.Burmeister AR, Hansen E, Cunningham JJ, Rego EH, Turner PE, Weitz JS, Hochberg ME. Bioessays. 2021 Mar; 2020 Dec 30. PMID: 33377530.
- The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.Tavares RCA, Mahadeshwar G, Wan H, Huston NC, Pyle AM. J Virol. 2021 Mar 1; 2020 Dec 2. PMID: 33268519.
- Thrombocytopathy and endotheliopathy: crucial contributors to COVID-19 thromboinflammation.Gu SX, Tyagi T, Jain K, Gu VW, Lee SH, Hwa JM, Kwan JM, Krause DS, Lee AI, Halene S, Martin KA, Chun HJ, Hwa J. Nat Rev Cardiol. 2021 Mar; 2020 Nov 19. PMID: 33214651.
- The emerging role of Janus kinase inhibitors in the treatment of autoimmune and inflammatory diseases.Damsky W, Peterson D, Ramseier J, Al-Bawardy B, Chun H, Proctor D, Strand V, Flavell RA, King B. J Allergy Clin Immunol. 2021 Mar; 2020 Oct 28. PMID: 33129886.
- Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways.Li X, Christenson SA, Modena B, Li H, Busse WW, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Hastie AT, Israel E, Jarjour NN, Levy BD, Moore WC, Woodruff PG, Kaminski N, Wenzel SE, Bleecker ER, Meyers DA. J Allergy Clin Immunol. 2021 Mar; 2020 Aug 11. PMID: 32795586.
- MAP3K2 augments Th1 cell differentiation via IL-18 to promote T cell-mediated colitis.Wu N, Chen D, Sun H, Tan J, Zhang Y, Zhang T, Han Y, Liu H, Ouyang X, Yang XD, Niu X, Zhong J, Wang Z, Su B. Sci China Life Sci. 2021 Mar; 2020 Jul 28. PMID: 32737854.
- TCP5 controls leaf margin development by regulating KNOX and BEL-like transcription factors in Arabidopsis.Yu H, Zhang L, Wang W, Tian P, Wang W, Wang K, Gao Z, Liu S, Zhang Y, Irish VF, Huang T. J Exp Bot. 2021 Feb 27. PMID: 33258902.
- To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.Xu J, Kudron MM, Victorsen A, Gao J, Ammouri HN, Navarro FCP, Gevirtzman L, Waterston RH, White KP, Reinke V, Gerstein M. Nucleic Acids Res. 2021 Feb 22. PMID: 33347581.
- Unlocking Pericyte Function in the Adult Blood Brain Barrier One Cell at a Time.Nicoli S, Grutzendler J. Circ Res. 2021 Feb 19; 2021 Feb 18. PMID: 33600230.
- A Genetic Code Expansion-Derived Molecular Beacon for the Detection of Intracellular Amyloid-β Peptide Generation.Sappakhaw K, Jantarug K, Slavoff SA, Israsena N, Uttamapinant C. Angew Chem Int Ed Engl. 2021 Feb 19; 2020 Dec 15. PMID: 33063327.
- Nonsurgical treatment of skin cancer with local delivery of bioadhesive nanoparticles.Hu JK, Suh HW, Qureshi M, Lewis JM, Yaqoob S, Moscato ZM, Griff S, Lee AK, Yin ES, Saltzman WM, Girardi M. Proc Natl Acad Sci U S A. 2021 Feb 16. PMID: 33526595.
- The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency.Mori L, Jenike K, Yeh YJ, Lacombe B, Li C, Getzler A, Mediouni S, Cameron M, Pipkin M, Ho YC, Ramirez BC, Valente S. J Virol. 2021 Feb 15; 2020 Nov 25. PMID: 33239456.
- Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries.Liu N, Neuenkirchen N, Zhong M, Lin H. G3 (Bethesda). 2021 Feb 9. PMID: 33609367.
- RNA stabilization by a poly(A) tail 3'-end binding pocket and other modes of poly(A)-RNA interaction.Torabi SF, Vaidya AT, Tycowski KT, DeGregorio SJ, Wang J, Shu MD, Steitz TA, Steitz JA. Science. 2021 Feb 5; 2021 Jan 7. PMID: 33414189.
- Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Mol Cell. 2021 Feb 4; 2021 Jan 1. PMID: 33444546.
- Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression.Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA. Mol Cell. 2021 Feb 4; 2021 Jan 4. PMID: 33400923.
- Loss of hepatic miR-33 improves metabolic homeostasis and liver function without altering body weight or atherosclerosis.Price NL, Zhang X, Fernández-Tussy P, Singh AK, Burnap SA, Rotllan N, Goedeke L, Sun J, Canfrán-Duque A, Aryal B, Mayr M, Suárez Y, Fernández-Hernando C. Proc Natl Acad Sci U S A. 2021 Feb 2. PMID: 33495342.
- Intercellular Mitochondria Transfer to Macrophages Regulates White Adipose Tissue Homeostasis and Is Impaired in Obesity.Brestoff JR, Wilen CB, Moley JR, Li Y, Zou W, Malvin NP, Rowen MN, Saunders BT, Ma H, Mack MR, Hykes BL Jr, Balce DR, Orvedahl A, Williams JW, Rohatgi N, Wang X, McAllaster MR, Handley SA, Kim BS, Doench JG, Zinselmeyer BH, Diamond MS, Virgin HW, Gelman AE, Teitelbaum SL. Cell Metab. 2021 Feb 2; 2020 Dec 4. PMID: 33278339.
- Introducing Selenocysteine into Recombinant Proteins in Escherichia coli.Chung CZ, Miller C, Söll D, Krahn N. Curr Protoc. 2021 Feb. PMID: 33566458.
- Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state.Omote N, Sakamoto K, Li Q, Schupp JC, Adams T, Ahangari F, Chioccioli M, DeIuliis G, Hashimoto N, Hasegawa Y, Kaminski N. Physiol Rep. 2021 Feb. PMID: 33527707.
- Publisher Correction: VEGF-C-driven lymphatic drainage enables immunosurveillance of brain tumours.Song E, Mao T, Dong H, Boisserand LSB, Antila S, Bosenberg M, Alitalo K, Thomas JL, Iwasaki A. Nature. 2021 Feb. PMID: 33500588.
- Bacteriophage therapy for infections in CF.Chan BK, Stanley G, Modak M, Koff JL, Turner PE. Pediatr Pulmonol. 2021 Feb. PMID: 33434411.
- Diverse Functional Autoantibodies in Patients with COVID-19.Wang EY, Mao T, Klein J, Dai Y, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Cruz CD, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. medRxiv. 2021 Feb 1; 2021 Feb 1. PMID: 33330894.
- Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency.Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Thorax. 2021 Feb; 2020 Dec 10. PMID: 33303696.
- Emerging roles of circular RNAs in innate immunity.Li I, Chen YG. Curr Opin Immunol. 2021 Feb; 2020 Nov 8. PMID: 33176221.
- A web tool for the design of prime-editing guide RNAs.Chow RD, Chen JS, Shen J, Chen S. Nat Biomed Eng. 2021 Feb; 2020 Sep 28. PMID: 32989284.
- How Pathogens Feel and Overcome Magnesium Limitation When in Host Tissues.Blanc-Potard AB, Groisman EA. Trends Microbiol. 2021 Feb; 2020 Aug 14. PMID: 32807623.
- Keratin 17 Expression Predicts Poor Clinical Outcome in Patients With Advanced Esophageal Squamous Cell Carcinoma.Haye K, Babu S, Oblein L, Gupta R, Akalin A, Escobar-Hoyos LF, Shroyer KR. Appl Immunohistochem Mol Morphol. 2021 Feb 1. PMID: 32554975.
- Controversies around the function of LARP1.Berman AJ, Thoreen CC, Dedeic Z, Chettle J, Roux PP, Blagden SP. RNA Biol. 2021 Feb; 2020 Apr 1. PMID: 32233986.
- FANCY: fast estimation of privacy risk in functional genomics data.Gürsoy G, Brannon CM, Navarro FCP, Gerstein M. Bioinformatics. 2021 Jan 29. PMID: 32726397.
- SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface.Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. medRxiv. 2021 Jan 26; 2021 Jan 26. PMID: 33532791.
- Reduced ATP-dependent proteolysis of functional proteins during nutrient limitation speeds the return of microbes to a growth state.Yeom J, Groisman EA. Sci Signal. 2021 Jan 26; 2021 Jan 26. PMID: 33500334.
- The RNA helicase Dhx15 mediates Wnt-induced antimicrobial protein expression in Paneth cells.Wang Y, He K, Sheng B, Lei X, Tao W, Zhu X, Wei Z, Fu R, Wang A, Bai S, Zhang Z, Hong N, Ye C, Tian Y, Wang J, Li M, Zhang K, Li L, Yang H, Li HB, Flavell RA, Zhu S. Proc Natl Acad Sci U S A. 2021 Jan 26. PMID: 33483420.
- MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease.Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. JCI Insight. 2021 Jan 25; 2021 Jan 25. PMID: 33290275.
- Sex differences in immune responses.Takahashi T, Iwasaki A. Science. 2021 Jan 22. PMID: 33479140.
- Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24.Cao X, Khitun A, Luo Y, Na Z, Phoodokmai T, Sappakhaw K, Olatunji E, Uttamapinant C, Slavoff SA. Nat Commun. 2021 Jan 21; 2021 Jan 21. PMID: 33479206.
- An in vivo screen of noncoding loci reveals that Daedalus is a gatekeeper of an Ikaros-dependent checkpoint during haematopoiesis.Harman CCD, Bailis W, Zhao J, Hill L, Qu R, Jackson RP, Shyer JA, Steach HR, Kluger Y, Goff LA, Rinn JL, Williams A, Henao-Mejia J, Flavell RA. Proc Natl Acad Sci U S A. 2021 Jan 19. PMID: 33446502.
- Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease.Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC. Cell Host Microbe. 2021 Jan 13; 2021 Jan 1. PMID: 33385335.
- CD300lf Conditional Knockout Mouse Reveals Strain-Specific Cellular Tropism of Murine Norovirus.Graziano VR, Alfajaro MM, Schmitz CO, Filler RB, Strine MS, Wei J, Hsieh LL, Baldridge MT, Nice TJ, Lee S, Orchard RC, Wilen CB. J Virol. 2021 Jan 13; 2021 Jan 13. PMID: 33177207.
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- Current understanding of human megakaryocytic-erythroid progenitors and their fate determinants.Kwon N, Thompson EN, Mayday MY, Scanlon V, Lu YC, Krause DS. Curr Opin Hematol. 2021 Jan. PMID: 33186151.
- The single-cell landscape of immunological responses of CD4+ T cells in HIV versus severe acute respiratory syndrome coronavirus 2.Collora JA, Liu R, Albrecht K, Ho YC. Curr Opin HIV AIDS. 2021 Jan. PMID: 33165008.
- Genetic characterization of an aggressive optic nerve pilocytic glioma.Hong CS, Fliney G, Fisayo A, An Y, Gopal PP, Omuro A, Pointdujour-Lim R, Erson-Omay EZ, Omay SB. Brain Tumor Pathol. 2021 Jan; 2020 Oct 24. PMID: 33098465.
- A second riboswitch class for the enzyme cofactor NAD().Panchapakesan SSS, Corey L, Malkowski SN, Higgs G, Breaker RR. RNA. 2021 Jan; 2020 Oct 21. PMID: 33087526.
- IL-4-BATF signaling directly modulates IL-9 producing mucosal mast cell (MMC9) function in experimental food allergy.Tomar S, Ganesan V, Sharma A, Zeng C, Waggoner L, Smith A, Kim CH, Licona-Limón P, Reinhardt RL, Flavell RA, Wang YH, Hogan SP. J Allergy Clin Immunol. 2021 Jan; 2020 Oct 15. PMID: 33069715.
- What reinfections mean for COVID-19.Iwasaki A. Lancet Infect Dis. 2021 Jan; 2020 Oct 12. PMID: 33058796.
- Genetic determinants of ammonia-induced acute lung injury in mice.Bein K, Ganguly K, Martin TM, Concel VJ, Brant KA, Di YPP, Upadhyay S, Fabisiak JP, Vuga LJ, Kaminski N, Kostem E, Eskin E, Prows DR, Jang AS, Leikauf GD. Am J Physiol Lung Cell Mol Physiol. 2021 Jan 1; 2020 Oct 14. PMID: 33050709.
- Lysis of cold-storage-induced microvascular obstructions for ex vivo revitalization of marginal human kidneys.DiRito JR, Hosgood SA, Reschke M, Albert C, Bracaglia LG, Ferdinand JR, Stewart BJ, Edwards CM, Vaish AG, Thiru S, Mulligan DC, Haakinson DJ, Clatworthy MR, Saltzman WM, Pober JS, Nicholson ML, Tietjen GT. Am J Transplant. 2021 Jan; 2020 Jul 5. PMID: 32627324.
2020
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- BMP-9 and LDL crosstalk regulates ALK-1 endocytosis and LDL transcytosis in endothelial cells.Tao B, Kraehling JR, Ghaffari S, Ramirez CM, Lee S, Fowler JW, Lee WL, Fernandez-Hernando C, Eichmann A, Sessa WC. J Biol Chem. 2020 Dec 25; 2020 Oct 23. PMID: 33097593.
- Kinetics of antibody responses dictate COVID-19 outcome.Lucas C, Klein J, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B, Wyllie AL, Vogels CBF, Muenker MC, Casanovas-Massana A, Schulz WL, Zell J, Campbell M, Fournier JB, Grubaugh ND, Farhadian S, Wisnewski AV, Cruz CD, Omer S, Ko AI, Ring A, Iwasaki A. medRxiv. 2020 Dec 22; 2020 Dec 22. PMID: 33398304.
- An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2.Tada T, Fan C, Chen JS, Kaur R, Stapleford KA, Gristick H, Dcosta BM, Wilen CB, Nimigean CM, Landau NR. Cell Rep. 2020 Dec 22; 2020 Dec 1. PMID: 33326798.
- Developmentally Regulated Novel Non-coding Anti-sense Regulators of mRNA Translation in Trypanosoma b rucei.Rajan KS, Doniger T, Cohen-Chalamish S, Rengaraj P, Galili B, Aryal S, Unger R, Tschudi C, Michaeli S. iScience. 2020 Dec 18; 2020 Nov 5. PMID: 33294788.
- The Interpretation of SARS-CoV-2 Diagnostic Tests.Stites EC, Wilen CB. Med. 2020 Dec 18; 2020 Aug 21. PMID: 32864639.
- Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.Yuan S, Peng L, Park JJ, Hu Y, Devarkar SC, Dong MB, Shen Q, Wu S, Chen S, Lomakin IB, Xiong Y. Mol Cell. 2020 Dec 17; 2020 Oct 29. PMID: 33188728.
- Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria.Salvail H, Balaji A, Yu D, Roth A, Breaker RR. Biochemistry. 2020 Dec 15; 2020 Nov 25. PMID: 33236895.
- Toward a Cell Atlas of the Human Airway.Schupp JC, Yan X, Kaminski N. Am J Respir Crit Care Med. 2020 Dec 15. PMID: 32841575.
- High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. Cell. 2020 Dec 10; 2020 Nov 13. PMID: 33188776.
- DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells.Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C. Nano Lett. 2020 Dec 9; 2020 Nov 9. PMID: 33164530.
- Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. bioRxiv. 2020 Dec 9; 2020 Dec 9. PMID: 32935102.
- STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.Lee D, Shi M, Moran J, Wall M, Zhang J, Liu J, Fitzgerald D, Kyono Y, Ma L, White KP, Gerstein M. Genome Biol. 2020 Dec 8; 2020 Dec 8. PMID: 33292397.
- Roadblock-qPCR: A simple and inexpensive strategy for targeted measurements of mRNA stability.Watson M, Park Y, Thoreen C. RNA. 2020 Dec 7; 2020 Dec 7. PMID: 33288682.
- Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling.Israelow B, Song E, Mao T, Lu P, Meir A, Liu F, Alfajaro MM, Wei J, Dong H, Homer RJ, Ring A, Wilen CB, Iwasaki A. J Exp Med. 2020 Dec 7. PMID: 32750141.
- The N-glycome regulates the endothelial-to-hematopoietic transition.Kasper DM, Hintzen J, Wu Y, Ghersi JJ, Mandl HK, Salinas KE, Armero W, He Z, Sheng Y, Xie Y, Heindel DW, Park EJ, Sessa WC, Mahal LK, Lebrilla C, Hirschi KK, Nicoli S. Science. 2020 Dec 4; 2020 Dec 3. PMID: 33273096.
- The role of RNA epigenetic modification in normal and malignant hematopoiesis.Vasic R, Gao Y, Liu C, Halene S. Curr Stem Cell Rep. 2020 Dec; 2020 Aug 12. PMID: 33777659.
- Preparation of Mammalian Nascent RNA for Long Read Sequencing.Reimer KA, Neugebauer KM. Curr Protoc Mol Biol. 2020 Dec. PMID: 33085989.
- Identification and characterization of functional long noncoding RNAs in cancer.Olivero CE, Dimitrova N. FASEB J. 2020 Dec; 2020 Oct 15. PMID: 33058262.
- The Idiopathic Pulmonary Fibrosis Cell Atlas.Neumark N, Cosme C Jr, Rose KA, Kaminski N. Am J Physiol Lung Cell Mol Physiol. 2020 Dec 1; 2020 Sep 30. PMID: 32996785.
- Glycogen synthase kinase-3β inhibition alleviates activation of the NLRP3 inflammasome in myocardial infarction.Wang S, Su X, Xu L, Chang C, Yao Y, Komal S, Cha X, Zang M, Ouyang X, Zhang L, Han S. J Mol Cell Cardiol. 2020 Dec; 2020 Sep 28. PMID: 32991876.
- Circular RNAs in Immune Response and Viral Infection.Yan L, Chen YG. Trends Biochem Sci. 2020 Dec; 2020 Sep 6. PMID: 32900574.
- CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade.Wang G, Chow RD, Zhu L, Bai Z, Ye L, Zhang F, Renauer PA, Dong MB, Dai X, Zhang X, Du Y, Cheng Y, Niu L, Chu Z, Kim K, Liao C, Clark P, Errami Y, Chen S. Cancer Discov. 2020 Dec; 2020 Sep 4. PMID: 32887696.
- Sex differences in immune responses that underlie COVID-19 disease outcomes.Takahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Nature. 2020 Dec; 2020 Aug 26. PMID: 32846427.
- A rare bacterial RNA motif is implicated in the regulation of the purF gene whose encoded enzyme synthesizes phosphoribosylamine.Malkowski SN, Atilho RM, Greenlee EB, Weinberg CE, Breaker RR. RNA. 2020 Dec; 2020 Aug 25. PMID: 32843366.
- Emerging roles for noncoding RNAs in female sex steroids and reproductive disease.Zhang R, Wesevich V, Chen Z, Zhang D, Kallen AN. Mol Cell Endocrinol. 2020 Dec 1; 2020 Jul 12. PMID: 32668269.
- The evolution of the human brain and disease susceptibility.Pattabiraman K, Muchnik SK, Sestan N. Curr Opin Genet Dev. 2020 Dec; 2020 Jul 3. PMID: 32629339.
- Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L. Nat Commun. 2020 Nov 30; 2020 Nov 30. PMID: 33257764.
- Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.Li B, Yang YT, Capra JA, Gerstein MB. PLoS Comput Biol. 2020 Nov; 2020 Nov 30. PMID: 33253214.
- Circulating markers of angiogenesis and endotheliopathy in COVID-19.Pine AB, Meizlish ML, Goshua G, Chang CH, Zhang H, Bishai J, Bahel P, Patel A, Gbyli R, Kwan JM, Won CH, Price C, Dela Cruz CS, Halene S, van Dijk D, Hwa J, Lee AI, Chun HJ. Pulm Circ. 2020 Oct-Dec; 2020 Nov 25. PMID: 33282193.
- Commensal Microbiota Modulation of Natural Resistance to Virus Infection.Stefan KL, Kim MV, Iwasaki A, Kasper DL. Cell. 2020 Nov 25; 2020 Nov 18. PMID: 33212011.
- Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors.Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Sanchez-San Martin C, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL. J Virol. 2020 Nov 23; 2020 Nov 23. PMID: 32999034.
- Regulation and Function of RNA Pseudouridylation in Human Cells.Borchardt EK, Martinez NM, Gilbert WV. Annu Rev Genet. 2020 Nov 23; 2020 Sep 1. PMID: 32870730.
- Insights into Lysosomal PI(3,5)P(2) Homeostasis from a Structural-Biochemical Analysis of the PIKfyve Lipid Kinase Complex.Lees JA, Li P, Kumar N, Weisman LS, Reinisch KM. Mol Cell. 2020 Nov 19; 2020 Oct 23. PMID: 33098764.
- Ovarian somatic Piwi regulates nurse cell proliferation and oocyte specification in Drosophila.Gonzalez LE, Zhu G, Lin H. MicroPubl Biol. 2020 Nov 18; 2020 Nov 18. PMID: 33274329.
- Piwi in the stem cell niche regulates nurse cell number and oocyte specification.Zhu G, Gonzalez LE, Lin H. MicroPubl Biol. 2020 Nov 18; 2020 Nov 18. PMID: 33274324.
- miR-27b Modulates Insulin Signaling in Hepatocytes by Regulating Insulin Receptor Expression.Benito-Vicente A, Uribe KB, Rotllan N, Ramírez CM, Jebari-Benslaiman S, Goedeke L, Canfrán-Duque A, Galicia-García U, Saenz De Urturi D, Aspichueta P, Suárez Y, Fernández-Hernando C, Martín C. Int J Mol Sci. 2020 Nov 17; 2020 Nov 17. PMID: 33212990.
- Lymphangiogenic therapy prevents cardiac dysfunction by ameliorating inflammation and hypertension.Song L, Chen X, Swanson TA, LaViolette B, Pang J, Cunio T, Nagle MW, Asano S, Hales K, Shipstone A, Sobon H, Al-Harthy SD, Ahn Y, Kreuser S, Robertson A, Ritenour C, Voigt F, Boucher M, Sun F, Sessa WC, Roth Flach RJ. Elife. 2020 Nov 17; 2020 Nov 17. PMID: 33200983.
- Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.Schupp JC, Khanal S, Gomez JL, Sauler M, Adams TS, Chupp GL, Yan X, Poli S, Zhao Y, Montgomery RR, Rosas IO, Dela Cruz CS, Bruscia EM, Egan ME, Kaminski N, Britto CJ. Am J Respir Crit Care Med. 2020 Nov 15. PMID: 32603604.
- Data Sanitization to Reduce Private Information Leakage from Functional Genomics.Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Cell. 2020 Nov 12. PMID: 33186529.
- SVFX: a machine learning framework to quantify the pathogenicity of structural variants.Kumar S, Harmanci A, Vytheeswaran J, Gerstein MB. Genome Biol. 2020 Nov 9; 2020 Nov 9. PMID: 33168059.
- Clinical Characteristics and Outcomes for 7,995 Patients with SARS-CoV-2 Infection.McPadden J, Warner F, Young HP, Hurley NC, Pulk RA, Singh A, Durant TJ, Gong G, Desai N, Haimovich A, Taylor RA, Gunel M, Cruz CSD, Farhadian SF, Siner J, Villanueva M, Churchwell K, Hsiao A, Torre CJ Jr, Velazquez EJ, Herbst RS, Iwasaki A, Ko AI, Mortazavi BJ, Krumholz HM, Schulz WL. medRxiv. 2020 Nov 8; 2020 Nov 8. PMID: 32743602.
- Publisher Correction: TGF-β signaling in Th17 cells promotes IL-22 production and colitis-associated colon cancer.Perez LG, Kempski J, McGee HM, Pelzcar P, Agalioti T, Giannou A, Konczalla L, Brockmann L, Wahib R, Xu H, Vesely MCA, Soukou S, Steglich B, Bedke T, Manthey C, Seiz O, Diercks BP, Gnafakis S, Guse AH, Perez D, Izbicki JR, Gagliani N, Flavell RA, Huber S. Nat Commun. 2020 Nov 6; 2020 Nov 6. PMID: 33159069.
- Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Nat Commun. 2020 Nov 6; 2020 Nov 6. PMID: 33159066.
- Transcriptional priming as a conserved mechanism of lineage diversification in the developing mouse and human neocortex.Li Z, Tyler WA, Zeldich E, Santpere Baró G, Okamoto M, Gao T, Li M, Sestan N, Haydar TF. Sci Adv. 2020 Nov; 2020 Nov 6. PMID: 33158872.
- Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence.Choi J, Groisman EA. Nucleic Acids Res. 2020 Nov 4. PMID: 33045730.
- Global Profiling of Cellular Substrates of Human Dcp2.Luo Y, Schofield JA, Simon MD, Slavoff SA. Biochemistry. 2020 Nov 3; 2020 May 14. PMID: 32365300.
- Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus.Jin SC, Dong W, Kundishora AJ, Panchagnula S, Moreno-De-Luca A, Furey CG, Allocco AA, Walker RL, Nelson-Williams C, Smith H, Dunbar A, Conine S, Lu Q, Zeng X, Sierant MC, Knight JR, Sullivan W, Duy PQ, DeSpenza T, Reeves BC, Karimy JK, Marlier A, Castaldi C, Tikhonova IR, Li B, Peña HP, Broach JR, Kabachelor EM, Ssenyonga P, Hehnly C, Ge L, Keren B, Timberlake AT, Goto J, Mangano FT, Johnston JM, Butler WE, Warf BC, Smith ER, Schiff SJ, Limbrick DD Jr, Heuer G, Jackson EM, Iskandar BJ, Mane S, Haider S, Guclu B, Bayri Y, Sahin Y, Duncan CC, Apuzzo MLJ, DiLuna ML, Hoffman EJ, Sestan N, Ment LR, Alper SL, Bilguvar K, Geschwind DH, Günel M, Lifton RP, Kahle KT. Nat Med. 2020 Nov; 2020 Oct 19. PMID: 33077954.
- Author Correction: metabolic signaling in T cells.Shyer JA, Flavell RA, Bailis W. Cell Res. 2020 Nov. PMID: 33028962.
- Hypoxia Induces Resistance to EGFR Inhibitors in Lung Cancer Cells via Upregulation of FGFR1 and the MAPK Pathway.Lu Y, Liu Y, Oeck S, Zhang GJ, Schramm A, Glazer PM. Cancer Res. 2020 Nov 1; 2020 Sep 1. PMID: 32873635.
- Tumor-targeted pH-low insertion peptide delivery of theranostic gadolinium nanoparticles for image-guided nanoparticle-enhanced radiation therapy.Liu W, Deacon J, Yan H, Sun B, Liu Y, Hegan D, Li Q, Coman D, Parent M, Hyder F, Roberts K, Nath R, Tillement O, Engelman D, Glazer P. Transl Oncol. 2020 Nov; 2020 Aug 4. PMID: 32763504.
- Sulfamethoxazole drug stress upregulates antioxidant immunomodulatory metabolites in Escherichia coli.Park HB, Wei Z, Oh J, Xu H, Kim CS, Wang R, Wyche TP, Piizzi G, Flavell RA, Crawford JM. Nat Microbiol. 2020 Nov; 2020 Jul 27. PMID: 32719505.
- Control of Murine Primordial Follicle Growth Activation by IκB/NFκB Signaling.Wright CJ, Cari EL, Sandoval J, Bales E, Sam PK, Zarate MA, Polotsky AJ, Kallen AN, Johnson J. Reprod Sci. 2020 Nov; 2020 Jun 15. PMID: 32542534.
- Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells.Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. bioRxiv. 2020 Oct 31; 2020 Oct 31. PMID: 33140047.
- DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines.Duprey A, Groisman EA. PLoS Genet. 2020 Oct; 2020 Oct 30. PMID: 33125364.
- Widespread Transcriptional Readthrough Caused by Nab2 Depletion Leads to Chimeric Transcripts with Retained Introns.Alpert T, Straube K, Carrillo Oesterreich F, Herzel L, Neugebauer KM. Cell Rep. 2020 Oct 27. PMID: 33113357.
- The NBDY Microprotein Regulates Cellular RNA Decapping.Na Z, Luo Y, Schofield JA, Smelyansky S, Khitun A, Muthukumar S, Valkov E, Simon MD, Slavoff SA. Biochemistry. 2020 Oct 27; 2020 Oct 15. PMID: 33059440.
- RUNX Binding Sites Are Enriched in Herpesvirus Genomes, and RUNX1 Overexpression Leads to Herpes Simplex Virus 1 Suppression.Kim DJ, Khoury-Hanold W, Jain PC, Klein J, Kong Y, Pope SD, Ge W, Medzhitov R, Iwasaki A. J Virol. 2020 Oct 27; 2020 Oct 27. PMID: 32878886.
- NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis.Zhang J, Liu J, McGillivray P, Yi C, Lochovsky L, Lee D, Gerstein M. BMC Bioinformatics. 2020 Oct 22; 2020 Oct 22. PMID: 33092526.
- Naturally Occurring tRNAs With Non-canonical Structures.Krahn N, Fischer JT, Söll D. Front Microbiol. 2020; 2020 Oct 21. PMID: 33193279.
- Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro.Sun Y, Abriola L, Surovtseva YV, Lindenbach BD, Guo JU. bioRxiv. 2020 Oct 21; 2020 Oct 21. PMID: 33106809.
- p120 catenin recruits HPV to γ-secretase to promote virus infection.Harwood MC, Dupzyk AJ, Inoue T, DiMaio D, Tsai B. PLoS Pathog. 2020 Oct; 2020 Oct 21. PMID: 33085724.
- Phosphoinositide 3'-Kinase γ Facilitates Polyomavirus Infection.Clark P, Gee GV, Albright BS, Assetta B, Han Y, Atwood WJ, DiMaio D. Viruses. 2020 Oct 20; 2020 Oct 20. PMID: 33092168.
- Using Genetic Code Expansion for Protein Biochemical Studies.Chung CZ, Amikura K, Söll D. Front Bioeng Biotechnol. 2020; 2020 Oct 19. PMID: 33195171.
- Why and How Vaccines Work.Iwasaki A, Omer SB. Cell. 2020 Oct 15. PMID: 33064982.
- Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients.Lou S, Li T, Spakowicz D, Yan X, Chupp GL, Gerstein M. BMC Bioinformatics. 2020 Oct 15; 2020 Oct 15. PMID: 33059594.
- Macrophage scavenger receptor 1 controls Chikungunya virus infection through autophagy in mice.Yang L, Geng T, Yang G, Ma J, Wang L, Ketkar H, Yang D, Lin T, Hwang J, Zhu S, Wang Y, Dai J, You F, Cheng G, Vella AT, Flavell RA, Fikrig E, Wang P. Commun Biol. 2020 Oct 8; 2020 Oct 8. PMID: 33033362.
- Detection of SARS-CoV-2 RNA by multiplex RT-qPCR.Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND, Iwasaki A. PLoS Biol. 2020 Oct; 2020 Oct 7. PMID: 33027248.
- Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection.Flynn RA, Belk JA, Qi Y, Yasumoto Y, Schmitz CO, Mumbach MR, Limaye A, Wei J, Alfajaro MM, Parker KR, Chang HY, Horvath TL, Carette JE, Bertozzi C, Wilen CB, Satpathy AT. bioRxiv. 2020 Oct 6; 2020 Oct 6. PMID: 33052334.
- Reduced development of COVID-19 in children reveals molecular checkpoints gating pathogenesis illuminating potential therapeutics.Steinman JB, Lum FM, Ho PP, Kaminski N, Steinman L. Proc Natl Acad Sci U S A. 2020 Oct 6; 2020 Sep 3. PMID: 32883878.
- The Role of Immune Factors in Shaping Fetal Neurodevelopment.Lu-Culligan A, Iwasaki A. Annu Rev Cell Dev Biol. 2020 Oct 6; 2020 Jul 28. PMID: 32722920.
- SV40 Polyomavirus Activates the Ras-MAPK Signaling Pathway for Vacuolization, Cell Death, and Virus Release.Motamedi N, Sewald X, Luo Y, Mothes W, DiMaio D. Viruses. 2020 Oct 5; 2020 Oct 5. PMID: 33028008.
- Trading-off and trading-up in the world of bacteria-phage evolution.Burmeister AR, Turner PE. Curr Biol. 2020 Oct 5. PMID: 33022253.
- COVID-19 therapy with mesenchymal stromal cells (MSC) and convalescent plasma must consider exosome involvement: Do the exosomes in convalescent plasma antagonize the weak immune antibodies?Askenase PW. J Extracell Vesicles. 2020 Oct; 2020 Nov 14. PMID: 33304473.
- One Ring to Rule Them All: Mitochondrial Circular RNAs Control Mitochondrial Function.Yan L, Chen YG. Cell. 2020 Oct 1. PMID: 33007261.
- Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics.Peccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Nat Biotechnol. 2020 Oct; 2020 Sep 18. PMID: 32948856.
- A special collection of reviews on frontiers in immunology.Xu C, Li HB, Flavell RA. Cell Res. 2020 Oct. PMID: 32859992.
- Differentiation of PTH-Expressing Cells From Human Pluripotent Stem Cells.Lawton BR, Martineau C, Sosa JA, Roman S, Gibson CE, Levine MA, Krause DS. Endocrinology. 2020 Oct 1. PMID: 32810225.
- Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT-qPCR primer-probe sets.Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Catherine Muenker M, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Tokuyama M, Venkataraman A, Weizman OE, Wong P, Yang Y, Cheemarla NR, White EB, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz CS, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND. Nat Microbiol. 2020 Oct; 2020 Jul 10. PMID: 32651556.
- IL22BP Mediates the Antitumor Effects of Lymphotoxin Against Colorectal Tumors in Mice and Humans.Kempski J, Giannou AD, Riecken K, Zhao L, Steglich B, Lücke J, Garcia-Perez L, Karstens KF, Wöstemeier A, Nawrocki M, Pelczar P, Witkowski M, Nilsson S, Konczalla L, Shiri AM, Kempska J, Wahib R, Brockmann L, Huber P, Gnirck AC, Turner JE, Zazara DE, Arck PC, Stein A, Simon R, Daubmann A, Meiners J, Perez D, Strowig T, Koni P, Kruglov AA, Sauter G, Izbicki JR, Guse AH, Rösch T, Lohse AW, Flavell RA, Gagliani N, Huber S. Gastroenterology. 2020 Oct; 2020 Jun 22. PMID: 32585307.
- Medication adherence and its correlates among patients affected by schizophrenia with an episodic course: A large-scale multi-center cross-sectional study in China.Wang D, Ross B, Xi C, Pan Y, Zhou L, Yang X, Wu G, Ouyang X, Si T, Liu Z, Hu X. Asian J Psychiatr. 2020 Oct; 2020 Jun 8. PMID: 32570097.
- Tocilizumab Treatment for Cytokine Release Syndrome in Hospitalized Patients With Coronavirus Disease 2019: Survival and Clinical Outcomes.Price CC, Altice FL, Shyr Y, Koff A, Pischel L, Goshua G, Azar MM, Mcmanus D, Chen SC, Gleeson SE, Britto CJ, Azmy V, Kaman K, Gaston DC, Davis M, Burrello T, Harris Z, Villanueva MS, Aoun-Barakat L, Kang I, Seropian S, Chupp G, Bucala R, Kaminski N, Lee AI, LoRusso PM, Topal JE, Dela Cruz C, Malinis M. Chest. 2020 Oct; 2020 Jun 15. PMID: 32553536.
- A New Coronavirus Emerges, This Time Causing a Pandemic.DiMaio D, Enquist LW, Dermody TS. Annu Rev Virol. 2020 Sep 29. PMID: 32315256.
- Seasonality of Respiratory Viral Infections.Moriyama M, Hugentobler WJ, Iwasaki A. Annu Rev Virol. 2020 Sep 29; 2020 Mar 20. PMID: 32196426.
- Corrigendum to "EOLA1 Inhibits Lipopolysaccharide-Induced Vascular Cell Adhesion Molecule-1 Expression by Association with MT2A in ECV304 Cells".Leng W, Lei X, Meng H, Ouyang X, Liang Z. Int J Inflam. 2020; 2020 Sep 27. PMID: 33062250.
- Cyclooxgenase-2 is induced by SARS-CoV-2 infection but does not affect viral entry or replication.Chen JS, Alfajaro MM, Wei J, Chow RD, Filler RB, Eisenbarth SC, Wilen CB. bioRxiv. 2020 Sep 25; 2020 Sep 25. PMID: 32995789.
- Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.Zuo Y, De S, Feng Y, Steitz TA. iScience. 2020 Sep 25; 2020 Aug 11. PMID: 32829286.
- Publisher Correction to: Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images.Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR, Samaras D, Kurc T, Saltz J. Diagn Pathol. 2020 Sep 24; 2020 Sep 24. PMID: 32972449.
- Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2.Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI. N Engl J Med. 2020 Sep 24; 2020 Aug 28. PMID: 32857487.
- Single-cell genomics reveals the genetic and molecular bases for escape from mutational epistasis in myeloid neoplasms.Taylor J, Mi X, North K, Binder M, Penson A, Lasho T, Knorr K, Haddadin M, Liu B, Pangallo J, Benbarche S, Wiseman D, Tefferi A, Halene S, Liang Y, Patnaik MM, Bradley RK, Abdel-Wahab O. Blood. 2020 Sep 24. PMID: 32640014.
- Neural Stem Cells Direct Axon Guidance via Their Radial Fiber Scaffold.Kaur N, Han W, Li Z, Madrigal MP, Shim S, Pochareddy S, Gulden FO, Li M, Xu X, Xing X, Takeo Y, Li Z, Lu K, Imamura Kawasawa Y, Ballester-Lurbe B, Moreno-Bravo JA, Chédotal A, Terrado J, Pérez-Roger I, Koleske AJ, Sestan N. Neuron. 2020 Sep 23; 2020 Jul 23. PMID: 32707082.
- Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L. Nat Commun. 2020 Sep 21; 2020 Sep 21. PMID: 32958763.
- Transcriptomic and clonal characterization of T cells in the human central nervous system.Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Sci Immunol. 2020 Sep 18. PMID: 32948672.
- Updates on molecular and environmental determinants of luteal progesterone production.DeWitt NA, Whirledge S, Kallen AN. Mol Cell Endocrinol. 2020 Sep 15; 2020 Jun 28. PMID: 32610113.
- Predicting the frequencies of drug side effects.Galeano D, Li S, Gerstein M, Paccanaro A. Nat Commun. 2020 Sep 11; 2020 Sep 11. PMID: 32917868.
- Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection.Weiss JJ, Attuquayefio TN, White EB, Li F, Herz RS, White TL, Campbell M, Geng B, Datta R, Wyllie AL, Grubaugh ND, Casanovas-Massana A, Muenker MC, Handoko R, Iwasaki A, Martinello RA, Ko AI, Small DM, Farhadian SF. medRxiv. 2020 Sep 10; 2020 Sep 10. PMID: 32935121.
- A Functional Non-coding RNA Is Produced from xbp-1 mRNA.Liu X, Beaudoin JD, Davison CA, Kosmaczewski SG, Meyer BI, Giraldez AJ, Hammarlund M. Neuron. 2020 Sep 9; 2020 Jul 7. PMID: 32640191.
- Kynurenic acid underlies sex-specific immune responses to COVID-19.Cai Y, Kim DJ, Takahashi T, Broadhurst DI, Ma S, Rattray NJW, Casanovas-Massana A, Israelow B, Klein J, Lucas C, Mao T, Moore AJ, Muenker MC, Oh J, Silva J, Wong P, Ko AI, Khan SA, Iwasaki A, Johnson CH. medRxiv. 2020 Sep 8; 2020 Sep 8. PMID: 32935119.
- Neuroinvasion of SARS-CoV-2 in human and mouse brain.Song E, Zhang C, Israelow B, Lu-Culligan A, Prado AV, Skriabine S, Lu P, Weizman OE, Liu F, Dai Y, Szigeti-Buck K, Yasumoto Y, Wang G, Castaldi C, Heltke J, Ng E, Wheeler J, Alfajaro MM, Levavasseur E, Fontes B, Ravindra NG, Van Dijk D, Mane S, Gunel M, Ring A, Kazmi SAJ, Zhang K, Wilen CB, Horvath TL, Plu I, Haik S, Thomas JL, Louvi A, Farhadian SF, Huttner A, Seilhean D, Renier N, Bilguvar K, Iwasaki A. bioRxiv. 2020 Sep 8; 2020 Sep 8. PMID: 32935108.
- Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells.Marczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Cancers (Basel). 2020 Sep 8; 2020 Sep 8. PMID: 32911681.
- PIWIL1 promotes gastric cancer via a piRNA-independent mechanism.Shi S, Yang ZZ, Liu S, Yang F, Lin H. Proc Natl Acad Sci U S A. 2020 Sep 8; 2020 Aug 26. PMID: 32848063.
- Long noncoding RNA amplified in lung cancer rewires cancer pathways.Martínez-Terroba E, Dimitrova N. J Cell Biol. 2020 Sep 7. PMID: 32858749.
- Pooling saliva to increase SARS-CoV-2 testing capacity.Watkins AE, Fenichel EP, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND, Wyllie AL. medRxiv. 2020 Sep 3; 2020 Sep 3. PMID: 32909003.
- LEARNING GENERAL TRANSFORMATIONS OF DATA FOR OUT-OF-SAMPLE EXTENSIONS.Amodio M, van Dijk D, Wolf G, Krishnaswamy S. IEEE Int Workshop Mach Learn Signal Process. 2020 Sep; 2020 Oct 20. PMID: 34557339.
- Recommendations for measuring HIV reservoir size in cure-directed clinical trials.Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ. Nat Med. 2020 Sep; 2020 Sep 7. PMID: 32895573.
- IL-7 receptor alpha defines heterogeneity and signature of human effector memory CD8(+) T cells in high dimensional analysis.Shin MS, Kim D, Yim K, Park HJ, You S, Dong X, Koumpouras F, Shaw AC, Fan R, Krishnaswamy S, Kang I. Cell Immunol. 2020 Sep; 2020 Jun 24. PMID: 32619811.
- SARS-CoV-2 infection of the placenta.Hosier H, Farhadian SF, Morotti RA, Deshmukh U, Lu-Culligan A, Campbell KH, Yasumoto Y, Vogels CB, Casanovas-Massana A, Vijayakumar P, Geng B, Odio CD, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy AM, Aguilar G, Fardelmann KL, Harigopal M, Taylor HS, Pettker CM, Wyllie AL, Cruz CD, Ring AM, Grubaugh ND, Ko AI, Horvath TL, Iwasaki A, Reddy UM, Lipkind HS. J Clin Invest. 2020 Sep 1. PMID: 32573498.
- Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation.Yeh YJ, Jenike KM, Calvi RM, Chiarella J, Hoh R, Deeks SG, Ho YC. J Clin Invest. 2020 Sep 1. PMID: 32573496.
- Clinical outcomes and characteristics of patients with TP53-mutated acute myeloid leukemia or myelodysplastic syndromes: a single center experience.Bewersdorf JP, Shallis RM, Gowda L, Wei W, Hager K, Isufi I, Kim TK, Pillai MM, Seropian S, Podoltsev NA, Gore SD, Siddon AJ, Zeidan AM. Leuk Lymphoma. 2020 Sep; 2020 May 2. PMID: 32362171.
- The minimal that kills: Why defining and targeting measurable residual disease is the "Sine Qua Non" for further progress in management of acute myeloid leukemia.Bewersdorf JP, Shallis RM, Boddu PC, Wood B, Radich J, Halene S, Zeidan AM. Blood Rev. 2020 Sep; 2019 Dec 20. PMID: 31883804.
- Hepatitis C virus NS3-4A protease regulates the lipid environment for RNA replication by cleaving host enzyme 24-dehydrocholesterol reductase.Tallorin L, Villareal VA, Hsia CY, Rodgers MA, Burri DJ, Pfeil MP, Llopis PM, Lindenbach BD, Yang PL. J Biol Chem. 2020 Aug 28; 2020 Jul 8. PMID: 32641492.
- Broadscale phage therapy is unlikely to select for widespread evolution of bacterial resistance to virus infection.Cohan FM, Zandi M, Turner PE. Virus Evol. 2020 Jul; 2020 Aug 25. PMID: 33365149.
- An allosteric site on MKP5 reveals a strategy for small-molecule inhibition.Gannam ZTK, Min K, Shillingford SR, Zhang L, Herrington J, Abriola L, Gareiss PC, Pantouris G, Tzouvelekis A, Kaminski N, Zhang X, Yu J, Jamali H, Ellman JA, Lolis E, Anderson KS, Bennett AM. Sci Signal. 2020 Aug 25; 2020 Aug 25. PMID: 32843541.
- Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation.Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Proc Natl Acad Sci U S A. 2020 Aug 25; 2020 Aug 12. PMID: 32817466.
- Real-time public health communication of local SARS-CoV-2 genomic epidemiology.Kalinich CC, Jensen CG, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF, Fauver JR, Grubaugh ND, Brito AF. PLoS Biol. 2020 Aug; 2020 Aug 21. PMID: 32822393.
- Imaginary Ribozymes.Breaker RR. ACS Chem Biol. 2020 Aug 21; 2020 Aug 3. PMID: 32687319.
- Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear.Grubaugh ND, Hanage WP, Rasmussen AL. Cell. 2020 Aug 20; 2020 Jul 3. PMID: 32697970.
- Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development.Farley-Barnes KI, Deniz E, Overton MM, Khokha MK, Baserga SJ. PLoS Genet. 2020 Aug; 2020 Aug 19. PMID: 32813698.
- Small proteins regulate Salmonella survival inside macrophages by controlling degradation of a magnesium transporter.Yeom J, Shao Y, Groisman EA. Proc Natl Acad Sci U S A. 2020 Aug 18; 2020 Aug 4. PMID: 32753384.
- MIWI prevents aneuploidy during meiosis by cleaving excess satellite RNA.Hsieh CL, Xia J, Lin H. EMBO J. 2020 Aug 17; 2020 Jul 17. PMID: 32677148.
- CD300LF Polymorphisms of Inbred Mouse Strains Confer Resistance to Murine Norovirus Infection in a Cell Type-Dependent Manner.Furlong K, Biering SB, Choi J, Wilen CB, Orchard RC, Wobus CE, Nelson CA, Fremont DH, Baldridge MT, Randall G, Hwang S. J Virol. 2020 Aug 17; 2020 Aug 17. PMID: 32581099.
- LabxDB: versatile databases for genomic sequencing and lab management.Vejnar CE, Giraldez AJ. Bioinformatics. 2020 Aug 15. PMID: 32502232.
- Estimation of the carrier frequency of fumarate hydratase alterations and implications for kidney cancer risk in hereditary leiomyomatosis and renal cancer.Shuch B, Li S, Risch H, Bindra RS, McGillivray PD, Gerstein M. Cancer. 2020 Aug 15; 2020 May 15. PMID: 32413184.
- Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.Escobar-Hoyos LF, Penson A, Kannan R, Cho H, Pan CH, Singh RK, Apken LH, Hobbs GA, Luo R, Lecomte N, Babu S, Pan FC, Alonso-Curbelo D, Morris JP 4th, Askan G, Grbovic-Huezo O, Ogrodowski P, Bermeo J, Saglimbeni J, Cruz CD, Ho YJ, Lawrence SA, Melchor JP, Goda GA, Bai K, Pastore A, Hogg SJ, Raghavan S, Bailey P, Chang DK, Biankin A, Shroyer KR, Wolpin BM, Aguirre AJ, Ventura A, Taylor B, Der CJ, Dominguez D, Kümmel D, Oeckinghaus A, Lowe SW, Bradley RK, Abdel-Wahab O, Leach SD. Cancer Cell. 2020 Aug 10; 2020 Jun 18. PMID: 32559497.
- Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines.Cao X, Khitun A, Na Z, Dumitrescu DG, Kubica M, Olatunji E, Slavoff SA. J Proteome Res. 2020 Aug 7; 2020 Jun 3. PMID: 32449352.
- Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.Ott IM, Strine MS, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL. medRxiv. 2020 Aug 4; 2020 Aug 4. PMID: 32793924.
- A Vectorial, ER-Mitochondria Link to Energy Homeostasis in the Vascular Endothelium.Boutagy NE, Fowler JW, Sessa WC. Cell Metab. 2020 Aug 4. PMID: 32755606.
- High-throughput discovery of phage receptors using transposon insertion sequencing of bacteria.Kortright KE, Chan BK, Turner PE. Proc Natl Acad Sci U S A. 2020 Aug 4; 2020 Jul 16. PMID: 32675236.
- Reprogramming of Stem Cell Activity to Convert Thorns into Branches.Zhang F, Rossignol P, Huang T, Wang Y, May A, Dupont C, Orbovic V, Irish VF. Curr Biol. 2020 Aug 3; 2020 Jun 18. PMID: 32559443.
- Tissue-resident memory T cell reactivation by diverse antigen-presenting cells imparts distinct functional responses.Low JS, Farsakoglu Y, Amezcua Vesely MC, Sefik E, Kelly JB, Harman CCD, Jackson R, Shyer JA, Jiang X, Cauley LS, Flavell RA, Kaech SM. J Exp Med. 2020 Aug 3. PMID: 32525985.
- NK cell receptor NKG2D enforces proinflammatory features and pathogenicity of Th1 and Th17 cells.Babic M, Dimitropoulos C, Hammer Q, Stehle C, Heinrich F, Sarsenbayeva A, Eisele A, Durek P, Mashreghi MF, Lisnic B, Van Snick J, Löhning M, Fillatreau S, Withers DR, Gagliani N, Huber S, Flavell RA, Polic B, Romagnani C. J Exp Med. 2020 Aug 3. PMID: 32453422.
- Orally Administered Exosomes Suppress Mouse Delayed-Type Hypersensitivity by Delivering miRNA-150 to Antigen-Primed Macrophage APC Targeted by Exosome-Surface Anti-Peptide Antibody Light Chains.Nazimek K, Bryniarski K, Ptak W, Groot Kormelink T, Askenase PW. Int J Mol Sci. 2020 Aug 2; 2020 Aug 2. PMID: 32748889.
- [Meningeal lymphatics, a potential target for the treatment of brain tumors].Thomas JL, Song E, Boisserand L, Iwasaki A. Med Sci (Paris). 2020 Aug-Sep; 2020 Aug 21. PMID: 32821046.
- Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.Sethi A, Gu M, Gumusgoz E, Chan L, Yan KK, Rozowsky J, Barozzi I, Afzal V, Akiyama JA, Plajzer-Frick I, Yan C, Novak CS, Kato M, Garvin TH, Pham Q, Harrington A, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, Visel A, Dickel DE, Yip KY, Sutton R, Pennacchio LA, Gerstein M. Nat Methods. 2020 Aug; 2020 Jul 29. PMID: 32737473.
- Longitudinal analyses reveal immunological misfiring in severe COVID-19.Lucas C, Wong P, Klein J, Castro TBR, Silva J, Sundaram M, Ellingson MK, Mao T, Oh JE, Israelow B, Takahashi T, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Muenker MC, Fournier JB, Campbell M, Odio CD, Casanovas-Massana A, Herbst R, Shaw AC, Medzhitov R, Schulz WL, Grubaugh ND, Dela Cruz C, Farhadian S, Ko AI, Omer SB, Iwasaki A. Nature. 2020 Aug; 2020 Jul 27. PMID: 32717743.
- Metabolic signaling in T cells.Shyer JA, Flavell RA, Bailis W. Cell Res. 2020 Aug; 2020 Jul 24. PMID: 32709897.
- Endotheliopathy in COVID-19-associated coagulopathy: evidence from a single-centre, cross-sectional study.Goshua G, Pine AB, Meizlish ML, Chang CH, Zhang H, Bahel P, Baluha A, Bar N, Bona RD, Burns AJ, Dela Cruz CS, Dumont A, Halene S, Hwa J, Koff J, Menninger H, Neparidze N, Price C, Siner JM, Tormey C, Rinder HM, Chun HJ, Lee AI. Lancet Haematol. 2020 Aug; 2020 Jun 30. PMID: 32619411.
- An unbiased high-throughput drug screen reveals a potential therapeutic vulnerability in the most lethal molecular subtype of pancreatic cancer.Pan CH, Otsuka Y, Sridharan B, Woo M, Leiton CV, Babu S, Torrente Gonçalves M, Kawalerski RR, K Bai JD, Chang DK, Biankin AV, Scampavia L, Spicer T, Escobar-Hoyos LF, Shroyer KR. Mol Oncol. 2020 Aug; 2020 Jul 4. PMID: 32533886.
- Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype.Camiolo M, Gauthier M, Kaminski N, Ray A, Wenzel SE. J Allergy Clin Immunol. 2020 Aug; 2020 Jun 10. PMID: 32531372.
- Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA.Zhang J, Teramoto T, Qiu C, Wine RN, Gonzalez LE, Baserga SJ, Tanaka Hall TM. RNA. 2020 Aug; 2020 May 5. PMID: 32371454.
- A bacterial riboswitch class senses xanthine and uric acid to regulate genes associated with purine oxidation.Yu D, Breaker RR. RNA. 2020 Aug; 2020 Apr 28. PMID: 32345632.
- Inter-organelle lipid transfer: a channel model for Vps13 and chorein-N motif proteins.Lees JA, Reinisch KM. Curr Opin Cell Biol. 2020 Aug; 2020 Mar 23. PMID: 32213462.
- RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.Zhang J, Liu J, Lee D, Feng JJ, Lochovsky L, Lou S, Rutenberg-Schoenberg M, Gerstein M. Genome Biol. 2020 Jul 30; 2020 Jul 30. PMID: 32727537.
- Transcriptional activity and strain-specific history of mouse pseudogenes.Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T, Harrow J, Gerstein M. Nat Commun. 2020 Jul 29; 2020 Jul 29. PMID: 32728065.
- An integrative ENCODE resource for cancer genomics.Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. Nat Commun. 2020 Jul 29; 2020 Jul 29. PMID: 32728046.
- FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo.Duprey A, Groisman EA. mBio. 2020 Jul 28; 2020 Jul 28. PMID: 32723920.
- Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images.Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR, Samaras D, Kurc T, Saltz J. Diagn Pathol. 2020 Jul 28; 2020 Jul 28. PMID: 32723384.
- Exploiting evolutionary trade-offs for posttreatment management of drug-resistant populations.Melnikov SV, Stevens DL, Fu X, Kwok HS, Zhang JT, Shen Y, Sabina J, Lee K, Lee H, Söll D. Proc Natl Acad Sci U S A. 2020 Jul 28; 2020 Jul 13. PMID: 32661175.
- La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region.Philippe L, Vasseur JJ, Debart F, Thoreen CC. Nucleic Acids Res. 2020 Jul 27. PMID: 32558918.
- Using blockchain to log genome dataset access: efficient storage and query.Gürsoy G, Bjornson R, Green ME, Gerstein M. BMC Med Genomics. 2020 Jul 21; 2020 Jul 21. PMID: 32693796.
- Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J, Beckmann R. PLoS Biol. 2020 Jul; 2020 Jul 20. PMID: 32687489.
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- The Development of a Practical Artificial Intelligence Tool for Diagnosing and Evaluating Autism Spectrum Disorder: Multicenter Study.Chen T, Chen Y, Yuan M, Gerstein M, Li T, Liang H, Froehlich T, Lu L. JMIR Med Inform. 2020 May 8; 2020 May 8. PMID: 32041690.
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- The Positively Charged Active Site of the Bacterial Toxin RelE Causes a Large Shift in the General Base pK(a).Hiller DA, Dunican BF, Nallur S, Li NS, Piccirilli JA, Strobel SA. Biochemistry. 2020 May 5; 2020 Apr 24. PMID: 32320214.
- Cryo-EM reconstruction of a VPS13 fragment reveals a long groove to channel lipids between membranes.Li P, Lees JA, Lusk CP, Reinisch KM. J Cell Biol. 2020 May 4. PMID: 32182622.
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- Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex.Werling DM, Pochareddy S, Choi J, An JY, Sheppard B, Peng M, Li Z, Dastmalchi C, Santpere G, Sousa AMM, Tebbenkamp ATN, Kaur N, Gulden FO, Breen MS, Liang L, Gilson MC, Zhao X, Dong S, Klei L, Cicek AE, Buxbaum JD, Adle-Biassette H, Thomas JL, Aldinger KA, O'Day DR, Glass IA, Zaitlen NA, Talkowski ME, Roeder K, State MW, Devlin B, Sanders SJ, Sestan N. Cell Rep. 2020 Apr 7. PMID: 32268104.
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- Randomized Controlled Trial of Paliperidone Extended Release Versus Risperidone for the Treatment of Methamphetamine-Associated Psychosis in Chinese Patients.Wang G, Ding F, Chawarski MC, Hao W, Liu X, Deng Q, Ouyang X. Front Psychiatry. 2020; 2020 Apr 1. PMID: 32296355.
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- Platform Effects on Regeneration by Pulmonary Basal Cells as Evaluated by Single-Cell RNA Sequencing.Greaney AM, Adams TS, Brickman Raredon MS, Gubbins E, Schupp JC, Engler AJ, Ghaedi M, Yuan Y, Kaminski N, Niklason LE. Cell Rep. 2020 Mar 24. PMID: 32209482.
- Method for Measuring Mucociliary Clearance and Cilia-generated Flow in Mice by ex vivo Imaging.Song E, Iwasaki A. Bio Protoc. 2020 Mar 20; 2020 Mar 20. PMID: 33659527.
- Crystal structure of the C-terminal domain of DENR.Lomakin IB, De S, Wang J, Borkar AN, Steitz TA. Comput Struct Biotechnol J. 2020; 2020 Mar 19. PMID: 32257053.
- Contribution of increasing plasma membrane to the energetic cost of early zebrafish embryogenesis.Rodenfels J, Sartori P, Golfier S, Nagendra K, Neugebauer KM, Howard J. Mol Biol Cell. 2020 Mar 19; 2020 Feb 12. PMID: 32049586.
- miR-181a Modulation of ERK-MAPK Signaling Sustains DC-SIGN Expression and Limits Activation of Monocyte-Derived Dendritic Cells.Lim CX, Lee B, Geiger O, Passegger C, Beitzinger M, Romberger J, Stracke A, Högenauer C, Stift A, Stoiber H, Poidinger M, Zebisch A, Meister G, Williams A, Flavell RA, Henao-Mejia J, Strobl H. Cell Rep. 2020 Mar 17. PMID: 32187550.
- Erratum for Townsend et al., "A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor".Townsend GE 2nd, Han W, Schwalm ND 3rd, Hong X, Bencivenga-Barry NA, Goodman AL, Groisman EA. mBio. 2020 Mar 17; 2020 Mar 17. PMID: 32184244.
- Cell-penetrating peptide inhibits retromer-mediated human papillomavirus trafficking during virus entry.Zhang P, Moreno R, Lambert PF, DiMaio D. Proc Natl Acad Sci U S A. 2020 Mar 17; 2020 Mar 2. PMID: 32123072.
- mRNA destabilization by BTG1 and BTG2 maintains T cell quiescence.Hwang SS, Lim J, Yu Z, Kong P, Sefik E, Xu H, Harman CCD, Kim LK, Lee GR, Li HB, Flavell RA. Science. 2020 Mar 13. PMID: 32165587.
- Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5' TOP motifs.Philippe L, van den Elzen AMG, Watson MJ, Thoreen CC. Proc Natl Acad Sci U S A. 2020 Mar 10; 2020 Feb 24. PMID: 32094190.
- Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures.Zhao Y, Amodio M, Vander Wyk B, Gerritsen B, Kumar MM, van Dijk D, Moon K, Wang X, Malawista A, Richards MM, Cahill ME, Desai A, Sivadasan J, Venkataswamy MM, Ravi V, Fikrig E, Kumar P, Kleinstein SH, Krishnaswamy S, Montgomery RR. PLoS Negl Trop Dis. 2020 Mar; 2020 Mar 9. PMID: 32150565.
- Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.Kumar S, Warrell J, Li S, McGillivray PD, Meyerson W, Salichos L, Harmanci A, Martinez-Fundichely A, Chan CWY, Nielsen MM, Lochovsky L, Zhang Y, Li X, Lou S, Pedersen JS, Herrmann C, Getz G, Khurana E, Gerstein MB. Cell. 2020 Mar 5; 2020 Feb 20. PMID: 32084333.
- Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin.Machyna M, Kiefer L, Simon MD. Nat Struct Mol Biol. 2020 Mar; 2020 Mar 10. PMID: 32157249.
- Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMC. Nat Genet. 2020 Mar; 2020 Feb 5. PMID: 32024998.
- Uncovering axes of variation among single-cell cancer specimens.Chen WS, Zivanovic N, van Dijk D, Wolf G, Bodenmiller B, Krishnaswamy S. Nat Methods. 2020 Mar; 2020 Jan 13. PMID: 31932777.
- Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis.Allen RJ, Guillen-Guio B, Oldham JM, Ma SF, Dressen A, Paynton ML, Kraven LM, Obeidat M, Li X, Ng M, Braybrooke R, Molina-Molina M, Hobbs BD, Putman RK, Sakornsakolpat P, Booth HL, Fahy WA, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Whyte MKB, Zhang Y, Kaminski N, Adegunsoye A, Strek ME, Neighbors M, Sheng XR, Gudmundsson G, Gudnason V, Hatabu H, Lederer DJ, Manichaikul A, Newell JD Jr, O'Connor GT, Ortega VE, Xu H, Fingerlin TE, Bossé Y, Hao K, Joubert P, Nickle DC, Sin DD, Timens W, Furniss D, Morris AP, Zondervan KT, Hall IP, Sayers I, Tobin MD, Maher TM, Cho MH, Hunninghake GM, Schwartz DA, Yaspan BL, Molyneaux PL, Flores C, Noth I, Jenkins RG, Wain LV. Am J Respir Crit Care Med. 2020 Mar 1. PMID: 31710517.
- The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea.Zhao C, Lyu Z, Long F, Akinyemi T, Manakongtreecheep K, Söll D, Whitman WB, Vinyard DJ, Liu Y. FEBS Lett. 2020 Mar; 2019 Nov 27. PMID: 31709520.
- Three Dimensional Bioprinting of a Vascularized and Perfusable Skin Graft Using Human Keratinocytes, Fibroblasts, Pericytes, and Endothelial Cells.Baltazar T, Merola J, Catarino C, Xie CB, Kirkiles-Smith NC, Lee V, Hotta S, Dai G, Xu X, Ferreira FC, Saltzman WM, Pober JS, Karande P. Tissue Eng Part A. 2020 Mar; 2019 Dec 3. PMID: 31672103.
- Characterization of Autoinducer-3 Structure and Biosynthesis in E. coli.Kim CS, Gatsios A, Cuesta S, Lam YC, Wei Z, Chen H, Russell RM, Shine EE, Wang R, Wyche TP, Piizzi G, Flavell RA, Palm NW, Sperandio V, Crawford JM. ACS Cent Sci. 2020 Feb 26; 2020 Jan 22. PMID: 32123737.
- Nucleolar localization of RAG1 modulates V(D)J recombination activity.Brecht RM, Liu CC, Beilinson HA, Khitun A, Slavoff SA, Schatz DG. Proc Natl Acad Sci U S A. 2020 Feb 25; 2020 Feb 11. PMID: 32047031.
- Mangroves give cause for conservation optimism, for now.Friess DA, Yando ES, Abuchahla GMO, Adams JB, Cannicci S, Canty SWJ, Cavanaugh KC, Connolly RM, Cormier N, Dahdouh-Guebas F, Diele K, Feller IC, Fratini S, Jennerjahn TC, Lee SY, Ogurcak DE, Ouyang X, Rogers K, Rowntree JK, Sharma S, Sloey TM, Wee AKS. Curr Biol. 2020 Feb 24. PMID: 32097637.
- Small-Molecule Antagonists of the RIG-I Innate Immune Receptor.Rawling DC, Jagdmann GE Jr, Potapova O, Pyle AM. ACS Chem Biol. 2020 Feb 21; 2020 Jan 27. PMID: 31944652.
- p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis.Olivero CE, Martínez-Terroba E, Zimmer J, Liao C, Tesfaye E, Hooshdaran N, Schofield JA, Bendor J, Fang D, Simon MD, Zamudio JR, Dimitrova N. Mol Cell. 2020 Feb 20; 2020 Jan 20. PMID: 31973890.
- High-throughput quantitative microscopy-based half-life measurements of intravenously injected agents.Bracaglia LG, Piotrowski-Daspit AS, Lin CY, Moscato ZM, Wang Y, Tietjen GT, Saltzman WM. Proc Natl Acad Sci U S A. 2020 Feb 18; 2020 Feb 3. PMID: 32015123.
- Initiation of Protein Synthesis with Non-Canonical Amino Acids In Vivo.Tharp JM, Ad O, Amikura K, Ward FR, Garcia EM, Cate JHD, Schepartz A, Söll D. Angew Chem Int Ed Engl. 2020 Feb 17; 2020 Jan 21. PMID: 31828898.
- Endothelial cell-glucocorticoid receptor interactions and regulation of Wnt signaling.Zhou H, Mehta S, Srivastava SP, Grabinska K, Zhang X, Wong C, Hedayat A, Perrotta P, Fernández-Hernando C, Sessa WC, Goodwin JE. JCI Insight. 2020 Feb 13; 2020 Feb 13. PMID: 32051336.
- Impact of hypoxia on DNA repair and genome integrity.Kaplan AR, Glazer PM. Mutagenesis. 2020 Feb 13. PMID: 31282537.
- Quantitating Endosomal Escape of a Library of Polymers for mRNA Delivery.Jiang Y, Lu Q, Wang Y, Xu E, Ho A, Singh P, Wang Y, Jiang Z, Yang F, Tietjen GT, Cresswell P, Saltzman WM. Nano Lett. 2020 Feb 12; 2020 Jan 31. PMID: 32003222.
- Peptide Nucleic Acids and Gene Editing: Perspectives on Structure and Repair.Economos NG, Oyaghire S, Quijano E, Ricciardi AS, Saltzman WM, Glazer PM. Molecules. 2020 Feb 8; 2020 Feb 8. PMID: 32046275.
- Estimating growth patterns and driver effects in tumor evolution from individual samples.Salichos L, Meyerson W, Warrell J, Gerstein M. Nat Commun. 2020 Feb 5; 2020 Feb 5. PMID: 32024824.
- Quantitative Models of Phage-Antibiotic Combination Therapy.Rodriguez-Gonzalez RA, Leung CY, Chan BK, Turner PE, Weitz JS. mSystems. 2020 Feb 4; 2020 Feb 4. PMID: 32019835.
- The stress-responsive gene GDPGP1/mcp-1 regulates neuronal glycogen metabolism and survival.Schulz A, Sekine Y, Oyeyemi MJ, Abrams AJ, Basavaraju M, Han SM, Groth M, Morrison H, Strittmatter SM, Hammarlund M. J Cell Biol. 2020 Feb 3. PMID: 31968056.
- An endothelial microRNA-1-regulated network controls eosinophil trafficking in asthma and chronic rhinosinusitis.Korde A, Ahangari F, Haslip M, Zhang X, Liu Q, Cohn L, Gomez JL, Chupp G, Pober JS, Gonzalez A, Takyar SS. J Allergy Clin Immunol. 2020 Feb. PMID: 32035607.
- Establishing a Global Standard for Wearable Devices in Sport and Fitness: Perspectives from the New England Chapter of the American College of Sports Medicine Members.Ash GI, Stults-Kolehmainen M, Busa MA, Gregory R, Garber CE, Liu J, Gerstein M, Casajus JA, Gonzalez-Aguero A, Constantinou D, Geistlinger M, Guppy FM, Pigozzi F, Pitsiladis YP. Curr Sports Med Rep. 2020 Feb. PMID: 32028347.
- Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Nature. 2020 Feb; 2020 Feb 5. PMID: 32025015.
- Select autophagy genes maintain quiescence of tissue-resident macrophages and increase susceptibility to Listeria monocytogenes.Wang YT, Zaitsev K, Lu Q, Li S, Schaiff WT, Kim KW, Droit L, Wilen CB, Desai C, Balce DR, Orchard RC, Orvedahl A, Park S, Kreamalmeyer D, Handley SA, Pfeifer JD, Baldridge MT, Artyomov MN, Stallings CL, Virgin HW. Nat Microbiol. 2020 Feb; 2020 Jan 20. PMID: 31959973.
- Treatment of Clostridioides difficile Infection and Non-compliance with Treatment Guidelines in Adults in 10 US Geographical Locations, 2013-2015.Novosad SA, Mu Y, Winston LG, Johnston H, Basiliere E, Olson DM, Farley MM, Revis A, Wilson L, Perlmutter R, Holzbauer SM, Whitten T, Phipps EC, Dumyati GK, Beldavs ZG, Ocampo VLS, Davis CM, Kainer M, Gerding DN, Guh AY. J Gen Intern Med. 2020 Feb; 2019 Nov 25. PMID: 31768906.
- Publisher Correction: MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors.Chen X, Burkhardt DB, Hartman AA, Hu X, Eastman AE, Sun C, Wang X, Zhong M, Krishnaswamy S, Guo S. Nat Commun. 2020 Jan 29; 2020 Jan 29. PMID: 31996673.
- A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor.Townsend GE 2nd, Han W, Schwalm ND 3rd, Hong X, Bencivenga-Barry NA, Goodman AL, Groisman EA. mBio. 2020 Jan 28; 2020 Jan 28. PMID: 31992627.
- Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex.Yang H, Kim J, Kim Y, Jang SW, Sestan N, Shim S. Biochem Biophys Res Commun. 2020 Jan 22; 2019 Nov 8. PMID: 31708105.
- Enteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity.Jarret A, Jackson R, Duizer C, Healy ME, Zhao J, Rone JM, Bielecki P, Sefik E, Roulis M, Rice T, Sivanathan KN, Zhou T, Solis AG, Honcharova-Biletska H, Vélez K, Hartner S, Low JS, Qu R, de Zoete MR, Palm NW, Ring AM, Weber A, Moor AE, Kluger Y, Nowarski R, Flavell RA. Cell. 2020 Jan 9. PMID: 31923399.
- The forces driving clonal expansion of the HIV-1 latent reservoir.Liu R, Simonetti FR, Ho YC. Virol J. 2020 Jan 7; 2020 Jan 7. PMID: 31910871.
- Engineering aminoacyl-tRNA synthetases for use in synthetic biology.Krahn N, Tharp JM, Crnković A, Söll D. Enzymes. 2020; 2020 Sep 8. PMID: 33837709.
- Harmonic Alignment.Stanley JS 3rd, Gigante S, Wolf G, Krishnaswamy S. Proc SIAM Int Conf Data Min. 2020. PMID: 33723496.
- Polymeric vehicles for nucleic acid delivery.Piotrowski-Daspit AS, Kauffman AC, Bracaglia LG, Saltzman WM. Adv Drug Deliv Rev. 2020; 2020 Jun 23. PMID: 32585159.
- Pharmacological methods to transcriptionally modulate double-strand break DNA repair.Kaplan AR, Glazer PM. Int Rev Cell Mol Biol. 2020; 2019 Dec 18. PMID: 32475473.
- Poly(Lactic-co-Glycolic Acid) Nanoparticle Delivery of Peptide Nucleic Acids In Vivo.Oyaghire SN, Quijano E, Piotrowski-Daspit AS, Saltzman WM, Glazer PM. Methods Mol Biol. 2020. PMID: 32088877.
- VEGF-C-driven lymphatic drainage enables immunosurveillance of brain tumours.Song E, Mao T, Dong H, Boisserand LSB, Antila S, Bosenberg M, Alitalo K, Thomas JL, Iwasaki A. Nature. 2020 Jan; 2020 Jan 15. PMID: 31942068.
- Author Correction: Visualizing structure and transitions in high-dimensional biological data.Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, van den Elzen A, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Nat Biotechnol. 2020 Jan. PMID: 31896828.
- Inflammasome Is Activated in the Liver of Cholestatic Patients and Aggravates Hepatic Injury in Bile Duct-Ligated Mouse.Cai SY, Ge M, Mennone A, Hoque R, Ouyang X, Boyer JL. Cell Mol Gastroenterol Hepatol. 2020; 2019 Dec 27. PMID: 31887435.
- Functional Analysis of Human Hematopoietic Stem Cells In Vivo in Humanized Mice.Song Y, Gbyli R, Fu X, Halene S. Methods Mol Biol. 2020. PMID: 31776933.
- The intestinal regionalization of acute norovirus infection is regulated by the microbiota via bile acid-mediated priming of type III interferon.Grau KR, Zhu S, Peterson ST, Helm EW, Philip D, Phillips M, Hernandez A, Turula H, Frasse P, Graziano VR, Wilen CB, Wobus CE, Baldridge MT, Karst SM. Nat Microbiol. 2020 Jan; 2019 Nov 25. PMID: 31768030.
- Evolvability Costs of Niche Expansion.Bono LM, Draghi JA, Turner PE. Trends Genet. 2020 Jan; 2019 Nov 5. PMID: 31699305.
- Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.Dong J, Chen H, Deng XW, Irish VF, Wei N. Plant Physiol. 2020 Jan; 2019 Nov 5. PMID: 31690709.
- Archaeal Ribosomal Proteins Possess Nuclear Localization Signal-Type Motifs: Implications for the Origin of the Cell Nucleus.Melnikov S, Kwok HS, Manakongtreecheep K, van den Elzen A, Thoreen CC, Söll D. Mol Biol Evol. 2020 Jan 1. PMID: 31501901.
- Perspectives on Burnout from Pulmonary, Critical Care, and Sleep Medicine Division Directors.Rinne ST, Swamy L, Anderson E, Shah T, Dixon AE, Kaminski N, Borok Z, Thomson CC. Am J Respir Crit Care Med. 2020 Jan 1. PMID: 31469580.
- Caveolae: The FAQs.Parton RG, Del Pozo MA, Vassilopoulos S, Nabi IR, Le Lay S, Lundmark R, Kenworthy AK, Camus A, Blouin CM, Sessa WC, Lamaze C. Traffic. 2020 Jan; 2019 Sep 9. PMID: 31448516.
2019
- Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen.Perkins KR, Atilho RM, Moon MH, Breaker RR. ACS Chem Biol. 2019 Dec 20; 2019 Nov 14. PMID: 31609568.
- MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors.Chen X, Burkhardt DB, Hartman AA, Hu X, Eastman AE, Sun C, Wang X, Zhong M, Krishnaswamy S, Guo S. Nat Commun. 2019 Dec 18; 2019 Dec 18. PMID: 31852898.
- RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling.Ren X, Linehan MM, Iwasaki A, Pyle AM. Cell Rep. 2019 Dec 17. PMID: 31851914.
- Homeobox protein Hhex negatively regulates Treg cells by inhibiting Foxp3 expression and function.Jang SW, Hwang SS, Kim HS, Kim MK, Lee WH, Hwang SU, Gwak J, Yew SK, Flavell RA, Lee GR. Proc Natl Acad Sci U S A. 2019 Dec 17; 2019 Dec 2. PMID: 31792183.
- Single-cell connectomic analysis of adult mammalian lungs.Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Sci Adv. 2019 Dec; 2019 Dec 4. PMID: 31840053.
- Elevated CO(2) regulates the Wnt signaling pathway in mammals, Drosophila melanogaster and Caenorhabditis elegans.Shigemura M, Lecuona E, Angulo M, Dada LA, Edwards MB, Welch LC, Casalino-Matsuda SM, Sporn PHS, Vadász I, Helenius IT, Nader GA, Gruenbaum Y, Sharabi K, Cummins E, Taylor C, Bharat A, Gottardi CJ, Beitel GJ, Kaminski N, Budinger GRS, Berdnikovs S, Sznajder JI. Sci Rep. 2019 Dec 3; 2019 Dec 3. PMID: 31796806.
- Suppressing miR-21 activity in tumor-associated macrophages promotes an antitumor immune response.Sahraei M, Chaube B, Liu Y, Sun J, Kaplan A, Price NL, Ding W, Oyaghire S, García-Milian R, Mehta S, Reshetnyak YK, Bahal R, Fiorina P, Glazer PM, Rimm DL, Fernández-Hernando C, Suárez Y. J Clin Invest. 2019 Dec 2. PMID: 31710308.
- Intratumoral delivery of RIG-I agonist SLR14 induces robust antitumor responses.Jiang X, Muthusamy V, Fedorova O, Kong Y, Kim DJ, Bosenberg M, Pyle AM, Iwasaki A. J Exp Med. 2019 Dec 2; 2019 Oct 10. PMID: 31601678.
- Joint Models for Time-to-Event Data and Longitudinal Biomarkers of High Dimension.Liu M, Sun J, Herazo-Maya JD, Kaminski N, Zhao H. Stat Biosci. 2019 Dec; 2019 Sep 23. PMID: 33281995.
- Coarse Graining of Data via Inhomogeneous Diffusion Condensation.Brugnone N, Gonopolskiy A, Moyle MW, Kuchroo M, van Dijk D, Moon KR, Colon-Ramos D, Wolf G, Hirn MJ, Krishnaswamy S. Proc IEEE Int Conf Big Data. 2019 Dec; 2020 Feb 24. PMID: 32747879.
- Mitochondrial DNA Stress Signalling Protects the Nuclear Genome.Wu Z, Oeck S, West AP, Mangalhara KC, Sainz AG, Newman LE, Zhang XO, Wu L, Yan Q, Bosenberg M, Liu Y, Sulkowski PL, Tripple V, Kaech SM, Glazer PM, Shadel GS. Nat Metab. 2019 Dec; 2019 Dec 9. PMID: 32395698.
- Human SNORA31 variations impair cortical neuron-intrinsic immunity to HSV-1 and underlie herpes simplex encephalitis.Lafaille FG, Harschnitz O, Lee YS, Zhang P, Hasek ML, Kerner G, Itan Y, Ewaleifoh O, Rapaport F, Carlile TM, Carter-Timofte ME, Paquet D, Dobbs K, Zimmer B, Gao D, Rojas-Duran MF, Kwart D, Rattina V, Ciancanelli MJ, McAlpine JL, Lorenzo L, Boucherit S, Rozenberg F, Halwani R, Henry B, Amenzoui N, Alsum Z, Marques L, Church JA, Al-Muhsen S, Tardieu M, Bousfiha AA, Paludan SR, Mogensen TH, Quintana-Murci L, Tessier-Lavigne M, Smith GA, Notarangelo LD, Studer L, Gilbert W, Abel L, Casanova JL, Zhang SY. Nat Med. 2019 Dec; 2019 Dec 5. PMID: 31806906.
- Visualizing structure and transitions in high-dimensional biological data.Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, Elzen AVD, Hirn MJ, Coifman RR, Ivanova NB, Wolf G, Krishnaswamy S. Nat Biotechnol. 2019 Dec; 2019 Dec 3. PMID: 31796933.
- Proteomic Detection and Validation of Translated Small Open Reading Frames.Khitun A, Slavoff SA. Curr Protoc Chem Biol. 2019 Dec. PMID: 31750990.
- Evidence that the nadA motif is a bacterial riboswitch for the ubiquitous enzyme cofactor NAD().Malkowski SN, Spencer TCJ, Breaker RR. RNA. 2019 Dec; 2019 Aug 29. PMID: 31467147.
- Leading Change and Negotiation Strategies for Division Leaders in Clinical Medicine.Nguyen HB, Thomson C, Jarjour NN, Dixon AE, Liesching TN, Schnapp LM, Madison JM, Murin S, Glenny R, Kaminski N. Chest. 2019 Dec; 2019 Jul 9. PMID: 31299244.
- Optimizing biodegradable nanoparticle size for tissue-specific delivery.Mandl HK, Quijano E, Suh HW, Sparago E, Oeck S, Grun M, Glazer PM, Saltzman WM. J Control Release. 2019 Nov 28; 2019 Oct 22. PMID: 31654688.
- Modeling the Evolution of Human Brain Development Using Organoids.Muchnik SK, Lorente-Galdos B, Santpere G, Sestan N. Cell. 2019 Nov 27. PMID: 31778651.
- LAM-003, a new drug for treatment of tyrosine kinase inhibitor-resistant FLT3-ITD-positive AML.Beeharry N, Landrette S, Gayle S, Hernandez M, Grotzke JE, Young PR, Beckett P, Zhang X, Carter BZ, Andreeff M, Halene S, Xu T, Rothberg J, Lichenstein H. Blood Adv. 2019 Nov 26. PMID: 31751472.
- Nitrate and Phosphate Transporters Rescue Fluoride Toxicity in Yeast.Johnston NR, Strobel SA. Chem Res Toxicol. 2019 Nov 18; 2019 Oct 16. PMID: 31576749.
- Ketogenic diet activates protective γδ T cell responses against influenza virus infection.Goldberg EL, Molony RD, Kudo E, Sidorov S, Kong Y, Dixit VD, Iwasaki A. Sci Immunol. 2019 Nov 15. PMID: 31732517.
- Genetic deficiency or pharmacological inhibition of miR-33 protects from kidney fibrosis.Price NL, Miguel V, Ding W, Singh AK, Malik S, Rotllan N, Moshnikova A, Toczek J, Zeiss C, Sadeghi MM, Arias N, Baldán Á, Andreev OA, Rodríguez-Puyol D, Bahal R, Reshetnyak YK, Suárez Y, Fernández-Hernando C, Lamas S. JCI Insight. 2019 Nov 14; 2019 Nov 14. PMID: 31613798.
- Transcriptional regulatory model of fibrosis progression in the human lung.McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. JCI Insight. 2019 Nov 14; 2019 Nov 14. PMID: 31600171.
- The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis.Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. Nat Commun. 2019 Nov 13; 2019 Nov 13. PMID: 31723143.
- Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM. Nat Commun. 2019 Nov 6; 2019 Nov 6. PMID: 31695033.
- Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates.Smith TS, Zoltek MA, Simon MD. J Am Chem Soc. 2019 Nov 6; 2019 Oct 28. PMID: 31626536.
- Author Correction: Mechanosensation of cyclical force by PIEZO1 is essential for innate immunity.Solis AG, Bielecki P, Steach HR, Sharma L, Harman CCD, Yun S, de Zoete MR, Warnock JN, To SDF, York AG, Mack M, Schwartz MA, Cruz CSD, Palm NW, Jackson R, Flavell RA. Nature. 2019 Nov. PMID: 31712625.
- Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin.Simon MD, Machyna M. Cold Spring Harb Perspect Biol. 2019 Nov 1; 2019 Nov 1. PMID: 31676573.
- Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity.Wang G, Chow RD, Bai Z, Zhu L, Errami Y, Dai X, Dong MB, Ye L, Zhang X, Renauer PA, Park JJ, Shen L, Ye H, Fuchs CS, Chen S. Nat Immunol. 2019 Nov; 2019 Oct 14. PMID: 31611701.
- Exploring single-cell data with deep multitasking neural networks.Amodio M, van Dijk D, Srinivasan K, Chen WS, Mohsen H, Moon KR, Campbell A, Zhao Y, Wang X, Venkataswamy M, Desai A, Ravi V, Kumar P, Montgomery R, Wolf G, Krishnaswamy S. Nat Methods. 2019 Nov; 2019 Oct 7. PMID: 31591579.
- In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma.Ye L, Park JJ, Dong MB, Yang Q, Chow RD, Peng L, Du Y, Guo J, Dai X, Wang G, Errami Y, Chen S. Nat Biotechnol. 2019 Nov; 2019 Sep 23. PMID: 31548728.
- A versatile flow-based assay for immunocyte-mediated cytotoxicity.Rabinovich PM, Zhang J, Kerr SR, Cheng BH, Komarovskaya M, Bersenev A, Hurwitz ME, Krause DS, Weissman SM, Katz SG. J Immunol Methods. 2019 Nov; 2019 Sep 13. PMID: 31525367.
- Role of dual-specificity protein phosphatase DUSP10/MKP-5 in pulmonary fibrosis.Xylourgidis N, Min K, Ahangari F, Yu G, Herazo-Maya JD, Karampitsakos T, Aidinis V, Binzenhöfer L, Bouros D, Bennett AM, Kaminski N, Tzouvelekis A. Am J Physiol Lung Cell Mol Physiol. 2019 Nov 1; 2019 Sep 4. PMID: 31483681.
- hnRNPA2B1: a nuclear DNA sensor in antiviral immunity.Zhang X, Flavell RA, Li HB. Cell Res. 2019 Nov. PMID: 31471560.
- Disruption of the OLE ribonucleoprotein complex causes magnesium toxicity in Bacillus halodurans.Harris KA, Odzer NB, Breaker RR. Mol Microbiol. 2019 Nov; 2019 Sep 22. PMID: 31461569.
- Murine Leukemia Virus Exploits Innate Sensing by Toll-Like Receptor 7 in B-1 Cells To Establish Infection and Locally Spread in Mice.Pi R, Iwasaki A, Sewald X, Mothes W, Uchil PD. J Virol. 2019 Nov 1; 2019 Oct 15. PMID: 31434732.
- Integrating multiomics longitudinal data to reconstruct networks underlying lung development.Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Am J Physiol Lung Cell Mol Physiol. 2019 Nov 1; 2019 Aug 21. PMID: 31432713.
- Syngeneic red blood cell-induced extracellular vesicles suppress delayed-type hypersensitivity to self-antigens in mice.Nazimek K, Bustos-Morán E, Blas-Rus N, Nowak B, Ptak W, Askenase PW, Sánchez-Madrid F, Bryniarski K. Clin Exp Allergy. 2019 Nov; 2019 Aug 26. PMID: 31365154.
- Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain.Hadfield J, Brito AF, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND. PLoS Pathog. 2019 Oct; 2019 Oct 31. PMID: 31671157.
- Low iron promotes megakaryocytic commitment of megakaryocytic-erythroid progenitors in humans and mice.Xavier-Ferrucio J, Scanlon V, Li X, Zhang PX, Lozovatsky L, Ayala-Lopez N, Tebaldi T, Halene S, Cao C, Fleming MD, Finberg KE, Krause DS. Blood. 2019 Oct 31. PMID: 31439541.
- The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA.Kolev NG, Rajan KS, Tycowski KT, Toh JY, Shi H, Lei Y, Michaeli S, Tschudi C. J Biol Chem. 2019 Oct 25; 2019 Aug 22. PMID: 31439669.
- Reply to Iñiguez et al.: ERVmap is a validated approach to mapping proviral endogenous retroviruses in the human genome.Tokuyama M, Kong Y, Iwasaki A. Proc Natl Acad Sci U S A. 2019 Oct 22; 2019 Oct 8. PMID: 31594852.
- Screening Legionella effectors for antiviral effects reveals Rab1 GTPase as a proviral factor coopted for tombusvirus replication.Inaba JI, Xu K, Kovalev N, Ramanathan H, Roy CR, Lindenbach BD, Nagy PD. Proc Natl Acad Sci U S A. 2019 Oct 22; 2019 Oct 7. PMID: 31591191.
- Progenitor-derived human endothelial cells evade alloimmunity by CRISPR/Cas9-mediated complete ablation of MHC expression.Merola J, Reschke M, Pierce RW, Qin L, Spindler S, Baltazar T, Manes TD, Lopez-Giraldez F, Li G, Bracaglia LG, Xie C, Kirkiles-Smith N, Saltzman WM, Tietjen GT, Tellides G, Pober JS. JCI Insight. 2019 Oct 17; 2019 Oct 17. PMID: 31527312.
- Human APOBEC3G Prevents Emergence of Infectious Endogenous Retrovirus in Mice.Treger RS, Tokuyama M, Dong H, Salas-Briceno K, Ross SR, Kong Y, Iwasaki A. J Virol. 2019 Oct 15; 2019 Sep 30. PMID: 31341050.
- N6-Methyladenosine Modification Controls Circular RNA Immunity.Chen YG, Chen R, Ahmad S, Verma R, Kasturi SP, Amaya L, Broughton JP, Kim J, Cadena C, Pulendran B, Hur S, Chang HY. Mol Cell. 2019 Oct 3; 2019 Aug 29. PMID: 31474572.
- mRNA structure determines modification by pseudouridine synthase 1.Carlile TM, Martinez NM, Schaening C, Su A, Bell TA, Zinshteyn B, Gilbert WV. Nat Chem Biol. 2019 Oct; 2019 Sep 2. PMID: 31477916.
- Publisher Correction: HER2 joins AKT to inhibit STING immunity.Odell ID, Flavell RA. Nat Cell Biol. 2019 Oct. PMID: 31444402.
- Digoxin improves steatohepatitis with differential involvement of liver cell subsets in mice through inhibition of PKM2 transactivation.Zhao P, Han SN, Arumugam S, Yousaf MN, Qin Y, Jiang JX, Torok NJ, Chen Y, Mankash MS, Liu J, Li J, Iwakiri Y, Ouyang X. Am J Physiol Gastrointest Liver Physiol. 2019 Oct 1; 2019 Aug 14. PMID: 31411894.
- Publisher Correction: Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues.Cella M, Gamini R, Sécca C, Collins PL, Zhao S, Peng V, Robinette ML, Schettini J, Zaitsev K, Gordon W, Bando JK, Yomogida K, Cortez V, Fronick C, Fulton R, Lin LL, Gilfillan S, Flavell RA, Shan L, Artyomov MN, Bowman M, Oltz EM, Jelinsky SA, Colonna M. Nat Immunol. 2019 Oct. PMID: 31388149.
- Ribosomopathies: Old Concepts, New Controversies.Farley-Barnes KI, Ogawa LM, Baserga SJ. Trends Genet. 2019 Oct; 2019 Jul 31. PMID: 31376929.
- BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications.Weathington N, O'Brien ME, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie AT, Jarjour NN, Meyers DA, Milosevic J, Moore WC, Tedrow JR, Trudeau JB, Wong HP, Wu W, Kaminski N, Wenzel SE, Modena BD. Am J Respir Crit Care Med. 2019 Oct 1. PMID: 31161938.
- Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology.Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Annu Rev Virol. 2019 Sep 29; 2019 Apr 30. PMID: 31039329.
- Pollen-derived RNAs Are Found in the Human Circulation.Koupenova M, Mick E, Corkrey HA, Singh A, Tanriverdi SE, Vitseva O, Levy D, Keeler AM, Ezzaty Mirhashemi M, ElMallah MK, Gerstein M, Rozowsky J, Tanriverdi K, Freedman JE. iScience. 2019 Sep 27; 2019 Aug 24. PMID: 31518900.
- Structural Basis for Target-Directed MicroRNA Degradation.Sheu-Gruttadauria J, Pawlica P, Klum SM, Wang S, Yario TA, Schirle Oakdale NT, Steitz JA, MacRae IJ. Mol Cell. 2019 Sep 19; 2019 Jul 25. PMID: 31353209.
- Leveraging protein dynamics to identify cancer mutational hotspots using 3D structures.Kumar S, Clarke D, Gerstein MB. Proc Natl Acad Sci U S A. 2019 Sep 17; 2019 Aug 28. PMID: 31462496.
- Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy.Tal R, Shaikh S, Pallavi P, Tal A, López-Giráldez F, Lyu F, Fang YY, Chinchanikar S, Liu Y, Kliman HJ, Alderman M 3rd, Pluchino N, Kayani J, Mamillapalli R, Krause DS, Taylor HS. PLoS Biol. 2019 Sep; 2019 Sep 12. PMID: 31513564.
- Discovery of N-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II.Van Zandt MC, Jagdmann GE, Whitehouse DL, Ji M, Savoy J, Potapova O, Cousido-Siah A, Mitschler A, Howard EI, Pyle AM, Podjarny AD. J Med Chem. 2019 Sep 12; 2019 Aug 23. PMID: 31408339.
- The expanded specificity and physiological role of a widespread N-degron recognin.Gao X, Yeom J, Groisman EA. Proc Natl Acad Sci U S A. 2019 Sep 10; 2019 Aug 26. PMID: 31451664.
- Biologically Active Ultra-Simple Proteins Reveal Principles of Transmembrane Domain Interactions.Federman RS, Boguraev AS, Heim EN, DiMaio D. J Mol Biol. 2019 Sep 6; 2019 Jul 10. PMID: 31301406.
- Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay.Fish L, Navickas A, Culbertson B, Xu Y, Nguyen HCB, Zhang S, Hochman M, Okimoto R, Dill BD, Molina H, Najafabadi HS, Alarcón C, Ruggero D, Goodarzi H. Mol Cell. 2019 Sep 5; 2019 Jul 9. PMID: 31300274.
- A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH. Neuron. 2019 Sep 4; 2019 Jul 11. PMID: 31303374.
- Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M. Structure. 2019 Sep 3; 2019 Jul 3. PMID: 31279629.
- The SGLT2 inhibitor dapagliflozin attenuates the activity of ROS-NLRP3 inflammasome axis in steatohepatitis with diabetes mellitus.Leng W, Wu M, Pan H, Lei X, Chen L, Wu Q, Ouyang X, Liang Z. Ann Transl Med. 2019 Sep. PMID: 31700865.
- Author Correction: Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.Bailis W, Shyer JA, Zhao J, Canaveras JCG, Al Khazal FJ, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ 3rd, Rabinowitz J, Craft J, Flavell RA. Nature. 2019 Sep. PMID: 31447485.
- Mechanosensation of cyclical force by PIEZO1 is essential for innate immunity.Solis AG, Bielecki P, Steach HR, Sharma L, Harman CCD, Yun S, de Zoete MR, Warnock JN, To SDF, York AG, Mack M, Schwartz MA, Dela Cruz CS, Palm NW, Jackson R, Flavell RA. Nature. 2019 Sep; 2019 Aug 21. PMID: 31435009.
- Why we need to increase diversity in the immunology research community.Iwasaki A. Nat Immunol. 2019 Sep. PMID: 31427777.
- From clonal hematopoiesis to myeloid leukemia and what happens in between: Will improved understanding lead to new therapeutic and preventive opportunities?Bewersdorf JP, Ardasheva A, Podoltsev NA, Singh A, Biancon G, Halene S, Zeidan AM. Blood Rev. 2019 Sep; 2019 Jul 4. PMID: 31400824.
- New insights into the development of the human cerebral cortex.Molnár Z, Clowry GJ, Šestan N, Alzu'bi A, Bakken T, Hevner RF, Hüppi PS, Kostović I, Rakic P, Anton ES, Edwards D, Garcez P, Hoerder-Suabedissen A, Kriegstein A. J Anat. 2019 Sep; 2019 Aug 2. PMID: 31373394.
- Activator of one protease transforms into inhibitor of another in response to nutritional signals.Yeom J, Groisman EA. Genes Dev. 2019 Sep 1; 2019 Aug 1. PMID: 31371438.
- Biochemical validation of a second class of tetrahydrofolate riboswitches in bacteria.Chen X, Mirihana Arachchilage G, Breaker RR. RNA. 2019 Sep; 2019 Jun 11. PMID: 31186369.
- Sin1/mTORC2 regulate B cell growth and metabolism by activating mTORC1 and Myc.Li M, Lazorchak AS, Ouyang X, Zhang H, Liu H, Arojo OA, Yan L, Jin J, Han Y, Qu G, Fu Y, Xu X, Liu X, Zhang W, Yang Z, Ruan C, Wang Q, Liu D, Huang C, Lu L, Jiang S, Li F, Su B. Cell Mol Immunol. 2019 Sep; 2019 Jan 31. PMID: 30705387.
- GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner.Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. PLoS Genet. 2019 Aug; 2019 Aug 30. PMID: 31469829.
- Plasma mitochondrial DNA is associated with extrapulmonary sarcoidosis.Ryu C, Brandsdorfer C, Adams T, Hu B, Kelleher DW, Yaggi M, Manning EP, Walia A, Reeves B, Pan H, Winkler J, Minasyan M, Dela Cruz CS, Kaminski N, Gulati M, Herzog EL. Eur Respir J. 2019 Aug; 2019 Aug 29. PMID: 31273041.
- Quantitative Fluorescence In Situ Hybridization (FISH) and Immunofluorescence (IF) of Specific Gene Products in KSHV-Infected Cells.Vallery TK, Steitz JA. J Vis Exp. 2019 Aug 27; 2019 Aug 27. PMID: 31524859.
- Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer.Craig M, Kaveh K, Woosley A, Brown AS, Goldman D, Eton E, Mehta RM, Dhawan A, Arai K, Rahman MM, Chen S, Nowak MA, Goldman A. PLoS Comput Biol. 2019 Aug; 2019 Aug 26. PMID: 31449515.
- A cysteinyl-tRNA synthetase variant confers resistance against selenite toxicity and decreases selenocysteine misincorporation.Hoffman KS, Vargas-Rodriguez O, Bak DW, Mukai T, Woodward LK, Weerapana E, Söll D, Reynolds NM. J Biol Chem. 2019 Aug 23; 2019 Jul 11. PMID: 31296657.
- Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells.Dong MB, Wang G, Chow RD, Ye L, Zhu L, Dai X, Park JJ, Kim HR, Errami Y, Guzman CD, Zhou X, Chen KY, Renauer PA, Du Y, Shen J, Lam SZ, Zhou JJ, Lannin DR, Herbst RS, Chen S. Cell. 2019 Aug 22. PMID: 31442407.
- Effector T(H)17 Cells Give Rise to Long-Lived T(RM) Cells that Are Essential for an Immediate Response against Bacterial Infection.Amezcua Vesely MC, Pallis P, Bielecki P, Low JS, Zhao J, Harman CCD, Kroehling L, Jackson R, Bailis W, Licona-Limón P, Xu H, Iijima N, Pillai PS, Kaplan DH, Weaver CT, Kluger Y, Kowalczyk MS, Iwasaki A, Pereira JP, Esplugues E, Gagliani N, Flavell RA. Cell. 2019 Aug 22. PMID: 31442406.
- Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW 4th, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. Cell. 2019 Aug 22. PMID: 31442400.
- Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions.Rajan KS, Doniger T, Cohen-Chalamish S, Chen D, Semo O, Aryal S, Glick Saar E, Chikne V, Gerber D, Unger R, Tschudi C, Michaeli S. Nucleic Acids Res. 2019 Aug 22. PMID: 31147702.
- Application of a Modified Smart-seq2 Sample Preparation Protocol for Rare Cell Full-length Single-cell mRNA Sequencing to Mouse Oocytes.Treger RS, Pope SD, Xing X, Iwasaki A. Bio Protoc. 2019 Aug 20; 2019 Aug 20. PMID: 33654848.
- TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. PLoS Comput Biol. 2019 Aug; 2019 Aug 19. PMID: 31425522.
- Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation.Hosmillo M, Lu J, McAllaster MR, Eaglesham JB, Wang X, Emmott E, Domingues P, Chaudhry Y, Fitzmaurice TJ, Tung MK, Panas MD, McInerney G, Locker N, Wilen CB, Goodfellow IG. Elife. 2019 Aug 12; 2019 Aug 12. PMID: 31403400.
- Successful application of prime and pull strategy for a therapeutic HSV vaccine.Bernstein DI, Cardin RD, Bravo FJ, Awasthi S, Lu P, Pullum DA, Dixon DA, Iwasaki A, Friedman HM. NPJ Vaccines. 2019; 2019 Aug 1. PMID: 31396405.
- HER2 joins AKT to inhibit STING immunity.Odell ID, Flavell RA. Nat Cell Biol. 2019 Aug. PMID: 31371829.
- Nascent RNA and the Coordination of Splicing with Transcription.Neugebauer KM. Cold Spring Harb Perspect Biol. 2019 Aug 1; 2019 Aug 1. PMID: 31371351.
- CELA2A mutations predispose to early-onset atherosclerosis and metabolic syndrome and affect plasma insulin and platelet activation.Esteghamat F, Broughton JS, Smith E, Cardone R, Tyagi T, Guerra M, Szabó A, Ugwu N, Mani MV, Azari B, Kayingo G, Chung S, Fathzadeh M, Weiss E, Bender J, Mane S, Lifton RP, Adeniran A, Nathanson MH, Gorelick FS, Hwa J, Sahin-Tóth M, Belfort-DeAguiar R, Kibbey RG, Mani A. Nat Genet. 2019 Aug; 2019 Jul 29. PMID: 31358993.
- ANGPTL4 in Metabolic and Cardiovascular Disease.Aryal B, Price NL, Suarez Y, Fernández-Hernando C. Trends Mol Med. 2019 Aug; 2019 Jun 21. PMID: 31235370.
- Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues.Cella M, Gamini R, Sécca C, Collins PL, Zhao S, Peng V, Robinette ML, Schettini J, Zaitsev K, Gordon W, Bando JK, Yomogida K, Cortez V, Fronick C, Fulton R, Lin LL, Gilfillan S, Flavell RA, Shan L, Artyomov MN, Bowman M, Oltz EM, Jelinsky SA, Colonna M. Nat Immunol. 2019 Aug; 2019 Jun 17. PMID: 31209406.
- Fas ligand and nitric oxide combination to control smooth muscle growth while sparing endothelium.Kural MH, Wang J, Gui L, Yuan Y, Li G, Leiby KL, Quijano E, Tellides G, Saltzman WM, Niklason LE. Biomaterials. 2019 Aug; 2019 May 7. PMID: 31102854.
- Mechanisms of injury-induced axon degeneration.Ding C, Hammarlund M. Curr Opin Neurobiol. 2019 Aug; 2019 May 6. PMID: 31071521.
- Slow growth determines nonheritable antibiotic resistance in Salmonella enterica.Pontes MH, Groisman EA. Sci Signal. 2019 Jul 30; 2019 Jul 30. PMID: 31363068.
- Transmembrane Protein Aptamer Induces Cooperative Signaling by the EPO Receptor and the Cytokine Receptor β-Common Subunit.He L, Cohen EB, Edwards APB, Xavier-Ferrucio J, Bugge K, Federman RS, Absher D, Myers RM, Kragelund BB, Krause DS, DiMaio D. iScience. 2019 Jul 26; 2019 Jun 21. PMID: 31279934.
- Translation of Diverse Aramid- and 1,3-Dicarbonyl-peptides by Wild Type Ribosomes in Vitro.Ad O, Hoffman KS, Cairns AG, Featherston AL, Miller SJ, Söll D, Schepartz A. ACS Cent Sci. 2019 Jul 24; 2019 Jun 26. PMID: 31403077.
- Longitudinal Trajectories of Psychotic-Like Experiences and Their Relationship to Emergent Mental Disorders Among Adolescents: A 3-Year Cohort Study.Zhang W, Zhu Y, Sun M, Guo R, Wu G, Wang Z, Xue Z, Shi J, Ouyang X, Pu W, Liu Z, Chiu HFK, Rosenheck R. J Clin Psychiatry. 2019 Jul 23; 2019 Jul 23. PMID: 31347795.
- Caveolin-1 Regulates Atherogenesis by Attenuating Low-Density Lipoprotein Transcytosis and Vascular Inflammation Independently of Endothelial Nitric Oxide Synthase Activation.Ramírez CM, Zhang X, Bandyopadhyay C, Rotllan N, Sugiyama MG, Aryal B, Liu X, He S, Kraehling JR, Ulrich V, Lin CS, Velazquez H, Lasunción MA, Li G, Suárez Y, Tellides G, Swirski FK, Lee WL, Schwartz MA, Sessa WC, Fernández-Hernando C. Circulation. 2019 Jul 16; 2019 Jun 3. PMID: 31154825.
- The Role of Orthogonality in Genetic Code Expansion.Arranz-Gibert P, Patel JR, Isaacs FJ. Life (Basel). 2019 Jul 5; 2019 Jul 5. PMID: 31284384.
- A novel, noncoding-RNA-mediated, post-transcriptional mechanism of anti-Mullerian hormone regulation by the H19/let-7 axis.Qin C, Xia X, Fan Y, Jiang Y, Chen Y, Zhang N, Uslu B, Johnson J, Kallen AN. Biol Reprod. 2019 Jul 1. PMID: 31286140.
- Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ. Genome Res. 2019 Jul; 2019 Jun 21. PMID: 31227602.
- Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function.Bailis W, Shyer JA, Zhao J, Canaveras JCG, Al Khazal FJ, Qu R, Steach HR, Bielecki P, Khan O, Jackson R, Kluger Y, Maher LJ 3rd, Rabinowitz J, Craft J, Flavell RA. Nature. 2019 Jul; 2019 Jun 19. PMID: 31217581.
- Migrant memory B cells secrete luminal antibody in the vagina.Oh JE, Iijima N, Song E, Lu P, Klein J, Jiang R, Kleinstein SH, Iwasaki A. Nature. 2019 Jul; 2019 Jun 12. PMID: 31189952.
- H19 lncRNA identified as a master regulator of genes that drive uterine leiomyomas.Cao T, Jiang Y, Wang Z, Zhang N, Al-Hendy A, Mamillapalli R, Kallen AN, Kodaman P, Taylor HS, Li D, Huang Y. Oncogene. 2019 Jul; 2019 May 15. PMID: 31089260.
- Structural and pharmacological evaluation of a novel non-nucleoside reverse transcriptase inhibitor as a promising long acting nanoformulation for treating HIV.Kudalkar SN, Ullah I, Bertoletti N, Mandl HK, Cisneros JA, Beloor J, Chan AH, Quijano E, Saltzman WM, Jorgensen WL, Kumar P, Anderson KS. Antiviral Res. 2019 Jul; 2019 Apr 26. PMID: 31034849.
- Climate change and lung health: presidential failure, professional responsibility.Hopkinson NS, Hart N, Jenkins G, Rosenfeld M, Smyth AR, Wilkinson AJK, Kaminski N. Thorax. 2019 Jul; 2019 Apr 21. PMID: 31010935.
- The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. Am J Respir Cell Mol Biol. 2019 Jul. PMID: 30995076.
- Poly(amine-co-ester) nanoparticles for effective Nogo-B knockdown in the liver.Cui J, Piotrowski-Daspit AS, Zhang J, Shao M, Bracaglia LG, Utsumi T, Seo YE, DiRito J, Song E, Wu C, Inada A, Tietjen GT, Pober JS, Iwakiri Y, Saltzman WM. J Control Release. 2019 Jun 28; 2019 May 1. PMID: 31054286.
- Heat shock protein DNAJA1 stabilizes PIWI proteins to support regeneration and homeostasis of planarian Schmidtea mediterranea.Wang C, Yang ZZ, Guo FH, Shi S, Han XS, Zeng A, Lin H, Jing Q. J Biol Chem. 2019 Jun 21; 2019 May 10. PMID: 31076507.
- Mouse Norovirus Infection Arrests Host Cell Translation Uncoupled from the Stress Granule-PKR-eIF2α Axis.Fritzlar S, Aktepe TE, Chao YW, Kenney ND, McAllaster MR, Wilen CB, White PA, Mackenzie JM. mBio. 2019 Jun 18; 2019 Jun 18. PMID: 31213553.
- Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation.Chan SH, Tang Y, Miao L, Darwich-Codore H, Vejnar CE, Beaudoin JD, Musaev D, Fernandez JP, Benitez MDJ, Bazzini AA, Moreno-Mateos MA, Giraldez AJ. Dev Cell. 2019 Jun 17. PMID: 31211993.
- Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression.Han M, Wei G, McManus CE, Hillier LW, Reinke V. BMC Genomics. 2019 Jun 17; 2019 Jun 17. PMID: 31208332.
- Absence of the long noncoding RNA H19 results in aberrant ovarian STAR and progesterone production.Chen Y, Wang J, Fan Y, Qin C, Xia X, Johnson J, Kallen AN. Mol Cell Endocrinol. 2019 Jun 15; 2019 Mar 25. PMID: 30922932.
- A Secreted Viral Nonstructural Protein Determines Intestinal Norovirus Pathogenesis.Lee S, Liu H, Wilen CB, Sychev ZE, Desai C, Hykes BL Jr, Orchard RC, McCune BT, Kim KW, Nice TJ, Handley SA, Baldridge MT, Amarasinghe GK, Virgin HW. Cell Host Microbe. 2019 Jun 12; 2019 May 23. PMID: 31130511.
- ATG2 transports lipids to promote autophagosome biogenesis.Valverde DP, Yu S, Boggavarapu V, Kumar N, Lees JA, Walz T, Reinisch KM, Melia TJ. J Cell Biol. 2019 Jun 3; 2019 Apr 5. PMID: 30952800.
- Protective Function of Mitogen-Activated Protein Kinase Phosphatase 5 in Aging- and Diet-Induced Hepatic Steatosis and Steatohepatitis.Tang P, Low HB, Png CW, Torta F, Kumar JK, Lim HY, Zhou Y, Yang H, Angeli V, Shabbir A, Tai ES, Flavell RA, Dong C, Wenk MR, Yang DY, Zhang Y. Hepatol Commun. 2019 Jun; 2019 Mar 1. PMID: 31168510.
- Monocytes Inadequately Fill In for Meningeal Macrophages.Song E, Iwasaki A. Trends Immunol. 2019 Jun; 2019 May 6. PMID: 31072686.
- A counterintuitive lesson in family planning? Patience first: taking a "gap year" after live birth from assisted reproductive technology before frozen embryo transfer is performed.Seifer DB, Kallen AN. Fertil Steril. 2019 Jun; 2019 May 2. PMID: 31056317.
- Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection.Rückert C, Prasad AN, Garcia-Luna SM, Robison A, Grubaugh ND, Weger-Lucarelli J, Ebel GD. Insect Biochem Mol Biol. 2019 Jun; 2019 Apr 5. PMID: 30959110.
- Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study.Scott MKD, Quinn K, Li Q, Carroll R, Warsinske H, Vallania F, Chen S, Carns MA, Aren K, Sun J, Koloms K, Lee J, Baral J, Kropski J, Zhao H, Herzog E, Martinez FJ, Moore BB, Hinchcliff M, Denny J, Kaminski N, Herazo-Maya JD, Shah NH, Khatri P. Lancet Respir Med. 2019 Jun; 2019 Mar 29. PMID: 30935881.
- Aedes aegypti AgBR1 antibodies modulate early Zika virus infection of mice.Uraki R, Hastings AK, Marin-Lopez A, Sumida T, Takahashi T, Grover JR, Iwasaki A, Hafler DA, Montgomery RR, Fikrig E. Nat Microbiol. 2019 Jun; 2019 Mar 11. PMID: 30858571.
- Androgens drive microvascular endothelial dysfunction in women with polycystic ovary syndrome: role of the endothelin B receptor.Usselman CW, Yarovinsky TO, Steele FE, Leone CA, Taylor HS, Bender JR, Stachenfeld NS. J Physiol. 2019 Jun; 2019 Mar 27. PMID: 30847930.
- The Combination of MEK Inhibitor With Immunomodulatory Antibodies Targeting Programmed Death 1 and Programmed Death Ligand 1 Results in Prolonged Survival in Kras/p53-Driven Lung Cancer.Lee JW, Zhang Y, Eoh KJ, Sharma R, Sanmamed MF, Wu J, Choi J, Park HS, Iwasaki A, Kaftan E, Chen L, Papadimitrakopoulou V, Herbst RS, Koo JS. J Thorac Oncol. 2019 Jun; 2019 Feb 13. PMID: 30771521.
- Shared and derived features of cellular diversity in the human cerebral cortex.Miller DJ, Bhaduri A, Sestan N, Kriegstein A. Curr Opin Neurobiol. 2019 Jun; 2019 Jan 21. PMID: 30677551.
- Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. J Biol Chem. 2019 May 31; 2019 Apr 22. PMID: 31010829.
- Norovirus Attachment and Entry.Graziano VR, Wei J, Wilen CB. Viruses. 2019 May 30; 2019 May 30. PMID: 31151248.
- Genomics and data science: an application within an umbrella.Navarro FCP, Mohsen H, Yan C, Li S, Gu M, Meyerson W, Gerstein M. Genome Biol. 2019 May 29; 2019 May 29. PMID: 31142351.
- Low ambient humidity impairs barrier function and innate resistance against influenza infection.Kudo E, Song E, Yockey LJ, Rakib T, Wong PW, Homer RJ, Iwasaki A. Proc Natl Acad Sci U S A. 2019 May 28; 2019 May 13. PMID: 31085641.
- Small size, big impact: how studies of small DNA tumour viruses revolutionized biology.DiMaio D. Philos Trans R Soc Lond B Biol Sci. 2019 May 27. PMID: 30955494.
- Uncoupling of nucleo-cytoplasmic RNA export and localization during stress.Hochberg-Laufer H, Schwed-Gross A, Neugebauer KM, Shav-Tal Y. Nucleic Acids Res. 2019 May 21. PMID: 30864659.
- Cediranib suppresses homology-directed DNA repair through down-regulation of BRCA1/2 and RAD51.Kaplan AR, Gueble SE, Liu Y, Oeck S, Kim H, Yun Z, Glazer PM. Sci Transl Med. 2019 May 15. PMID: 31092693.
- Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases.Crnković A, Vargas-Rodriguez O, Söll D. Int J Mol Sci. 2019 May 9; 2019 May 9. PMID: 31075874.
- IFN-γ binds TPO to inhibit hematopoiesis.Krause DS. Blood. 2019 May 9. PMID: 31072961.
- miR-181a/b downregulation exerts a protective action on mitochondrial disease models.Indrieri A, Carrella S, Romano A, Spaziano A, Marrocco E, Fernandez-Vizarra E, Barbato S, Pizzo M, Ezhova Y, Golia FM, Ciampi L, Tammaro R, Henao-Mejia J, Williams A, Flavell RA, De Leonibus E, Zeviani M, Surace EM, Banfi S, Franco B. EMBO Mol Med. 2019 May. PMID: 30979712.
- In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens.Chow RD, Wang G, Ye L, Codina A, Kim HR, Shen L, Dong MB, Errami Y, Chen S. Nat Methods. 2019 May; 2019 Apr 8. PMID: 30962622.
- The Transcription Factors TCP4 and PIF3 Antagonistically Regulate Organ-Specific Light Induction of SAUR Genes to Modulate Cotyledon Opening during De-Etiolation in Arabidopsis.Dong J, Sun N, Yang J, Deng Z, Lan J, Qin G, He H, Deng XW, Irish VF, Chen H, Wei N. Plant Cell. 2019 May; 2019 Mar 25. PMID: 30914467.
- Epithelial (E)-Cadherin is a Novel Mediator of Platelet Aggregation and Clot Stability.Scanlon VM, Teixeira AM, Tyagi T, Zou S, Zhang PX, Booth CJ, Kowalska MA, Bao J, Hwa J, Hayes V, Marks MS, Poncz M, Krause DS. Thromb Haemost. 2019 May; 2019 Mar 12. PMID: 30861547.
- Misperceived Risks of Zika-related Microcephaly in India.Grubaugh ND, Ishtiaq F, Setoh YX, Ko AI. Trends Microbiol. 2019 May; 2019 Feb 27. PMID: 30826180.
- Nanoparticle-mediated intratumoral inhibition of miR-21 for improved survival in glioblastoma.Seo YE, Suh HW, Bahal R, Josowitz A, Zhang J, Song E, Cui J, Noorbakhsh S, Jackson C, Bu T, Piotrowski-Daspit A, Bindra R, Saltzman WM. Biomaterials. 2019 May; 2019 Feb 14. PMID: 30802686.
- Immunity, microbiota and kidney disease.Knauf F, Brewer JR, Flavell RA. Nat Rev Nephrol. 2019 May. PMID: 30796361.
- Assessing Patterns of Palliative Care Referral and Location of Death in Patients with Idiopathic Pulmonary Fibrosis: A Sixteen-Year Single-Center Retrospective Cohort Study.Zou RH, Nouraie M, Chen X, Saul MI, Kaminski N, Gibson KF, Kass DJ, Lindell KO. J Palliat Med. 2019 May; 2019 Jan 7. PMID: 30615545.
- Dynamic and Cell-Specific DACH1 Expression in Human Neocortical and Striatal Development.Castiglioni V, Faedo A, Onorati M, Bocchi VD, Li Z, Iennaco R, Vuono R, Bulfamante GP, Muzio L, Martino G, Sestan N, Barker RA, Cattaneo E. Cereb Cortex. 2019 May 1. PMID: 29688344.
- Aberrant splicing contributes to severe α-spectrin-linked congenital hemolytic anemia.Gallagher PG, Maksimova Y, Lezon-Geyda K, Newburger PE, Medeiros D, Hanson RD, Rothman J, Israels S, Wall DA, Sidonio RF Jr, Sieff C, Gowans LK, Mittal N, Rivera-Santiago R, Speicher DW, Baserga SJ, Schulz VP. J Clin Invest. 2019 Apr 30; 2019 Apr 30. PMID: 31038472.
- exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M. Cell Syst. 2019 Apr 24; 2019 Apr 4. PMID: 30956140.
- Delayed-Type Hypersensitivity Underlying Casein Allergy Is Suppressed by Extracellular Vesicles Carrying miRNA-150.Wąsik M, Nazimek K, Nowak B, Askenase PW, Bryniarski K. Nutrients. 2019 Apr 23; 2019 Apr 23. PMID: 31018604.
- Aminoacyl-tRNA Synthetases and tRNAs for an Expanded Genetic Code: What Makes them Orthogonal?Melnikov SV, Söll D. Int J Mol Sci. 2019 Apr 19; 2019 Apr 19. PMID: 31010123.
- Engineered Aminoacyl-tRNA Synthetases with Improved Selectivity toward Noncanonical Amino Acids.Kwok HS, Vargas-Rodriguez O, Melnikov SV, Söll D. ACS Chem Biol. 2019 Apr 19; 2019 Apr 9. PMID: 30933556.
- Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice.Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Cell. 2019 Apr 18; 2019 Apr 4. PMID: 30955885.
- Multi-platform discovery of haplotype-resolved structural variation in human genomes.Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Nat Commun. 2019 Apr 16; 2019 Apr 16. PMID: 30992455.
- YTHDF1 Control of Dendritic Cell Cross-Priming as a Possible Target of Cancer Immunotherapy.Kim DJ, Iwasaki A. Biochemistry. 2019 Apr 16; 2019 Apr 3. PMID: 30943019.
- MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation.Hu X, Liu ZZ, Chen X, Schulz VP, Kumar A, Hartman AA, Weinstein J, Johnston JF, Rodriguez EC, Eastman AE, Cheng J, Min L, Zhong M, Carroll C, Gallagher PG, Lu J, Schwartz M, King MC, Krause DS, Guo S. Nat Commun. 2019 Apr 12; 2019 Apr 12. PMID: 30979898.
- Stella's Role in Oocyte DNA Methylation Suggests Additional Activities of DNMT1.Kiefer L, Simon MD. Biochemistry. 2019 Apr 9; 2019 Mar 28. PMID: 30920202.
- A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer.Atilho RM, Mirihana Arachchilage G, Greenlee EB, Knecht KM, Breaker RR. Elife. 2019 Apr 5; 2019 Apr 5. PMID: 30950790.
- Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.Tavares RCA, Pyle AM, Somarowthu S. J Mol Biol. 2019 Apr 5; 2019 Mar 16. PMID: 30890332.
- exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A. Cell. 2019 Apr 4. PMID: 30951672.
- The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.Das S, Ansel KM, Bitzer M, Breakefield XO, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, Saugstad JA, Van Keuren-Jensen K, Weaver AM, Laurent LC. Cell. 2019 Apr 4. PMID: 30951667.
- Restoration of brain circulation and cellular functions hours post-mortem.Vrselja Z, Daniele SG, Silbereis J, Talpo F, Morozov YM, Sousa AMM, Tanaka BS, Skarica M, Pletikos M, Kaur N, Zhuang ZW, Liu Z, Alkawadri R, Sinusas AJ, Latham SR, Waxman SG, Sestan N. Nature. 2019 Apr; 2019 Apr 17. PMID: 30996318.
- Genetic compensation triggered by mutant mRNA degradation.El-Brolosy MA, Kontarakis Z, Rossi A, Kuenne C, Günther S, Fukuda N, Kikhi K, Boezio GLM, Takacs CM, Lai SL, Fukuda R, Gerri C, Giraldez AJ, Stainier DYR. Nature. 2019 Apr; 2019 Apr 3. PMID: 30944477.
- Commentary on cell polarity in plants: Quatrano 1973.Irish V. Dev Biol. 2019 Apr 1. PMID: 30885317.
- Small open reading frames and cellular stress responses.Khitun A, Ness TJ, Slavoff SA. Mol Omics. 2019 Apr 1; 2019 Feb 27. PMID: 30810554.
- Stimulation of Caveolin-1 Signaling Improves Arteriovenous Fistula Patency.Hashimoto T, Isaji T, Hu H, Yamamoto K, Bai H, Santana JM, Kuo A, Kuwahara G, Foster TR, Hanisch JJ, Yatsula BA, Sessa WC, Hoshina K, Dardik A. Arterioscler Thromb Vasc Biol. 2019 Apr. PMID: 30786746.
- Promoters to Study Vascular Smooth Muscle.Chakraborty R, Saddouk FZ, Carrao AC, Krause DS, Greif DM, Martin KA. Arterioscler Thromb Vasc Biol. 2019 Apr. PMID: 30727757.
- Insights into genetics, human biology and disease gleaned from family based genomic studies.Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Genet Med. 2019 Apr; 2019 Jan 18. PMID: 30655598.
- The Yale Center for Biomedical Innovation and Technology (CBIT): One Model to Accelerate Impact From Academic Health Care Innovation.Siefert AL, Cartiera MS, Khalid AN, Nantel MC, Loose CR, Schulam PG, Saltzman WM, Dempsey MK. Acad Med. 2019 Apr. PMID: 30520807.
- Genome-wide discovery of structured noncoding RNAs in bacteria.Stav S, Atilho RM, Mirihana Arachchilage G, Nguyen G, Higgs G, Breaker RR. BMC Microbiol. 2019 Mar 22; 2019 Mar 22. PMID: 30902049.
- Coming together to define membrane contact sites.Scorrano L, De Matteis MA, Emr S, Giordano F, Hajnóczky G, Kornmann B, Lackner LL, Levine TP, Pellegrini L, Reinisch K, Rizzuto R, Simmen T, Stenmark H, Ungermann C, Schuldiner M. Nat Commun. 2019 Mar 20; 2019 Mar 20. PMID: 30894536.
- Membrane-cytoskeletal crosstalk mediated by myosin-I regulates adhesion turnover during phagocytosis.Barger SR, Reilly NS, Shutova MS, Li Q, Maiuri P, Heddleston JM, Mooseker MS, Flavell RA, Svitkina T, Oakes PW, Krendel M, Gauthier NC. Nat Commun. 2019 Mar 19; 2019 Mar 19. PMID: 30890704.
- Measuring the reproducibility and quality of Hi-C data.Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS. Genome Biol. 2019 Mar 19; 2019 Mar 19. PMID: 30890172.
- Small nucleolar RNAs controlling rRNA processing in Trypanosoma brucei.Chikne V, Shanmugha Rajan K, Shalev-Benami M, Decker K, Cohen-Chalamish S, Madmoni H, Biswas VK, Kumar Gupta S, Doniger T, Unger R, Tschudi C, Ullu E, Michaeli S. Nucleic Acids Res. 2019 Mar 18. PMID: 30605535.
- The Reduced Expression of EOLA1 May Be Related to Refractory Diabetic Foot Ulcer.Wu M, Leng W, Pan H, Lei X, Chen L, Ouyang X, Liang Z. Mediators Inflamm. 2019; 2019 Mar 17. PMID: 31007603.
- Specific Disruption of Abca1 Targeting Largely Mimics the Effects of miR-33 Knockout on Macrophage Cholesterol Efflux and Atherosclerotic Plaque Development.Price NL, Rotllan N, Zhang X, Canfrán-Duque A, Nottoli T, Suarez Y, Fernández-Hernando C. Circ Res. 2019 Mar 15. PMID: 30707082.
- Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling.Rodenfels J, Neugebauer KM, Howard J. Dev Cell. 2019 Mar 11; 2019 Jan 31. PMID: 30713074.
- Sialylation of MUC4β N-glycans by ST6GAL1 orchestrates human airway epithelial cell differentiation associated with type-2 inflammation.Zhou X, Kinlough CL, Hughey RP, Jin M, Inoue H, Etling E, Modena BD, Kaminski N, Bleecker ER, Meyers DA, Jarjour NN, Trudeau JB, Holguin F, Ray A, Wenzel SE. JCI Insight. 2019 Mar 7; 2019 Mar 7. PMID: 30730306.
- Publisher's Note: Phage treatment of an aortic graft infected with Pseudomonas aeruginosa.Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Evol Med Public Health. 2019; 2019 Mar 4. PMID: 30847220.
- Epithelial endoplasmic reticulum stress orchestrates a protective IgA response.Grootjans J, Krupka N, Hosomi S, Matute JD, Hanley T, Saveljeva S, Gensollen T, Heijmans J, Li H, Limenitakis JP, Ganal-Vonarburg SC, Suo S, Luoma AM, Shimodaira Y, Duan J, Shih DQ, Conner ME, Glickman JN, Fuhler GM, Palm NW, de Zoete MR, van der Woude CJ, Yuan GC, Wucherpfennig KW, Targan SR, Rosenstiel P, Flavell RA, McCoy KD, Macpherson AJ, Kaser A, Blumberg RS. Science. 2019 Mar 1. PMID: 30819965.
- One-step generation of modular CAR-T cells with AAV-Cpf1.Dai X, Park JJ, Du Y, Kim HR, Wang G, Errami Y, Chen S. Nat Methods. 2019 Mar; 2019 Feb 25. PMID: 30804551.
- Antiviral immunity: a link to bile acids.Wang J, Flavell RA, Li HB. Cell Res. 2019 Mar. PMID: 30778178.
- MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis.Moro A, Driscoll TP, Boraas LC, Armero W, Kasper DM, Baeyens N, Jouy C, Mallikarjun V, Swift J, Ahn SJ, Lee D, Zhang J, Gu M, Gerstein M, Schwartz M, Nicoli S. Nat Cell Biol. 2019 Mar; 2019 Feb 11. PMID: 30742093.
- Dissecting alterations in human CD8+ T cells with aging by high-dimensional single cell mass cytometry.Shin MS, Yim K, Moon K, Park HJ, Mohanty S, Kim JW, Montgomery RR, Shaw AC, Krishnaswamy S, Kang I. Clin Immunol. 2019 Mar; 2019 Jan 16. PMID: 30659916.
- Regularized Latent Class Model for Joint Analysis of High-Dimensional Longitudinal Biomarkers and a Time-to-Event Outcome.Sun J, Herazo-Maya JD, Molyneaux PL, Maher TM, Kaminski N, Zhao H. Biometrics. 2019 Mar; 2018 Dec 5. PMID: 30178494.
- BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis.Prasse A, Binder H, Schupp JC, Kayser G, Bargagli E, Jaeger B, Hess M, Rittinghausen S, Vuga L, Lynn H, Violette S, Jung B, Quast K, Vanaudenaerde B, Xu Y, Hohlfeld JM, Krug N, Herazo-Maya JD, Rottoli P, Wuyts WA, Kaminski N. Am J Respir Crit Care Med. 2019 Mar 1. PMID: 30141961.
- Non-coding RNA regulation of endothelial and macrophage functions during atherosclerosis.Aryal B, Suárez Y. Vascul Pharmacol. 2019 Mar; 2018 Mar 15. PMID: 29551552.
- High-throughput Evaluation of Protein Migration and Localization after Laser Micro-Irradiation.Oeck S, Malewicz NM, Krysztofiak A, Turchick A, Jendrossek V, Glazer PM. Sci Rep. 2019 Feb 28; 2019 Feb 28. PMID: 30816253.
- Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS. Nucleic Acids Res. 2019 Feb 28. PMID: 30520988.
- Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo.Codina A, Renauer PA, Wang G, Chow RD, Park JJ, Ye H, Zhang K, Dong MB, Gassaway B, Ye L, Errami Y, Shen L, Chang A, Jain D, Herbst RS, Bosenberg M, Rinehart J, Fan R, Chen S. Cell Syst. 2019 Feb 27; 2019 Feb 20. PMID: 30797773.
- RIG-I Selectively Discriminates against 5'-Monophosphate RNA.Ren X, Linehan MM, Iwasaki A, Pyle AM. Cell Rep. 2019 Feb 19. PMID: 30784585.
- The Lupus Susceptibility Locus Sgp3 Encodes the Suppressor of Endogenous Retrovirus Expression SNERV.Treger RS, Pope SD, Kong Y, Tokuyama M, Taura M, Iwasaki A. Immunity. 2019 Feb 19; 2019 Jan 29. PMID: 30709743.
- Identification of Dihydrofuro[3,4- d]pyrimidine Derivatives as Novel HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors with Promising Antiviral Activities and Desirable Physicochemical Properties.Kang D, Zhang H, Wang Z, Zhao T, Ginex T, Luque FJ, Yang Y, Wu G, Feng D, Wei F, Zhang J, De Clercq E, Pannecouque C, Chen CH, Lee KH, Murugan NA, Steitz TA, Zhan P, Liu X. J Med Chem. 2019 Feb 14; 2019 Jan 18. PMID: 30624934.
- Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria.Kortright KE, Chan BK, Koff JL, Turner PE. Cell Host Microbe. 2019 Feb 13. PMID: 30763536.
- LCox: a tool for selecting genes related to survival outcomes using longitudinal gene expression data.Sun J, Herazo-Maya JD, Wang JL, Kaminski N, Zhao H. Stat Appl Genet Mol Biol. 2019 Feb 13; 2019 Feb 13. PMID: 30759070.
- Synthetic lethality of a cell-penetrating anti-RAD51 antibody in PTEN-deficient melanoma and glioma cells.Turchick A, Liu Y, Zhao W, Cohen I, Glazer PM. Oncotarget. 2019 Feb 12; 2019 Feb 12. PMID: 30863489.
- MARCH8 Ubiquitinates the Hepatitis C Virus Nonstructural 2 Protein and Mediates Viral Envelopment.Kumar S, Barouch-Bentov R, Xiao F, Schor S, Pu S, Biquand E, Lu A, Lindenbach BD, Jacob Y, Demeret C, Einav S. Cell Rep. 2019 Feb 12. PMID: 30759391.
- Fanconi anemia protein FANCI functions in ribosome biogenesis.Sondalle SB, Longerich S, Ogawa LM, Sung P, Baserga SJ. Proc Natl Acad Sci U S A. 2019 Feb 12; 2019 Jan 28. PMID: 30692263.
- Apobec3A maintains HIV-1 latency through recruitment of epigenetic silencing machinery to the long terminal repeat.Taura M, Song E, Ho YC, Iwasaki A. Proc Natl Acad Sci U S A. 2019 Feb 5; 2019 Jan 22. PMID: 30670656.
- Precision epidemiology for infectious disease control.Ladner JT, Grubaugh ND, Pybus OG, Andersen KG. Nat Med. 2019 Feb; 2019 Feb 6. PMID: 30728537.
- A quantitative approach for measuring the reservoir of latent HIV-1 proviruses.Bruner KM, Wang Z, Simonetti FR, Bender AM, Kwon KJ, Sengupta S, Fray EJ, Beg SA, Antar AAR, Jenike KM, Bertagnolli LN, Capoferri AA, Kufera JT, Timmons A, Nobles C, Gregg J, Wada N, Ho YC, Zhang H, Margolick JB, Blankson JN, Deeks SG, Bushman FD, Siliciano JD, Laird GM, Siliciano RF. Nature. 2019 Feb; 2019 Jan 30. PMID: 30700913.
- Spatial distribution of marker gene activity in the mouse lung during alveolarization.Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Data Brief. 2019 Feb; 2018 Nov 3. PMID: 30596133.
- BPIFA1 regulates lung neutrophil recruitment and interferon signaling during acute inflammation.Britto CJ, Niu N, Khanal S, Huleihel L, Herazo-Maya JD, Thompson A, Sauler M, Slade MD, Sharma L, Dela Cruz CS, Kaminski N, Cohn LE. Am J Physiol Lung Cell Mol Physiol. 2019 Feb 1; 2018 Nov 21. PMID: 30461288.
- Metabolic regulation of T cell development by Sin1-mTORC2 is mediated by pyruvate kinase M2.Ouyang X, Han Y, Qu G, Li M, Wu N, Liu H, Arojo O, Sun H, Liu X, Liu D, Chen L, Zou Q, Su B. J Mol Cell Biol. 2019 Feb 1. PMID: 30428057.
- Glycoprotein-130 Expression Is Associated with Aggressive Bladder Cancer and Is a Potential Therapeutic Target.Martin DT, Shen H, Steinbach-Rankins JM, Zhu X, Johnson KK, Syed J, Saltzman WM, Weiss RM. Mol Cancer Ther. 2019 Feb; 2018 Oct 31. PMID: 30381445.
- Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis.McDonough JE, Kaminski N, Thienpont B, Hogg JC, Vanaudenaerde BM, Wuyts WA. Thorax. 2019 Feb; 2018 Oct 26. PMID: 30366970.
- Degenerate minigene library analysis enables identification of altered branch point utilization by mutant splicing factor 3B1 (SF3B1).Gupta AK, Murthy T, Paul KV, Ramirez O, Fisher JB, Rao S, Rosenberg AB, Seelig G, Minella AC, Pillai MM. Nucleic Acids Res. 2019 Jan 25. PMID: 30462273.
- Arbovirus coinfection and co-transmission: A neglected public health concern?Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. PLoS Biol. 2019 Jan; 2019 Jan 22. PMID: 30668574.
- A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies.Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S. Nat Commun. 2019 Jan 21; 2019 Jan 21. PMID: 30664659.
- Oligosaccharyltransferase Inhibition Reduces Receptor Tyrosine Kinase Activation and Enhances Glioma Radiosensitivity.Baro M, Lopez Sambrooks C, Quijano A, Saltzman WM, Contessa J. Clin Cancer Res. 2019 Jan 15; 2018 Jul 2. PMID: 29967251.
- Next-Generation Sequencing to Diagnose Suspected Genetic Disorders.Li S, Gerstein MB. N Engl J Med. 2019 Jan 10. PMID: 30628427.
- Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation.Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R, Lu J. Nat Commun. 2019 Jan 9; 2019 Jan 9. PMID: 30626865.
- Active Targeting of Cancer Cells by Nanobody Decorated Polypeptide Micelle with Bio-orthogonally Conjugated Drug.Costa SA, Mozhdehi D, Dzuricky MJ, Isaacs FJ, Brustad EM, Chilkoti A. Nano Lett. 2019 Jan 9; 2018 Dec 14. PMID: 30540482.
- An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG. Genome Biol. 2019 Jan 8; 2019 Jan 8. PMID: 30621750.
- Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation.Lomakin IB, Dmitriev SE, Steitz TA. Proc Natl Acad Sci U S A. 2019 Jan 8; 2018 Dec 24. PMID: 30584092.
- GENCODE reference annotation for the human and mouse genomes.Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P. Nucleic Acids Res. 2019 Jan 8. PMID: 30357393.
- Dietary sugar silences a colonization factor in a mammalian gut symbiont.Townsend GE 2nd, Han W, Schwalm ND 3rd, Raghavan V, Barry NA, Goodman AL, Groisman EA. Proc Natl Acad Sci U S A. 2019 Jan 2; 2018 Dec 17. PMID: 30559205.
- Pre-mRNA Splicing in the Nuclear Landscape.Carrocci TJ, Neugebauer KM. Cold Spring Harb Symp Quant Biol. 2019; 2020 Jun 3. PMID: 32493763.
- How Complementary Targets Expose the microRNA 3' End for Tailing and Trimming during Target-Directed microRNA Degradation.Pawlica P, Sheu-Gruttadauria J, MacRae IJ, Steitz JA. Cold Spring Harb Symp Quant Biol. 2019; 2020 Feb 4. PMID: 32019864.
- Transmissible inflammation-induced colorectal cancer in inflammasome-deficient mice.Hu B, Friedman G, Elinav E, Flavell RA. Oncoimmunology. 2019; 2018 May 7. PMID: 31646062.
- Shear Stress Attenuates Inward Remodeling in Cultured Mouse Thoracodorsal Arteries in an eNOS-Dependent, but Not Hemodynamic Manner, and Increases Cx37 Expression.Looft-Wilson RC, Billig JE, Sessa WC. J Vasc Res. 2019; 2019 Oct 1. PMID: 31574503.
- Intravenously administered contact allergens coupled to syngeneic erythrocytes induce in mice tolerance rather than effector immune response.Nazimek K, Wąsik M, Askenase PW, Bryniarski K. Folia Med Cracov. 2019. PMID: 31180076.
- Biodegradable bioadhesive nanoparticle incorporation of broad-spectrum organic sunscreen agents.Suh HW, Lewis J, Fong L, Ramseier JY, Carlson K, Peng ZH, Yin ES, Saltzman WM, Girardi M. Bioeng Transl Med. 2019 Jan; 2018 Jul 6. PMID: 30680324.
- Tracking virus outbreaks in the twenty-first century.Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG. Nat Microbiol. 2019 Jan; 2018 Dec 13. PMID: 30546099.
- The Role of Maternal HP1a in Early Drosophila Embryogenesis via Regulation of Maternal Transcript Production.Park AR, Liu N, Neuenkirchen N, Guo Q, Lin H. Genetics. 2019 Jan; 2018 Nov 15. PMID: 30442760.
- Alginate microparticles loaded with basic fibroblast growth factor induce tissue coverage in a rat model of myelomeningocele.Farrelly JS, Bianchi AH, Ricciardi AS, Buzzelli GL, Ahle SL, Freedman-Weiss MR, Luks VL, Saltzman WM, Stitelman DH. J Pediatr Surg. 2019 Jan; 2018 Oct 5. PMID: 30414695.
- Carbodiimide reagents for the chemical probing of RNA structure in cells.Wang PY, Sexton AN, Culligan WJ, Simon MD. RNA. 2019 Jan; 2018 Nov 2. PMID: 30389828.
- Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine.Duffy EE, Schofield JA, Simon MD. Wiley Interdiscip Rev RNA. 2019 Jan; 2018 Oct 28. PMID: 30370679.
- The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL.Murthy T, Paul KV, Minella AC, Pillai MM. Methods Mol Biol. 2019. PMID: 30350199.
- Endothelial NOS: perspective and recent developments.Garcia V, Sessa WC. Br J Pharmacol. 2019 Jan; 2018 Dec 9. PMID: 30341769.
- Rare variants of the FMN riboswitch class in Clostridium difficile and other bacteria exhibit altered ligand specificity.Atilho RM, Perkins KR, Breaker RR. RNA. 2019 Jan; 2018 Oct 4. PMID: 30287481.
- A novel, noncoding-RNA-mediated, post-transcriptional mechanism of anti-Mullerian hormone regulation by the H19/let-7 axis.Qin C, Xia X, Fan Y, Jiang Y, Chen Y, Zhang N, Uslu B, Johnson J, Kallen AN. Biol Reprod. 2019 Jan 1. PMID: 30137224.
- Macrophage Migration Inhibitory Factor Regulates U1 Small Nuclear RNP Immune Complex-Mediated Activation of the NLRP3 Inflammasome.Shin MS, Kang Y, Wahl ER, Park HJ, Lazova R, Leng L, Mamula M, Krishnaswamy S, Bucala R, Kang I. Arthritis Rheumatol. 2019 Jan; 2018 Dec 4. PMID: 30009530.
2018
- Molecular and functional heterogeneity of IL-10-producing CD4(+) T cells.Brockmann L, Soukou S, Steglich B, Czarnewski P, Zhao L, Wende S, Bedke T, Ergen C, Manthey C, Agalioti T, Geffken M, Seiz O, Parigi SM, Sorini C, Geginat J, Fujio K, Jacobs T, Roesch T, Izbicki JR, Lohse AW, Flavell RA, Krebs C, Gustafsson JA, Antonson P, Roncarolo MG, Villablanca EJ, Gagliani N, Huber S. Nat Commun. 2018 Dec 21; 2018 Dec 21. PMID: 30575716.
- Muller's Ratchet and Ribosome Degeneration in the Obligate Intracellular Parasites Microsporidia.Melnikov SV, Manakongtreecheep K, Rivera KD, Makarenko A, Pappin DJ, Söll D. Int J Mol Sci. 2018 Dec 19; 2018 Dec 19. PMID: 30572624.
- The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes.Meng Q, Wang K, Brunetti T, Xia Y, Jiao C, Dai R, Fitzgerald D, Thomas A, Jay L, Eckart H, Grennan K, Imamura-Kawasawa Y, Li M, Sestan N, White KP, Chen C, Liu C. Sci Transl Med. 2018 Dec 19; 2018 Dec 13. PMID: 30545965.
- Colitis Promotes a Pathological Condition of the Liver in the Absence of Foxp3(+) Regulatory T Cells.Mathies F, Steffens N, Kleinschmidt D, Stuhlmann F, Huber FJ, Roy U, Meyer T, Luetgehetmann M, von Petersdorff M, Seiz O, Herkel J, Schramm C, Flavell RA, Gagliani N, Krebs C, Panzer U, Abdullah Z, Strowig T, Bedke T, Huber S. J Immunol. 2018 Dec 15; 2018 Nov 16. PMID: 30446566.
- Spatiotemporal transcriptomic divergence across human and macaque brain development.Zhu Y, Sousa AMM, Gao T, Skarica M, Li M, Santpere G, Esteller-Cucala P, Juan D, Ferrández-Peral L, Gulden FO, Yang M, Miller DJ, Marques-Bonet T, Imamura Kawasawa Y, Zhao H, Sestan N. Science. 2018 Dec 14; 2018 Dec 13. PMID: 30545855.
- Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ. Science. 2018 Dec 14. PMID: 30545852.
- ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses.Tokuyama M, Kong Y, Song E, Jayewickreme T, Kang I, Iwasaki A. Proc Natl Acad Sci U S A. 2018 Dec 11; 2018 Nov 19. PMID: 30455304.
- Electron-Mediated Aminyl and Iminyl Radicals from C5 Azido-Modified Pyrimidine Nucleosides Augment Radiation Damage to Cancer Cells.Wen Z, Peng J, Tuttle PR, Ren Y, Garcia C, Debnath D, Rishi S, Hanson C, Ward S, Kumar A, Liu Y, Zhao W, Glazer PM, Liu Y, Sevilla MD, Adhikary A, Wnuk SF. Org Lett. 2018 Dec 7; 2018 Nov 20. PMID: 30457873.
- Loss of protein synthesis quality control in host-restricted organisms.Melnikov SV, van den Elzen A, Stevens DL, Thoreen CC, Söll D. Proc Natl Acad Sci U S A. 2018 Dec 4; 2018 Nov 19. PMID: 30455292.
- Microbiota-driven interleukin-17-producing cells and eosinophils synergize to accelerate multiple myeloma progression.Calcinotto A, Brevi A, Chesi M, Ferrarese R, Garcia Perez L, Grioni M, Kumar S, Garbitt VM, Sharik ME, Henderson KJ, Tonon G, Tomura M, Miwa Y, Esplugues E, Flavell RA, Huber S, Canducci F, Rajkumar VS, Bergsagel PL, Bellone M. Nat Commun. 2018 Dec 3; 2018 Dec 3. PMID: 30510245.
- Blocking immunoinhibitory receptor LILRB2 reprograms tumor-associated myeloid cells and promotes antitumor immunity.Chen HM, van der Touw W, Wang YS, Kang K, Mai S, Zhang J, Alsina-Beauchamp D, Duty JA, Mungamuri SK, Zhang B, Moran T, Flavell R, Aaronson S, Hu HM, Arase H, Ramanathan S, Flores R, Pan PY, Chen SH. J Clin Invest. 2018 Dec 3; 2018 Oct 22. PMID: 30352428.
- The translation of non-canonical open reading frames controls mucosal immunity.Jackson R, Kroehling L, Khitun A, Bailis W, Jarret A, York AG, Khan OM, Brewer JR, Skadow MH, Duizer C, Harman CCD, Chang L, Bielecki P, Solis AG, Steach HR, Slavoff S, Flavell RA. Nature. 2018 Dec; 2018 Dec 12. PMID: 30542152.
- Managing the emergence of pathogen resistance via spatially targeted antimicrobial use.Okamoto KW, Post DM, Vasseur DA, Turner PE. Evol Appl. 2018 Dec; 2018 Sep 26. PMID: 30459832.
- Temperature shift activates bloodstream VSG expression site promoters in Trypanosoma brucei.Kolev NG, Ramsdell TK, Tschudi C. Mol Biochem Parasitol. 2018 Dec; 2018 Nov 3. PMID: 30399391.
- Small molecules that target group II introns are potent antifungal agents.Fedorova O, Jagdmann GE Jr, Adams RL, Yuan L, Van Zandt MC, Pyle AM. Nat Chem Biol. 2018 Dec; 2018 Oct 15. PMID: 30323219.
- Pathologic Oxidation of PTPN12 Underlies ABL1 Phosphorylation in Hereditary Leiomyomatosis and Renal Cell Carcinoma.Xu Y, Taylor P, Andrade J, Ueberheide B, Shuch B, Glazer PM, Bindra RS, Moran MF, Linehan WM, Neel BG. Cancer Res. 2018 Dec 1; 2018 Oct 8. PMID: 30297534.
- Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching.Torgerson CD, Hiller DA, Stav S, Strobel SA. RNA. 2018 Dec; 2018 Sep 20. PMID: 30237163.
- Addressing Gender Inequality in Our Disciplines: Report from the Association of Pulmonary, Critical Care, and Sleep Division Chiefs.Thomson CC, Riekert KA, Bates CK, Jena AB, Borok Z, McCallister JW, Schnapp LM, Lama VN, Kraft M, Davis SD, Finn P, Carson SS, Beck JM, Powell CA, Tanoue LT, Kaminski N, Dixon AE. Ann Am Thorac Soc. 2018 Dec. PMID: 30153425.
- Sno-derived RNAs are prevalent molecular markers of cancer immunity.Chow RD, Chen S. Oncogene. 2018 Dec; 2018 Aug 2. PMID: 30072739.
- SRSF2 mutations drive oncogenesis by activating a global program of aberrant alternative splicing in hematopoietic cells.Liang Y, Tebaldi T, Rejeski K, Joshi P, Stefani G, Taylor A, Song Y, Vasic R, Maziarz J, Balasubramanian K, Ardasheva A, Ding A, Quattrone A, Halene S. Leukemia. 2018 Dec; 2018 Jun 1. PMID: 29858584.
- Rotavirus VP3 targets MAVS for degradation to inhibit type III interferon expression in intestinal epithelial cells.Ding S, Zhu S, Ren L, Feng N, Song Y, Ge X, Li B, Flavell RA, Greenberg HB. Elife. 2018 Nov 21; 2018 Nov 21. PMID: 30460894.
- The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification.Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS. Cell Rep. 2018 Nov 20. PMID: 30463007.
- SMAD4 Prevents Flow Induced Arteriovenous Malformations by Inhibiting Casein Kinase 2.Ola R, Künzel SH, Zhang F, Genet G, Chakraborty R, Pibouin-Fragner L, Martin K, Sessa W, Dubrac A, Eichmann A. Circulation. 2018 Nov 20. PMID: 29976569.
- Versatility of Synthetic tRNAs in Genetic Code Expansion.Hoffman KS, Crnković A, Söll D. Genes (Basel). 2018 Nov 7; 2018 Nov 7. PMID: 30405060.
- Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine.Kiefer L, Schofield JA, Simon MD. J Am Chem Soc. 2018 Nov 7; 2018 Oct 24. PMID: 30353734.
- Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C. Cell Rep. 2018 Nov 6. PMID: 30404001.
- Inhibition of profibrotic microRNA-21 affects platelets and their releasate.Barwari T, Eminaga S, Mayr U, Lu R, Armstrong PC, Chan MV, Sahraei M, Fernández-Fuertes M, Moreau T, Barallobre-Barreiro J, Lynch M, Yin X, Schulte C, Baig F, Pechlaner R, Langley SR, Zampetaki A, Santer P, Weger M, Plasenzotti R, Schosserer M, Grillari J, Kiechl S, Willeit J, Shah AM, Ghevaert C, Warner TD, Fernández-Hernando C, Suárez Y, Mayr M. JCI Insight. 2018 Nov 2; 2018 Nov 2. PMID: 30385722.
- A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria.Klähn S, Bolay P, Wright PR, Atilho RM, Brewer KI, Hagemann M, Breaker RR, Hess WR. Nucleic Acids Res. 2018 Nov 2. PMID: 30085248.
- Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci.Withers JB, Li ES, Vallery TK, Yario TA, Steitz JA. PLoS Pathog. 2018 Nov; 2018 Nov 1. PMID: 30383841.
- The 7q11.23 Protein DNAJC30 Interacts with ATP Synthase and Links Mitochondria to Brain Development.Tebbenkamp ATN, Varela L, Choi J, Paredes MI, Giani AM, Song JE, Sestan-Pesa M, Franjic D, Sousa AMM, Liu ZW, Li M, Bichsel C, Koch M, Szigeti-Buck K, Liu F, Li Z, Kawasawa YI, Paspalas CD, Mineur YS, Prontera P, Merla G, Picciotto MR, Arnsten AFT, Horvath TL, Sestan N. Cell. 2018 Nov 1. PMID: 30318146.
- Designing seryl-tRNA synthetase for improved serylation of selenocysteine tRNAs.Fu X, Crnković A, Sevostyanova A, Söll D. FEBS Lett. 2018 Nov; 2018 Oct 24. PMID: 30317559.
- Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Nat Genet. 2018 Nov; 2018 Oct 1. PMID: 30275530.
- Optimized CRISPR-Cpf1 system for genome editing in zebrafish.Fernandez JP, Vejnar CE, Giraldez AJ, Rouet R, Moreno-Mateos MA. Methods. 2018 Nov 1; 2018 Jun 28. PMID: 29964176.
- Riboswitches and Translation Control.Breaker RR. Cold Spring Harb Perspect Biol. 2018 Nov 1; 2018 Nov 1. PMID: 29844057.
- Intestinal IFN-γ-producing type 1 regulatory T cells coexpress CCR5 and programmed cell death protein 1 and downregulate IL-10 in the inflamed guts of patients with inflammatory bowel disease.Alfen JS, Larghi P, Facciotti F, Gagliani N, Bosotti R, Paroni M, Maglie S, Gruarin P, Vasco CM, Ranzani V, Frusteri C, Iseppon A, Moro M, Crosti MC, Gatti S, Pagani M, Caprioli F, Abrignani S, Flavell RA, Geginat J. J Allergy Clin Immunol. 2018 Nov; 2018 Jan 31. PMID: 29369775.
- Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue.Ma NJ, Hemez CF, Barber KW, Rinehart J, Isaacs FJ. Elife. 2018 Oct 30; 2018 Oct 30. PMID: 30375330.
- Learning time-varying information flow from single-cell epithelial to mesenchymal transition data.Krishnaswamy S, Zivanovic N, Sharma R, Pe'er D, Bodenmiller B. PLoS One. 2018; 2018 Oct 29. PMID: 30372433.
- Aberrant information transfer interferes with functional axon regeneration.Ding C, Hammarlund M. Elife. 2018 Oct 29; 2018 Oct 29. PMID: 30371349.
- Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder.Sestan N, State MW. Neuron. 2018 Oct 24. PMID: 30359605.
- MRTFA augments megakaryocyte maturation by enhancing the SRF regulatory axis.Rahman NT, Schulz VP, Wang L, Gallagher PG, Denisenko O, Gualdrini F, Esnault C, Krause DS. Blood Adv. 2018 Oct 23. PMID: 30337297.
- A role of Pumilio 1 in mammalian oocyte maturation and maternal phase of embryogenesis.Mak W, Xia J, Cheng EC, Lowther K, Lin H. Cell Biosci. 2018; 2018 Oct 19. PMID: 30364263.
- RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus.Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, Deniz E, Baserga SJ, Khokha MK. Development. 2018 Oct 18; 2018 Oct 18. PMID: 30337486.
- γ-Neurexin and Frizzled Mediate Parallel Synapse Assembly Pathways Antagonized by Receptor Endocytosis.Kurshan PT, Merrill SA, Dong Y, Ding C, Hammarlund M, Bai J, Jorgensen EM, Shen K. Neuron. 2018 Oct 10; 2018 Sep 27. PMID: 30269993.
- Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.Carlyle BC, Kitchen RR, Zhang J, Wilson RS, Lam TT, Rozowsky JS, Williams KR, Sestan N, Gerstein MB, Nairn AC. J Proteome Res. 2018 Oct 5; 2018 Sep 6. PMID: 30125121.
- The DNA repair transcriptome in severe COPD.Sauler M, Lamontagne M, Finnemore E, Herazo-Maya JD, Tedrow J, Zhang X, Morneau JE, Sciurba F, Timens W, Paré PD, Lee PJ, Kaminski N, Bossé Y, Gomez JL. Eur Respir J. 2018 Oct; 2018 Oct 4. PMID: 30190272.
- Characteristics of lung cancer among patients with idiopathic pulmonary fibrosis and interstitial lung disease - analysis of institutional and population data.Yoon JH, Nouraie M, Chen X, Zou RH, Sellares J, Veraldi KL, Chiarchiaro J, Lindell K, Wilson DO, Kaminski N, Burns T, Trejo Bittar H, Yousem S, Gibson K, Kass DJ. Respir Res. 2018 Oct 3; 2018 Oct 3. PMID: 30285867.
- Estrogen Reduces LDL (Low-Density Lipoprotein) Transcytosis.Sessa WC. Arterioscler Thromb Vasc Biol. 2018 Oct. PMID: 30354224.
- Differential expression analysis of transcriptome data of Trypanosoma brucei RBP6 induction in procyclics leading to infectious metacyclics and bloodstream forms in vitro.Shi H, Butler K, Tschudi C. Data Brief. 2018 Oct; 2018 Sep 1. PMID: 30225310.
- cGAS activation in phased droplets.Liu Y, Li HB, Flavell RA. Cell Res. 2018 Oct. PMID: 30218060.
- Mcp1 Promotes Macrophage-Dependent Cyst Expansion in Autosomal Dominant Polycystic Kidney Disease.Cassini MF, Kakade VR, Kurtz E, Sulkowski P, Glazer P, Torres R, Somlo S, Cantley LG. J Am Soc Nephrol. 2018 Oct; 2018 Sep 12. PMID: 30209078.
- The multi-dimensional role of intestinal HIFs in liver pathobiology.Ouyang X, Mehal WZ. J Hepatol. 2018 Oct; 2018 Aug 10. PMID: 30104025.
- VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites.Kumar N, Leonzino M, Hancock-Cerutti W, Horenkamp FA, Li P, Lees JA, Wheeler H, Reinisch KM, De Camilli P. J Cell Biol. 2018 Oct 1; 2018 Aug 9. PMID: 30093493.
- Next-generation genetic code expansion.Arranz-Gibert P, Vanderschuren K, Isaacs FJ. Curr Opin Chem Biol. 2018 Oct; 2018 Jul 30. PMID: 30072242.
- Upgrading aminoacyl-tRNA synthetases for genetic code expansion.Vargas-Rodriguez O, Sevostyanova A, Söll D, Crnković A. Curr Opin Chem Biol. 2018 Oct; 2018 Jul 27. PMID: 30059834.
- γ-Secretase promotes membrane insertion of the human papillomavirus L2 capsid protein during virus infection.Inoue T, Zhang P, Zhang W, Goodner-Bingham K, Dupzyk A, DiMaio D, Tsai B. J Cell Biol. 2018 Oct 1; 2018 Jul 13. PMID: 30006461.
- Hypoxia Promotes Resistance to EGFR Inhibition in NSCLC Cells via the Histone Demethylases, LSD1 and PLU-1.Lu Y, Liu Y, Oeck S, Glazer PM. Mol Cancer Res. 2018 Oct; 2018 Jun 22. PMID: 29934325.
- Reductio ad Intellectum.DiMaio D, Dermody TS, Enquist LW. Annu Rev Virol. 2018 Sep 29. PMID: 30265630.
- Lysine Acetylation Regulates Alanyl-tRNA Synthetase Activity in Escherichia coli.Umehara T, Kosono S, Söll D, Tamura K. Genes (Basel). 2018 Sep 28; 2018 Sep 28. PMID: 30274179.
- Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Science. 2018 Sep 28; 2018 Aug 23. PMID: 30139913.
- PD-1 up-regulation on CD4(+) T cells promotes pulmonary fibrosis through STAT3-mediated IL-17A and TGF-β1 production.Celada LJ, Kropski JA, Herazo-Maya JD, Luo W, Creecy A, Abad AT, Chioma OS, Lee G, Hassell NE, Shaginurova GI, Wang Y, Johnson JE, Kerrigan A, Mason WR, Baughman RP, Ayers GD, Bernard GR, Culver DA, Montgomery CG, Maher TM, Molyneaux PL, Noth I, Mutsaers SE, Prele CM, Peebles RS Jr, Newcomb DC, Kaminski N, Blackwell TS, Van Kaer L, Drake WP. Sci Transl Med. 2018 Sep 26. PMID: 30257954.
- Endothelial Transcytosis of Lipoproteins in Atherosclerosis.Zhang X, Sessa WC, Fernández-Hernando C. Front Cardiovasc Med. 2018; 2018 Sep 25. PMID: 30320124.
- Interferons and Proinflammatory Cytokines in Pregnancy and Fetal Development.Yockey LJ, Iwasaki A. Immunity. 2018 Sep 18. PMID: 30231982.
- Lack of Sprouty 1 and 2 enhances survival of effector CD8(+) T cells and yields more protective memory cells.Shehata HM, Khan S, Chen E, Fields PE, Flavell RA, Sanjabi S. Proc Natl Acad Sci U S A. 2018 Sep 18; 2018 Aug 20. PMID: 30126987.
- Identification and Analysis of Islet Antigen-Specific CD8(+) T Cells with T Cell Libraries.Ogura H, Preston-Hurlburt P, Perdigoto AL, Amodio M, Krishnaswamy S, Clark P, Yu H, Egli D, Fouts A, Steck AK, Herold KC. J Immunol. 2018 Sep 15; 2018 Aug 6. PMID: 30082321.
- MIWI2 targets RNAs transcribed from piRNA-dependent regions to drive DNA methylation in mouse prospermatogonia.Watanabe T, Cui X, Yuan Z, Qi H, Lin H. EMBO J. 2018 Sep 14; 2018 Aug 14. PMID: 30108053.
- NLRP1 restricts butyrate producing commensals to exacerbate inflammatory bowel disease.Tye H, Yu CH, Simms LA, de Zoete MR, Kim ML, Zakrzewski M, Penington JS, Harapas CR, Souza-Fonseca-Guimaraes F, Wockner LF, Preaudet A, Mielke LA, Wilcox SA, Ogura Y, Corr SC, Kanojia K, Kouremenos KA, De Souza DP, McConville MJ, Flavell RA, Gerlic M, Kile BT, Papenfuss AT, Putoczki TL, Radford-Smith GL, Masters SL. Nat Commun. 2018 Sep 13; 2018 Sep 13. PMID: 30214011.
- Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast.Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV. PLoS Biol. 2018 Sep; 2018 Sep 12. PMID: 30208026.
- Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus.Mihaylova VT, Kong Y, Fedorova O, Sharma L, Dela Cruz CS, Pyle AM, Iwasaki A, Foxman EF. Cell Rep. 2018 Sep 11. PMID: 30208323.
- Antibody Light Chains Dictate the Specificity of Contact Hypersensitivity Effector Cell Suppression Mediated by Exosomes.Nazimek K, Askenase PW, Bryniarski K. Int J Mol Sci. 2018 Sep 7; 2018 Sep 7. PMID: 30205452.
- Cell-Penetrating Peptide Mediates Intracellular Membrane Passage of Human Papillomavirus L2 Protein to Trigger Retrograde Trafficking.Zhang P, Monteiro da Silva G, Deatherage C, Burd C, DiMaio D. Cell. 2018 Sep 6; 2018 Aug 16. PMID: 30122350.
- An Antiviral Branch of the IL-1 Signaling Pathway Restricts Immune-Evasive Virus Replication.Orzalli MH, Smith A, Jurado KA, Iwasaki A, Garlick JA, Kagan JC. Mol Cell. 2018 Sep 6; 2018 Aug 9. PMID: 30100266.
- Hypercapnia increases airway smooth muscle contractility via caspase-7-mediated miR-133a-RhoA signaling.Shigemura M, Lecuona E, Angulo M, Homma T, Rodríguez DA, Gonzalez-Gonzalez FJ, Welch LC, Amarelle L, Kim SJ, Kaminski N, Budinger GRS, Solway J, Sznajder JI. Sci Transl Med. 2018 Sep 5. PMID: 30185650.
- Debugging the genetic code: non-viral in vivo delivery of therapeutic genome editing technologies.Piotrowski-Daspit AS, Glaze PM, Saltzman WM. Curr Opin Biomed Eng. 2018 Sep; 2018 Aug 21. PMID: 30984891.
- Pre-mRNA modifications and their role in nuclear processing.Martinez NM, Gilbert WV. Quant Biol. 2018 Sep; 2018 Sep 4. PMID: 30533247.
- A single-point mutation in the RNA-binding protein 6 generates Trypanosoma brucei metacyclics that are able to progress to bloodstream forms in vitro.Shi H, Butler K, Tschudi C. Mol Biochem Parasitol. 2018 Sep; 2018 Jul 25. PMID: 30055184.
- Oligosaccharyltransferase Inhibition Overcomes Therapeutic Resistance to EGFR Tyrosine Kinase Inhibitors.Lopez Sambrooks C, Baro M, Quijano A, Narayan A, Cui W, Greninger P, Egan R, Patel A, Benes CH, Saltzman WM, Contessa JN. Cancer Res. 2018 Sep 1; 2018 Jul 19. PMID: 30026325.
- Biodegradable PEG-poly(ω-pentadecalactone-co-p-dioxanone) nanoparticles for enhanced and sustained drug delivery to treat brain tumors.Chen EM, Quijano AR, Seo YE, Jackson C, Josowitz AD, Noorbakhsh S, Merlettini A, Sundaram RK, Focarete ML, Jiang Z, Bindra RS, Saltzman WM. Biomaterials. 2018 Sep; 2018 Jun 18. PMID: 29936153.
- A "top-down" approach to actuate poly(amine-co-ester) terpolymers for potent and safe mRNA delivery.Jiang Y, Gaudin A, Zhang J, Agarwal T, Song E, Kauffman AC, Tietjen GT, Wang Y, Jiang Z, Cheng CJ, Saltzman WM. Biomaterials. 2018 Sep; 2018 May 25. PMID: 29879653.
- β-Hydroxybutyrate protects from alcohol-induced liver injury via a Hcar2-cAMP dependent pathway.Chen Y, Ouyang X, Hoque R, Garcia-Martinez I, Yousaf MN, Tonack S, Offermanns S, Dubuquoy L, Louvet A, Mathurin P, Massey V, Schnabl B, Bataller RA, Mehal WZ. J Hepatol. 2018 Sep; 2018 Apr 27. PMID: 29705237.
- Posttranscriptional regulation of lipid metabolism by non-coding RNAs and RNA binding proteins.Singh AK, Aryal B, Zhang X, Fan Y, Price NL, Suárez Y, Fernández-Hernando C. Semin Cell Dev Biol. 2018 Sep; 2017 Dec 6. PMID: 29183708.
- Blood Relatives: Splicing Mechanisms underlying Erythropoiesis in Health and Disease.Reimer KA, Neugebauer KM. F1000Res. 2018; 2018 Aug 30. PMID: 30228869.
- Associations Among Suicidal Ideation, White Matter Integrity and Cognitive Deficit in First-Episode Schizophrenia.Long Y, Ouyang X, Liu Z, Chen X, Hu X, Lee E, Chen EYH, Pu W, Shan B, Rohrbaugh RM. Front Psychiatry. 2018; 2018 Aug 28. PMID: 30210372.
- Reply to Pandey et al.: Understanding the efficacy of a potential antiretroviral drug candidate in humanized mouse model of HIV infection.Kudalkar SN, Beloor J, Quijano E, Spasov KA, Lee WG, Cisneros JA, Saltzman WM, Kumar P, Jorgensen WL, Anderson KS. Proc Natl Acad Sci U S A. 2018 Aug 28; 2018 Aug 10. PMID: 30097540.
- Human neuroepithelial stem cell regional specificity enables spinal cord repair through a relay circuit.Dell'Anno MT, Wang X, Onorati M, Li M, Talpo F, Sekine Y, Ma S, Liu F, Cafferty WBJ, Sestan N, Strittmatter SM. Nat Commun. 2018 Aug 24; 2018 Aug 24. PMID: 30143638.
- Role of alternative splicing in hematopoietic stem cells during development.Gao Y, Vasic R, Halene S. Stem Cell Investig. 2018; 2018 Aug 23. PMID: 30221171.
- Solid phase chemistry to covalently and reversibly capture thiolated RNA.Duffy EE, Canzio D, Maniatis T, Simon MD. Nucleic Acids Res. 2018 Aug 21. PMID: 29986098.
- Lacteal junction zippering protects against diet-induced obesity.Zhang F, Zarkada G, Han J, Li J, Dubrac A, Ola R, Genet G, Boyé K, Michon P, Künzel SE, Camporez JP, Singh AK, Fong GH, Simons M, Tso P, Fernández-Hernando C, Shulman GI, Sessa WC, Eichmann A. Science. 2018 Aug 10. PMID: 30093598.
- WNT5a in Extracellular Vesicles - A New Frontier for Pulmonary Fibrosis.Ahangari F, Kaminski N. Am J Respir Crit Care Med. 2018 Aug 9; 2018 Aug 9. PMID: 30092145.
- The CeNGEN Project: The Complete Gene Expression Map of an Entire Nervous System.Hammarlund M, Hobert O, Miller DM 3rd, Sestan N. Neuron. 2018 Aug 8. PMID: 30092212.
- Critical role of CD4(+) T cells and IFNγ signaling in antibody-mediated resistance to Zika virus infection.Lucas CGO, Kitoko JZ, Ferreira FM, Suzart VG, Papa MP, Coelho SVA, Cavazzoni CB, Paula-Neto HA, Olsen PC, Iwasaki A, Pereira RM, Pimentel-Coelho PM, Vale AM, de Arruda LB, Bozza MT. Nat Commun. 2018 Aug 7; 2018 Aug 7. PMID: 30087337.
- KDM5 histone demethylases repress immune response via suppression of STING.Wu L, Cao J, Cai WL, Lang SM, Horton JR, Jansen DJ, Liu ZZ, Chen JF, Zhang M, Mott BT, Pohida K, Rai G, Kales SC, Henderson MJ, Hu X, Jadhav A, Maloney DJ, Simeonov A, Zhu S, Iwasaki A, Hall MD, Cheng X, Shadel GS, Yan Q. PLoS Biol. 2018 Aug; 2018 Aug 6. PMID: 30080846.
- RNA m(6)A modification and its function in diseases.Tong J, Flavell RA, Li HB. Front Med. 2018 Aug; 2018 Aug 10. PMID: 30097961.
- Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ. Nat Struct Mol Biol. 2018 Aug; 2018 Jul 30. PMID: 30061596.
- miR-221/222 activate the Wnt/β-catenin signaling to promote triple-negative breast cancer.Liu S, Wang Z, Liu Z, Shi S, Zhang Z, Zhang J, Lin H. J Mol Cell Biol. 2018 Aug 1. PMID: 30053090.
- Krebs-cycle-deficient hereditary cancer syndromes are defined by defects in homologous-recombination DNA repair.Sulkowski PL, Sundaram RK, Oeck S, Corso CD, Liu Y, Noorbakhsh S, Niger M, Boeke M, Ueno D, Kalathil AN, Bao X, Li J, Shuch B, Bindra RS, Glazer PM. Nat Genet. 2018 Aug; 2018 Jul 16. PMID: 30013182.
- Reducing protein oxidation reverses lung fibrosis.Anathy V, Lahue KG, Chapman DG, Chia SB, Casey DT, Aboushousha R, van der Velden JLJ, Elko E, Hoffman SM, McMillan DH, Jones JT, Nolin JD, Abdalla S, Schneider R, Seward DJ, Roberson EC, Liptak MD, Cousins ME, Butnor KJ, Taatjes DJ, Budd RC, Irvin CG, Ho YS, Hakem R, Brown KK, Matsui R, Bachschmid MM, Gomez JL, Kaminski N, van der Vliet A, Janssen-Heininger YMW. Nat Med. 2018 Aug; 2018 Jul 9. PMID: 29988126.
- Active mTORC2 Signaling in Naive T Cells Suppresses Bone Marrow Homing by Inhibiting CXCR4 Expression.Arojo OA, Ouyang X, Liu D, Meng T, Kaech SM, Pereira JP, Su B. J Immunol. 2018 Aug 1; 2018 Jun 22. PMID: 29934471.
- Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions.Barber KW, Muir P, Szeligowski RV, Rogulina S, Gerstein M, Sampson JR, Isaacs FJ, Rinehart J. Nat Biotechnol. 2018 Aug; 2018 Jun 11. PMID: 29889213.
- PTEN Regulates Nonhomologous End Joining By Epigenetic Induction of NHEJ1/XLF.Sulkowski PL, Scanlon SE, Oeck S, Glazer PM. Mol Cancer Res. 2018 Aug; 2018 May 8. PMID: 29739874.
- Concise Review: Bipotent Megakaryocytic-Erythroid Progenitors: Concepts and Controversies.Xavier-Ferrucio J, Krause DS. Stem Cells. 2018 Aug; 2018 May 2. PMID: 29658164.
- S100A12 as a marker of worse cardiac output and mortality in pulmonary hypertension.Tzouvelekis A, Herazo-Maya JD, Ryu C, Chu JH, Zhang Y, Gibson KF, Adonteng-Boateng PK, Li Q, Pan H, Cherry B, Ahmad F, Ford HJ, Herzog EL, Kaminski N, Fares WH. Respirology. 2018 Aug; 2018 Apr 2. PMID: 29611244.
- Fibrosis: Lessons from OMICS analyses of the human lung.Yu G, Ibarra GH, Kaminski N. Matrix Biol. 2018 Aug; 2018 Mar 19. PMID: 29567123.
- The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. Cell. 2018 Jul 26. PMID: 30053424.
- T cell LFA-1-induced proinflammatory mRNA stabilization is mediated by the p38 pathway kinase MK2 in a process regulated by hnRNPs C, H1 and K.Rao GK, Wong A, Collinge M, Sarhan J, Yarovinsky TO, Ramgolam VS, Gaestel M, Pardi R, Bender JR. PLoS One. 2018; 2018 Jul 26. PMID: 30048492.
- Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.van Dijk D, Sharma R, Nainys J, Yim K, Kathail P, Carr AJ, Burdziak C, Moon KR, Chaffer CL, Pattabiraman D, Bierie B, Mazutis L, Wolf G, Krishnaswamy S, Pe'er D. Cell. 2018 Jul 26; 2018 Jun 28. PMID: 29961576.
- Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors.Yang Y, Kang D, Nguyen LA, Smithline ZB, Pannecouque C, Zhan P, Liu X, Steitz TA. Elife. 2018 Jul 25; 2018 Jul 25. PMID: 30044217.
- Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9.Ye L, Wang C, Hong L, Sun N, Chen D, Chen S, Han F. Cell Discov. 2018; 2018 Jul 24. PMID: 30062046.
- A protein that controls the onset of a Salmonella virulence program.Yeom J, Pontes MH, Choi J, Groisman EA. EMBO J. 2018 Jul 13; 2018 Jun 1. PMID: 29858228.
- A role for telomere length and chromosomal damage in idiopathic pulmonary fibrosis.McDonough JE, Martens DS, Tanabe N, Ahangari F, Verleden SE, Maes K, Verleden GM, Kaminski N, Hogg JC, Nawrot TS, Wuyts WA, Vanaudenaerde BM. Respir Res. 2018 Jul 9; 2018 Jul 9. PMID: 29986708.
- KBase: The United States Department of Energy Systems Biology Knowledgebase.Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. Nat Biotechnol. 2018 Jul 6. PMID: 29979655.
- RES complex is associated with intron definition and required for zebrafish early embryogenesis.Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ. PLoS Genet. 2018 Jul; 2018 Jul 3. PMID: 29969449.
- Error-prone protein synthesis in parasites with the smallest eukaryotic genome.Melnikov SV, Rivera KD, Ostapenko D, Makarenko A, Sanscrainte ND, Becnel JJ, Solomon MJ, Texier C, Pappin DJ, Söll D. Proc Natl Acad Sci U S A. 2018 Jul 3; 2018 Jun 18. PMID: 29915081.
- A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex.Harris KA, Zhou Z, Peters ML, Wilkins SG, Breaker RR. Proc Natl Acad Sci U S A. 2018 Jul 3; 2018 Jun 18. PMID: 29915070.
- Large Noncoding RNAs in Bacteria.Harris KA, Breaker RR. Microbiol Spectr. 2018 Jul. PMID: 29992899.
- Long-read sequencing of nascent RNA reveals coupling among RNA processing events.Herzel L, Straube K, Neugebauer KM. Genome Res. 2018 Jul; 2018 Jun 14. PMID: 29903723.
- Focus on Fundamentals: Achieving Effective Nanoparticle Targeting.Tietjen GT, Bracaglia LG, Saltzman WM, Pober JS. Trends Mol Med. 2018 Jul; 2018 Jun 5. PMID: 29884540.
- IL-10 Receptor Signaling Empowers Regulatory T Cells to Control Th17 Responses and Protect from GN.Diefenhardt P, Nosko A, Kluger MA, Richter JV, Wegscheid C, Kobayashi Y, Tiegs G, Huber S, Flavell RA, Stahl RAK, Steinmetz OM. J Am Soc Nephrol. 2018 Jul; 2018 Jun 4. PMID: 29866800.
- Kaposi's Sarcoma-Associated Herpesvirus mRNA Accumulation in Nuclear Foci Is Influenced by Viral DNA Replication and Viral Noncoding Polyadenylated Nuclear RNA.Vallery TK, Withers JB, Andoh JA, Steitz JA. J Virol. 2018 Jul 1; 2018 Jun 13. PMID: 29643239.
- Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life.Melnikov S, Manakongtreecheep K, Söll D. Mol Biol Evol. 2018 Jul 1. PMID: 29529322.
- Association between migrant worker experience, limitations on insurance coverage, and hospitalization for schizophrenia in Hunan Province, China.Zhu Y, Hu X, Yang B, Wu G, Wang Z, Xue Z, Shi J, Ouyang X, Liu Z, Rosenheck R. Schizophr Res. 2018 Jul; 2017 Nov 28. PMID: 29195746.
- Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin.Murthy T, Bluemn T, Gupta AK, Reimer M Jr, Rao S, Pillai MM, Minella AC. J Biol Chem. 2018 Jun 29; 2018 May 15. PMID: 29764937.
- Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development.Stefanski HE, Xing Y, Taylor PA, Maio S, Henao-Meija J, Williams A, Flavell RA, Hollander GA, Blazar BR. PLoS One. 2018; 2018 Jun 27. PMID: 29949604.
- Caution needs to be taken when assigning transcription start sites to ends of protein-coding genes: a rebuttal.Sabath N, Vilborg A, Steitz JA, Shalgi R. Hum Genomics. 2018 Jun 27; 2018 Jun 27. PMID: 29945683.
- In utero nanoparticle delivery for site-specific genome editing.Ricciardi AS, Bahal R, Farrelly JS, Quijano E, Bianchi AH, Luks VL, Putman R, López-Giráldez F, Coşkun S, Song E, Liu Y, Hsieh WC, Ly DH, Stitelman DH, Glazer PM, Saltzman WM. Nat Commun. 2018 Jun 26; 2018 Jun 26. PMID: 29946143.
- Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.Harmanci A, Gerstein M. Nat Commun. 2018 Jun 22; 2018 Jun 22. PMID: 29934598.
- Parallel Evolution of Host-Attachment Proteins in Phage PP01 Populations Adapting to Escherichia coli O157:H7.Akusobi C, Chan BK, Williams ESCP, Wertz JE, Turner PE. Pharmaceuticals (Basel). 2018 Jun 20; 2018 Jun 20. PMID: 29925767.
- Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.Lin J, Zhou D, Steitz TA, Polikanov YS, Gagnon MG. Annu Rev Biochem. 2018 Jun 20; 2018 Mar 23. PMID: 29570352.
- A critical role for nucleoporin 358 (Nup358) in transposon silencing and piRNA biogenesis in Drosophila.Parikh RY, Lin H, Gangaraju VK. J Biol Chem. 2018 Jun 15; 2018 May 7. PMID: 29735528.
- [A facile method for producing selenocysteine-containing proteins].Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. Angew Chem Weinheim Bergstr Ger. 2018 Jun 11; 2018 Apr 6. PMID: 30002564.
- A Facile Method for Producing Selenocysteine-Containing Proteins.Mukai T, Sevostyanova A, Suzuki T, Fu X, Söll D. Angew Chem Int Ed Engl. 2018 Jun 11; 2018 May 9. PMID: 29631320.
- Regulation of C-C chemokine receptor 5 (CCR5) stability by Lys(197) and by transmembrane protein aptamers that target it for lysosomal degradation.Petti LM, Marlatt SA, Luo Y, Scheideman EH, Shelar A, DiMaio D. J Biol Chem. 2018 Jun 8; 2018 Apr 20. PMID: 29678881.
- CLOCK phosphorylation by AKT regulates its nuclear accumulation and circadian gene expression in peripheral tissues.Luciano AK, Zhou W, Santana JM, Kyriakides C, Velazquez H, Sessa WC. J Biol Chem. 2018 Jun 8; 2018 Mar 27. PMID: 29588368.
- Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.Knappenberger AJ, Reiss CW, Strobel SA. Elife. 2018 Jun 7; 2018 Jun 7. PMID: 29877798.
- Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems.Sherlock ME, Sudarsan N, Breaker RR. Proc Natl Acad Sci U S A. 2018 Jun 5; 2018 May 21. PMID: 29784782.
- Chikungunya virus evolution following a large 3'UTR deletion results in host-specific molecular changes in protein-coding regions.Morley VJ, Noval MG, Chen R, Weaver SC, Vignuzzi M, Stapleford KA, Turner PE. Virus Evol. 2018 Jan; 2018 Jun 4. PMID: 29942653.
- Leadership Primer for Current and Aspiring Pulmonary, Critical Care, and Sleep Medicine Academic Division Chiefs.Nguyen HB, Thomson CC, Kaminski N, Schnapp LM, Madison JM, Glenny RW, Dixon AE. Ann Am Thorac Soc. 2018 Jun. PMID: 29485911.
- The Psychiatry Major: A Curricular Innovation to Improve Undergraduate Psychiatry Education in China.Jing L, Chang WC, Rohrbaugh R, Ouyang X, Chen E, Liu Z, Hu X. Acad Psychiatry. 2018 Jun; 2017 Jun 2. PMID: 28577115.
- Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis.Frankowski KJ, Wang C, Patnaik S, Schoenen FJ, Southall N, Li D, Teper Y, Sun W, Kandela I, Hu D, Dextras C, Knotts Z, Bian Y, Norton J, Titus S, Lewandowska MA, Wen Y, Farley KI, Griner LM, Sultan J, Meng Z, Zhou M, Vilimas T, Powers AS, Kozlov S, Nagashima K, Quadri HS, Fang M, Long C, Khanolkar O, Chen W, Kang J, Huang H, Chow E, Goldberg E, Feldman C, Xi R, Kim HR, Sahagian G, Baserga SJ, Mazar A, Ferrer M, Zheng W, Shilatifard A, Aubé J, Rudloff U, Marugan JJ, Huang S. Sci Transl Med. 2018 May 16. PMID: 29769289.
- Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion.Chow RD, Kim HR, Chen S. Nat Commun. 2018 May 15; 2018 May 15. PMID: 29765043.
- The aging lung: tissue telomere shortening in health and disease.Everaerts S, Lammertyn EJ, Martens DS, De Sadeleer LJ, Maes K, van Batenburg AA, Goldschmeding R, van Moorsel CHM, Dupont LJ, Wuyts WA, Vos R, Gayan-Ramirez G, Kaminski N, Hogg JC, Janssens W, Verleden GM, Nawrot TS, Verleden SE, McDonough JE, Vanaudenaerde BM. Respir Res. 2018 May 11; 2018 May 11. PMID: 29751799.
- Gene expression kinetics governs stimulus-specific decoration of the Salmonella outer membrane.Hong X, Chen HD, Groisman EA. Sci Signal. 2018 May 8; 2018 May 8. PMID: 29739882.
- Reduction in adaptor amounts establishes degradation hierarchy among protease substrates.Yeom J, Gao X, Groisman EA. Proc Natl Acad Sci U S A. 2018 May 8; 2018 Apr 23. PMID: 29686082.
- The interaction between IKKα and LC3 promotes type I interferon production through the TLR9-containing LAPosome.Hayashi K, Taura M, Iwasaki A. Sci Signal. 2018 May 1; 2018 May 1. PMID: 29717061.
- Cancer CRISPR Screens In Vivo.Chow RD, Chen S. Trends Cancer. 2018 May; 2018 Mar 30. PMID: 29709259.
- Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner.Gopinath S, Kim MV, Rakib T, Wong PW, van Zandt M, Barry NA, Kaisho T, Goodman AL, Iwasaki A. Nat Microbiol. 2018 May; 2018 Apr 9. PMID: 29632368.
- Brown adipose tissue derived ANGPTL4 controls glucose and lipid metabolism and regulates thermogenesis.Singh AK, Aryal B, Chaube B, Rotllan N, Varela L, Horvath TL, Suárez Y, Fernández-Hernando C. Mol Metab. 2018 May; 2018 Mar 29. PMID: 29627378.
- MicroRNAs in endothelial cell homeostasis and vascular disease.Fernández-Hernando C, Suárez Y. Curr Opin Hematol. 2018 May. PMID: 29547400.
- Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux.Saffer AM, Irish VF. Plant J. 2018 May; 2018 Apr 6. PMID: 29505161.
- Dynamics and Function of Nuclear Bodies during Embryogenesis.Arias Escayola D, Neugebauer KM. Biochemistry. 2018 May 1; 2018 Mar 7. PMID: 29473743.
- P-Bodies: Composition, Properties, and Functions.Luo Y, Na Z, Slavoff SA. Biochemistry. 2018 May 1; 2018 Jan 30. PMID: 29381060.
- Surfactant protein C dampens inflammation by decreasing JAK/STAT activation during lung repair.Jin H, Ciechanowicz AK, Kaplan AR, Wang L, Zhang PX, Lu YC, Tobin RE, Tobin BA, Cohn L, Zeiss CJ, Lee PJ, Bruscia EM, Krause DS. Am J Physiol Lung Cell Mol Physiol. 2018 May 1; 2018 Jan 18. PMID: 29345196.
- An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ. Nat Genet. 2018 Apr 26; 2018 Apr 26. PMID: 29700473.
- A comprehensive catalog of predicted functional upstream open reading frames in humans.McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M. Nucleic Acids Res. 2018 Apr 20. PMID: 29562350.
- Antigen-mediated regulation in monoclonal gammopathies and myeloma.Nair S, Sng J, Boddupalli CS, Seckinger A, Chesi M, Fulciniti M, Zhang L, Rauniyar N, Lopez M, Neparidze N, Parker T, Munshi NC, Sexton R, Barlogie B, Orlowski R, Bergsagel L, Hose D, Flavell RA, Mistry PK, Meffre E, Dhodapkar MV. JCI Insight. 2018 Apr 19; 2018 Apr 19. PMID: 29669929.
- NLRP6 and Dysbiosis: Avoiding the Luring Attraction of Over-Simplification.Elinav E, Henao-Mejia J, Strowig T, Flavell R. Immunity. 2018 Apr 17. PMID: 29669238.
- KLRG1(+) Effector CD8(+) T Cells Lose KLRG1, Differentiate into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity.Herndler-Brandstetter D, Ishigame H, Shinnakasu R, Plajer V, Stecher C, Zhao J, Lietzenmayer M, Kroehling L, Takumi A, Kometani K, Inoue T, Kluger Y, Kaech SM, Kurosaki T, Okada T, Flavell RA. Immunity. 2018 Apr 17; 2018 Apr 3. PMID: 29625895.
- Functional Genome-wide Screen Identifies Pathways Restricting Central Nervous System Axonal Regeneration.Sekine Y, Lin-Moore A, Chenette DM, Wang X, Jiang Z, Cafferty WB, Hammarlund M, Strittmatter SM. Cell Rep. 2018 Apr 10. PMID: 29642001.
- Enzymatic synthesis of cyclic dinucleotide analogs by a promiscuous cyclic-AMP-GMP synthetase and analysis of cyclic dinucleotide responsive riboswitches.Launer-Felty KD, Strobel SA. Nucleic Acids Res. 2018 Apr 6. PMID: 29514227.
- Early emergence of cortical interneuron diversity in the mouse embryo.Mi D, Li Z, Lim L, Li M, Moissidis M, Yang Y, Gao T, Hu TX, Pratt T, Price DJ, Sestan N, Marín O. Science. 2018 Apr 6; 2018 Feb 22. PMID: 29472441.
- Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis.Vukmirovic M, Kaminski N. Front Med (Lausanne). 2018; 2018 Apr 4. PMID: 29670881.
- Small Cell Variant of Intravascular Large B-Cell Lymphoma: Highlighting a Potentially Fatal and Easily Missed Diagnosis.Rahmani M, Halene S, Xu ML. Biomed Res Int. 2018; 2018 Apr 3. PMID: 29850589.
- ZEB1, ZEB2, and the miR-200 family form a counterregulatory network to regulate CD8(+) T cell fates.Guan T, Dominguez CX, Amezquita RA, Laidlaw BJ, Cheng J, Henao-Mejia J, Williams A, Flavell RA, Lu J, Kaech SM. J Exp Med. 2018 Apr 2; 2018 Feb 15. PMID: 29449309.
- Emerging Roles for the Nucleolus 2017.Baserga SJ, DiMario PJ. Mol Biol Cell. 2018 Apr 1. PMID: 31917828.
- Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Genome Res. 2018 Apr; 2018 Mar 21. PMID: 29563166.
- Endothelial Cell Autonomous Role of Akt1: Regulation of Vascular Tone and Ischemia-Induced Arteriogenesis.Lee MY, Gamez-Mendez A, Zhang J, Zhuang Z, Vinyard DJ, Kraehling J, Velazquez H, Brudvig GW, Kyriakides TR, Simons M, Sessa WC. Arterioscler Thromb Vasc Biol. 2018 Apr; 2018 Feb 15. PMID: 29449333.
- Reciprocal Connections Between Cortex and Thalamus Contribute to Retinal Axon Targeting to Dorsal Lateral Geniculate Nucleus.Diao Y, Cui L, Chen Y, Burbridge TJ, Han W, Wirth B, Sestan N, Crair MC, Zhang J. Cereb Cortex. 2018 Apr 1. PMID: 28334242.
- Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids.Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG, Thomas PM, Majewska NI, Chen CX, Marcum RD, Weiss MG, Stoddart AE, Amiram M, Ranji Charna AK, Patel JR, Isaacs FJ, Kelleher NL, Hong SH, Jewett MC. Nat Commun. 2018 Mar 23; 2018 Mar 23. PMID: 29572528.
- Absence of ANGPTL4 in adipose tissue improves glucose tolerance and attenuates atherogenesis.Aryal B, Singh AK, Zhang X, Varela L, Rotllan N, Goedeke L, Chaube B, Camporez JP, Vatner DF, Horvath TL, Shulman GI, Suárez Y, Fernández-Hernando C. JCI Insight. 2018 Mar 22; 2018 Mar 22. PMID: 29563332.
- FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. Genome Biol. 2018 Mar 20; 2018 Mar 20. PMID: 29559002.
- Critical challenges and emerging opportunities in hepatitis C virus research in an era of potent antiviral therapy: Considerations for scientists and funding agencies.Bartenschlager R, Baumert TF, Bukh J, Houghton M, Lemon SM, Lindenbach BD, Lohmann V, Moradpour D, Pietschmann T, Rice CM, Thimme R, Wakita T. Virus Res. 2018 Mar 15; 2018 Mar 2. PMID: 29477639.
- Molecular basis for sterol transport by StART-like lipid transfer domains.Horenkamp FA, Valverde DP, Nunnari J, Reinisch KM. EMBO J. 2018 Mar 15; 2018 Feb 21. PMID: 29467216.
- MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.Lochovsky L, Zhang J, Gerstein M. Bioinformatics. 2018 Mar 15. PMID: 29121169.
- iDREM: Interactive visualization of dynamic regulatory networks.Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. PLoS Comput Biol. 2018 Mar; 2018 Mar 14. PMID: 29538379.
- Interactions between the Hepatitis C Virus Nonstructural 2 Protein and Host Adaptor Proteins 1 and 4 Orchestrate Virus Release.Xiao F, Wang S, Barouch-Bentov R, Neveu G, Pu S, Beer M, Schor S, Kumar S, Nicolaescu V, Lindenbach BD, Randall G, Einav S. mBio. 2018 Mar 13; 2018 Mar 13. PMID: 29535204.
- Expanded cellular clones carrying replication-competent HIV-1 persist, wax, and wane.Wang Z, Gurule EE, Brennan TP, Gerold JM, Kwon KJ, Hosmane NN, Kumar MR, Beg SA, Capoferri AA, Ray SC, Ho YC, Hill AL, Siliciano JD, Siliciano RF. Proc Natl Acad Sci U S A. 2018 Mar 13; 2018 Feb 26. PMID: 29483265.
- Peptide Nucleic Acids as a Tool for Site-Specific Gene Editing.Ricciardi AS, Quijano E, Putman R, Saltzman WM, Glazer PM. Molecules. 2018 Mar 11; 2018 Mar 11. PMID: 29534473.
- Phage treatment of an aortic graft infected with Pseudomonas aeruginosa.Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Evol Med Public Health. 2018; 2018 Mar 8. PMID: 29588855.
- An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm.Lino Cardenas CL, Kessinger CW, Cheng Y, MacDonald C, MacGillivray T, Ghoshhajra B, Huleihel L, Nuri S, Yeri AS, Jaffer FA, Kaminski N, Ellinor P, Weintraub NL, Malhotra R, Isselbacher EM, Lindsay ME. Nat Commun. 2018 Mar 8; 2018 Mar 8. PMID: 29520069.
- The hypoxic tumor microenvironment in vivo selects the cancer stem cell fate of breast cancer cells.Kim H, Lin Q, Glazer PM, Yun Z. Breast Cancer Res. 2018 Mar 6; 2018 Mar 6. PMID: 29510720.
- Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria.Sherlock ME, Sudarsan N, Stav S, Breaker RR. Elife. 2018 Mar 5; 2018 Mar 5. PMID: 29504937.
- Challenges of ligand identification for the second wave of orphan riboswitch candidates.Greenlee EB, Stav S, Atilho RM, Brewer KI, Harris KA, Malkowski SN, Mirihana Arachchilage G, Perkins KR, Sherlock ME, Breaker RR. RNA Biol. 2018 Mar 4; 2018 Feb 1. PMID: 29135333.
- SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities to SAM-III riboswitches.Mirihana Arachchilage G, Sherlock ME, Weinberg Z, Breaker RR. RNA Biol. 2018 Mar 4; 2018 Feb 12. PMID: 29106323.
- Epigenetic and Epitranscriptomic Factors Make a Mark on Hematopoietic Stem Cell Development.Kasper DM, Nicoli S. Curr Stem Cell Rep. 2018 Mar; 2018 Feb 3. PMID: 29910999.
- RNA tales - how embryos read and discard messages from mom.Despic V, Neugebauer KM. J Cell Sci. 2018 Mar 1; 2018 Mar 1. PMID: 29467249.
- Evolution of mutualism from parasitism in experimental virus populations.Shapiro JW, Turner PE. Evolution. 2018 Mar. PMID: 29380361.
- TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding.Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. Nat Methods. 2018 Mar; 2018 Jan 22. PMID: 29355846.
- The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH. Genetics. 2018 Mar; 2017 Dec 28. PMID: 29284660.
- Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening.Wang G, Chow RD, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ, Chen S. Sci Adv. 2018 Feb; 2018 Feb 28. PMID: 29503867.
- Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP. Cell Syst. 2018 Feb 28; 2018 Jan 17. PMID: 29361466.
- Generalized Growth of Estuarine, Household and Clinical Isolates of Pseudomonas aeruginosa.Diaz KE, Remold SK, Onyiri O, Bozeman M, Raymond PA, Turner PE. Front Microbiol. 2018; 2018 Feb 27. PMID: 29599754.
- Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira.Adhikarla H, Wunder EA Jr, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Front Cell Infect Microbiol. 2018; 2018 Feb 23. PMID: 29600195.
- A minimal RNA ligand for potent RIG-I activation in living mice.Linehan MM, Dickey TH, Molinari ES, Fitzgerald ME, Potapova O, Iwasaki A, Pyle AM. Sci Adv. 2018 Feb; 2018 Feb 21. PMID: 29492454.
- Genetic Ablation of miR-33 Increases Food Intake, Enhances Adipose Tissue Expansion, and Promotes Obesity and Insulin Resistance.Price NL, Singh AK, Rotllan N, Goedeke L, Wing A, Canfrán-Duque A, Diaz-Ruiz A, Araldi E, Baldán Á, Camporez JP, Suárez Y, Rodeheffer MS, Shulman GI, de Cabo R, Fernández-Hernando C. Cell Rep. 2018 Feb 20. PMID: 29466739.
- The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5.Jin D, Wu M, Li B, Bücker B, Keil P, Zhang S, Li J, Kang D, Liu J, Dong J, Deng XW, Irish V, Wei N. PLoS Genet. 2018 Feb; 2018 Feb 20. PMID: 29462139.
- La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region.Philippe L, Vasseur JJ, Debart F, Thoreen CC. Nucleic Acids Res. 2018 Feb 16. PMID: 29244122.
- Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications.Pyzocha NK, Chen S. ACS Chem Biol. 2018 Feb 16; 2017 Dec 5. PMID: 29121460.
- How many human proteoforms are there?Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. Nat Chem Biol. 2018 Feb 14. PMID: 29443976.
- Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number.Farley-Barnes KI, McCann KL, Ogawa LM, Merkel J, Surovtseva YV, Baserga SJ. Cell Rep. 2018 Feb 13. PMID: 29444442.
- Circuit Design Features of a Stable Two-Cell System.Zhou X, Franklin RA, Adler M, Jacox JB, Bailis W, Shyer JA, Flavell RA, Mayo A, Alon U, Medzhitov R. Cell. 2018 Feb 8; 2018 Feb 1. PMID: 29398113.
- Digoxin Suppresses Pyruvate Kinase M2-Promoted HIF-1α Transactivation in Steatohepatitis.Ouyang X, Han SN, Zhang JY, Dioletis E, Nemeth BT, Pacher P, Feng D, Bataller R, Cabezas J, Stärkel P, Caballeria J, Pongratz RL, Cai SY, Schnabl B, Hoque R, Chen Y, Yang WH, Garcia-Martinez I, Wang FS, Gao B, Torok NJ, Kibbey RG, Mehal WZ. Cell Metab. 2018 Feb 6. PMID: 29414684.
- Immunoprecipitation of Tri-methylated Capped RNA.Hayes KE, Barr JA, Xie M, Steitz JA, Martinez I. Bio Protoc. 2018 Feb 5. PMID: 29527542.
- Commentary: Pitfalls in the Neuroimaging of Glioblastoma in the Era of Antiangiogenic and Immuno/Targeted Therapy.Skolnik AD, Wang S, Gopal PP, Mohan S. Front Neurol. 2018; 2018 Feb 5. PMID: 29459848.
- Distance-correlation based gene set analysis in longitudinal studies.Sun J, Herazo-Maya JD, Huang X, Kaminski N, Zhao H. Stat Appl Genet Mol Biol. 2018 Feb 5; 2018 Feb 5. PMID: 29397393.
- Effects of Heterologous tRNA Modifications on the Production of Proteins Containing Noncanonical Amino Acids.Crnković A, Vargas-Rodriguez O, Merkuryev A, Söll D. Bioengineering (Basel). 2018 Feb 2; 2018 Feb 2. PMID: 29393901.
- Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.Bae T, Tomasini L, Mariani J, Zhou B, Roychowdhury T, Franjic D, Pletikos M, Pattni R, Chen BJ, Venturini E, Riley-Gillis B, Sestan N, Urban AE, Abyzov A, Vaccarino FM. Science. 2018 Feb 2; 2017 Dec 7. PMID: 29217587.
- Time for a change: is idiopathic pulmonary fibrosis still idiopathic and only fibrotic?Wolters PJ, Blackwell TS, Eickelberg O, Loyd JE, Kaminski N, Jenkins G, Maher TM, Molina-Molina M, Noble PW, Raghu G, Richeldi L, Schwarz MI, Selman M, Wuyts WA, Schwartz DA. Lancet Respir Med. 2018 Feb. PMID: 29413083.
- m(6)A mRNA methylation sustains Treg suppressive functions.Tong J, Cao G, Zhang T, Sefik E, Amezcua Vesely MC, Broughton JP, Zhu S, Li H, Li B, Chen L, Chang HY, Su B, Flavell RA, Li HB. Cell Res. 2018 Feb; 2018 Jan 5. PMID: 29303144.
- Photo-Crosslinkable Unnatural Amino Acids Enable Facile Synthesis of Thermoresponsive Nano- to Microgels of Intrinsically Disordered Polypeptides.Costa SA, Simon JR, Amiram M, Tang L, Zauscher S, Brustad EM, Isaacs FJ, Chilkoti A. Adv Mater. 2018 Feb; 2017 Dec 11. PMID: 29226470.
- The Germline-Specific Factor OEF-1 Facilitates Coordinated Progression Through Germ Cell Development in Caenorhabditis elegans.McManus CE, Reinke V. Genetics. 2018 Feb; 2017 Nov 22. PMID: 29167199.
- Antiviral CD8 T cells induce Zika-virus-associated paralysis in mice.Jurado KA, Yockey LJ, Wong PW, Lee S, Huttner AJ, Iwasaki A. Nat Microbiol. 2018 Feb; 2017 Nov 20. PMID: 29158604.
- Harnessing the power of regulatory T-cells to control autoimmune diabetes: overview and perspective.Yu H, Paiva R, Flavell RA. Immunology. 2018 Feb; 2017 Dec 11. PMID: 29155454.
- An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron.Zhao C, Liu F, Pyle AM. RNA. 2018 Feb; 2017 Nov 6. PMID: 29109157.
- Novel evidence for a PIWI-interacting RNA (piRNA) as an oncogenic mediator of disease progression, and a potential prognostic biomarker in colorectal cancer.Weng W, Liu N, Toiyama Y, Kusunoki M, Nagasaka T, Fujiwara T, Wei Q, Qin H, Lin H, Ma Y, Goel A. Mol Cancer. 2018 Jan 30; 2018 Jan 30. PMID: 29382334.
- From in silico hit to long-acting late-stage preclinical candidate to combat HIV-1 infection.Kudalkar SN, Beloor J, Quijano E, Spasov KA, Lee WG, Cisneros JA, Saltzman WM, Kumar P, Jorgensen WL, Anderson KS. Proc Natl Acad Sci U S A. 2018 Jan 23; 2017 Dec 26. PMID: 29279368.
- Caveolin-1 regulates lipid droplet metabolism in endothelial cells via autocrine prostacyclin-stimulated, cAMP-mediated lipolysis.Kuo A, Lee MY, Yang K, Gross RW, Sessa WC. J Biol Chem. 2018 Jan 19; 2017 Dec 4. PMID: 29203526.
- Recovery of Infectious Hepatitis C Virus From Injection Paraphernalia: Implications for Prevention Programs Serving People Who Inject Drugs.Heimer R, Binka M, Koester S, Grund JC, Patel A, Paintsil E, Lindenbach BD. J Infect Dis. 2018 Jan 17. PMID: 28968665.
- Oxysterol Sensing through the Receptor GPR183 Promotes the Lymphoid-Tissue-Inducing Function of Innate Lymphoid Cells and Colonic Inflammation.Emgård J, Kammoun H, García-Cassani B, Chesné J, Parigi SM, Jacob JM, Cheng HW, Evren E, Das S, Czarnewski P, Sleiers N, Melo-Gonzalez F, Kvedaraite E, Svensson M, Scandella E, Hepworth MR, Huber S, Ludewig B, Peduto L, Villablanca EJ, Veiga-Fernandes H, Pereira JP, Flavell RA, Willinger T. Immunity. 2018 Jan 16. PMID: 29343433.
- Engineering posttranslational proofreading to discriminate nonstandard amino acids.Kunjapur AM, Stork DA, Kuru E, Vargas-Rodriguez O, Landon M, Söll D, Church GM. Proc Natl Acad Sci U S A. 2018 Jan 16; 2018 Jan 4. PMID: 29301968.
- Correction for Gyrd-Hansen et al., "Apoptosome-Independent Activation of the Lysosomal Cell Death Pathway by Caspase-9".Gyrd-Hansen M, Farkas T, Fehrenbacher N, Bastholm L, Høyer-Hansen M, Elling F, Wallach D, Flavell R, Kroemer G, Nylandsted J, Jäättelä M. Mol Cell Biol. 2018 Jan 15; 2017 Dec 29. PMID: 29288151.
- Suppression of homology-dependent DNA double-strand break repair induces PARP inhibitor sensitivity in VHL-deficient human renal cell carcinoma.Scanlon SE, Hegan DC, Sulkowski PL, Glazer PM. Oncotarget. 2018 Jan 12; 2017 Dec 19. PMID: 29435132.
- Erratum: Author Correction: Successful amplification of DNA aboard the International Space Station.Boguraev AS, Christensen HC, Bonneau AR, Pezza JA, Nichols NM, Giraldez AJ, Gray MM, Wagner BM, Aken JT, Foley KD, Copeland DS, Kraves S, Saavedra EA. NPJ Microgravity. 2018; 2018 Jan 10. PMID: 29355237.
- Erratum for Barouch-Bentov et al., "Hepatitis C Virus Proteins Interact with the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery via Ubiquitination To Facilitate Viral Envelopment".Barouch-Bentov R, Neveu G, Xiao F, Beer M, Bekerman E, Schor S, Campbell J, Boonyaratanakornkit J, Lindenbach B, Lu A, Jacob Y, Einav S. mBio. 2018 Jan 9; 2018 Jan 9. PMID: 29317514.
- Reconstructing differentiation networks and their regulation from time series single-cell expression data.Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Genome Res. 2018 Jan 9; 2018 Jan 9. PMID: 29317474.
- Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein.Yuan P, D'Lima NG, Slavoff SA. Biochemistry. 2018 Jan 9; 2017 Oct 17. PMID: 29039649.
- Type I interferons instigate fetal demise after Zika virus infection.Yockey LJ, Jurado KA, Arora N, Millet A, Rakib T, Milano KM, Hastings AK, Fikrig E, Kong Y, Horvath TL, Weatherbee S, Kliman HJ, Coyne CB, Iwasaki A. Sci Immunol. 2018 Jan 5. PMID: 29305462.
- Intravenously delivered mesenchymal stem cell-derived exosomes target M2-type macrophages in the injured spinal cord.Lankford KL, Arroyo EJ, Nazimek K, Bryniarski K, Askenase PW, Kocsis JD. PLoS One. 2018; 2018 Jan 2. PMID: 29293592.
- Role of IL-10 Receptor Signaling in the Function of CD4+ T-Regulatory Type 1 cells: T-Cell Therapy in Patients with Inflammatory Bowel Disease.Soukou S, Brockmann L, Bedke T, Gagliani N, Flavell RA, Huber S. Crit Rev Immunol. 2018. PMID: 30806217.
- Transfer RNA function and evolution.O'Donoghue P, Ling J, Söll D. RNA Biol. 2018. PMID: 30099966.
- Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA(Cys) and elongation factor SelB.Vargas-Rodriguez O, Englert M, Merkuryev A, Mukai T, Söll D. RNA Biol. 2018; 2018 Jun 18. PMID: 29879865.
- Challenges of site-specific selenocysteine incorporation into proteins by Escherichia coli.Fu X, Söll D, Sevostyanova A. RNA Biol. 2018; 2018 Mar 12. PMID: 29447106.
- Protein synthesis controls phosphate homeostasis.Pontes MH, Groisman EA. Genes Dev. 2018 Jan 1; 2018 Feb 1. PMID: 29437726.
- Drugging tRNA aminoacylation.Ho JM, Bakkalbasi E, Söll D, Miller CA. RNA Biol. 2018; 2018 Feb 2. PMID: 29345185.
- Hematopoietic defects in response to reduced Arhgap21.Xavier-Ferrucio J, Ricon L, Vieira K, Longhini AL, Lazarini M, Bigarella CL, Franchi G Jr, Krause DS, Saad STO. Stem Cell Res. 2018 Jan; 2017 Nov 23. PMID: 29212046.
- Thyroid hormone inhibits lung fibrosis in mice by improving epithelial mitochondrial function.Yu G, Tzouvelekis A, Wang R, Herazo-Maya JD, Ibarra GH, Srivastava A, de Castro JPW, DeIuliis G, Ahangari F, Woolard T, Aurelien N, Arrojo E Drigo R, Gan Y, Graham M, Liu X, Homer RJ, Scanlan TS, Mannam P, Lee PJ, Herzog EL, Bianco AC, Kaminski N. Nat Med. 2018 Jan; 2017 Dec 4. PMID: 29200204.
- Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress.LeBlanc C, Zhang F, Mendez J, Lozano Y, Chatpar K, Irish VF, Jacob Y. Plant J. 2018 Jan; 2017 Dec 22. PMID: 29161464.
- NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA.Zhou T, Ren X, Adams RL, Pyle AM. J Virol. 2018 Jan 1; 2017 Dec 14. PMID: 29070684.
- The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes.Vincent NG, Charette JM, Baserga SJ. RNA. 2018 Jan; 2017 Oct 20. PMID: 29054886.
- Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Gerstein M, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, Rozowsky J, Wong DTW. Bioinformatics. 2018 Jan 1. PMID: 28961734.
- HIF-1α represses the expression of the angiogenesis inhibitor thrombospondin-2.MacLauchlan SC, Calabro NE, Huang Y, Krishna M, Bancroft T, Sharma T, Yu J, Sessa WC, Giordano F, Kyriakides TR. Matrix Biol. 2018 Jan; 2017 Aug 5. PMID: 28789925.
2017
- Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure.Gálvez EJC, Iljazovic A, Gronow A, Flavell R, Strowig T. Cell Rep. 2017 Dec 26. PMID: 29281837.
- Architecture of the human PI4KIIIα lipid kinase complex.Lees JA, Zhang Y, Oh MS, Schauder CM, Yu X, Baskin JM, Dobbs K, Notarangelo LD, De Camilli P, Walz T, Reinisch KM. Proc Natl Acad Sci U S A. 2017 Dec 26; 2017 Dec 11. PMID: 29229838.
- Therapeutic Peptide Nucleic Acids: Principles, Limitations, and Opportunities.Quijano E, Bahal R, Ricciardi A, Saltzman WM, Glazer PM. Yale J Biol Med. 2017 Dec; 2017 Dec 19. PMID: 29259523.
- The amino-terminus of the hepatitis C virus (HCV) p7 viroporin and its cleavage from glycoprotein E2-p7 precursor determine specific infectivity and secretion levels of HCV particle types.Denolly S, Mialon C, Bourlet T, Amirache F, Penin F, Lindenbach B, Boson B, Cosset FL. PLoS Pathog. 2017 Dec; 2017 Dec 18. PMID: 29253880.
- Anti-tumor Activity of miniPEG-γ-Modified PNAs to Inhibit MicroRNA-210 for Cancer Therapy.Gupta A, Quijano E, Liu Y, Bahal R, Scanlon SE, Song E, Hsieh WC, Braddock DE, Ly DH, Saltzman WM, Glazer PM. Mol Ther Nucleic Acids. 2017 Dec 15; 2017 Sep 12. PMID: 29246289.
- A Protective Function of IL-22BP in Ischemia Reperfusion and Acetaminophen-Induced Liver Injury.Kleinschmidt D, Giannou AD, McGee HM, Kempski J, Steglich B, Huber FJ, Ernst TM, Shiri AM, Wegscheid C, Tasika E, Hübener P, Huber P, Bedke T, Steffens N, Agalioti T, Fuchs T, Noll J, Lotter H, Tiegs G, Lohse AW, Axelrod JH, Galun E, Flavell RA, Gagliani N, Huber S. J Immunol. 2017 Dec 15; 2017 Nov 6. PMID: 29109123.
- Extracellular Mitochondrial DNA Is Generated by Fibroblasts and Predicts Death in Idiopathic Pulmonary Fibrosis.Ryu C, Sun H, Gulati M, Herazo-Maya JD, Chen Y, Osafo-Addo A, Brandsdorfer C, Winkler J, Blaul C, Faunce J, Pan H, Woolard T, Tzouvelekis A, Antin-Ozerkis DE, Puchalski JT, Slade M, Gonzalez AL, Bogenhagen DF, Kirillov V, Feghali-Bostwick C, Gibson K, Lindell K, Herzog RI, Dela Cruz CS, Mehal W, Kaminski N, Herzog EL, Trujillo G. Am J Respir Crit Care Med. 2017 Dec 15. PMID: 28783377.
- IRF8-dependent molecular complexes control the Th9 transcriptional program.Humblin E, Thibaudin M, Chalmin F, Derangère V, Limagne E, Richard C, Flavell RA, Chevrier S, Ladoire S, Berger H, Boidot R, Apetoh L, Végran F, Ghiringhelli F. Nat Commun. 2017 Dec 12; 2017 Dec 12. PMID: 29233972.
- Aging impairs both primary and secondary RIG-I signaling for interferon induction in human monocytes.Molony RD, Nguyen JT, Kong Y, Montgomery RR, Shaw AC, Iwasaki A. Sci Signal. 2017 Dec 12; 2017 Dec 12. PMID: 29233916.
- CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ. Nat Commun. 2017 Dec 8; 2017 Dec 8. PMID: 29222508.
- Anti-SIRPα antibody immunotherapy enhances neutrophil and macrophage antitumor activity.Ring NG, Herndler-Brandstetter D, Weiskopf K, Shan L, Volkmer JP, George BM, Lietzenmayer M, McKenna KM, Naik TJ, McCarty A, Zheng Y, Ring AM, Flavell RA, Weissman IL. Proc Natl Acad Sci U S A. 2017 Dec 5; 2017 Nov 20. PMID: 29158380.
- Nanomaterials for convection-enhanced delivery of agents to treat brain tumors.Seo YE, Bu T, Saltzman WM. Curr Opin Biomed Eng. 2017 Dec; 2017 Sep 22. PMID: 29333521.
- A multiregional proteomic survey of the postnatal human brain.Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC. Nat Neurosci. 2017 Dec; 2017 Nov 13. PMID: 29184206.
- Application of "Omics" and Systems Biology to Sarcoidosis Research.Crouser ED, Fingerlin TE, Yang IV, Maier LA, Nana-Sinkam P, Collman RG, Kaminski N. Ann Am Thorac Soc. 2017 Dec. PMID: 29053026.
- Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.Suzuki T, Miller C, Guo LT, Ho JML, Bryson DI, Wang YS, Liu DR, Söll D. Nat Chem Biol. 2017 Dec; 2017 Oct 16. PMID: 29035363.
- Continuous directed evolution of aminoacyl-tRNA synthetases.Bryson DI, Fan C, Guo LT, Miller C, Söll D, Liu DR. Nat Chem Biol. 2017 Dec; 2017 Oct 16. PMID: 29035361.
- Opposing Actions of AKT (Protein Kinase B) Isoforms in Vascular Smooth Muscle Injury and Therapeutic Response.Jin Y, Xie Y, Ostriker AC, Zhang X, Liu R, Lee MY, Leslie KL, Tang W, Du J, Lee SH, Wang Y, Sessa WC, Hwa J, Yu J, Martin KA. Arterioscler Thromb Vasc Biol. 2017 Dec; 2017 Oct 12. PMID: 29025710.
- Long-Chain Polyprenols Promote Spore Wall Formation in Saccharomyces cerevisiae.Hoffmann R, Grabińska K, Guan Z, Sessa WC, Neiman AM. Genetics. 2017 Dec; 2017 Oct 4. PMID: 28978675.
- Improved threshold selection for the determination of volume of distribution of nanoparticles administered by convection-enhanced delivery.Chi DL, Song E, Gaudin A, Saltzman WM. Comput Med Imaging Graph. 2017 Dec; 2017 Aug 24. PMID: 28927549.
- Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes.Gillen AE, Brechbuhl HM, Yamamoto TM, Kline E, Pillai MM, Hesselberth JR, Kabos P. Mol Cancer Res. 2017 Dec; 2017 Sep 14. PMID: 28912168.
- Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter.Zhang F, LeBlanc C, Irish VF, Jacob Y. Plant Cell Rep. 2017 Dec; 2017 Sep 1. PMID: 28864834.
- Lung Endothelial MicroRNA-1 Regulates Tumor Growth and Angiogenesis.Korde A, Jin L, Zhang JG, Ramaswamy A, Hu B, Kolahian S, Guardela BJ, Herazo-Maya J, Siegfried JM, Stabile L, Pisani MA, Herbst RS, Kaminski N, Elias JA, Puchalski JT, Takyar SS. Am J Respir Crit Care Med. 2017 Dec 1. PMID: 28853613.
- Navigating the Gut Buffet: Control of Polysaccharide Utilization in Bacteroides spp.Schwalm ND 3rd, Groisman EA. Trends Microbiol. 2017 Dec; 2017 Jul 18. PMID: 28733133.
- Population-averaged macaque brain atlas with high-resolution ex vivo DTI integrated into in vivo space.Feng L, Jeon T, Yu Q, Ouyang M, Peng Q, Mishra V, Pletikos M, Sestan N, Miller MI, Mori S, Hsiao S, Liu S, Huang H. Brain Struct Funct. 2017 Dec; 2017 Jun 20. PMID: 28634624.
- The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand.Zhao C, Pyle AM. Curr Opin Struct Biol. 2017 Dec; 2017 May 18. PMID: 28528306.
- Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes.Barbieri EM, Muir P, Akhuetie-Oni BO, Yellman CM, Isaacs FJ. Cell. 2017 Nov 30; 2017 Nov 16. PMID: 29153834.
- Nanoparticle targeting to the endothelium during normothermic machine perfusion of human kidneys.Tietjen GT, Hosgood SA, DiRito J, Cui J, Deep D, Song E, Kraehling JR, Piotrowski-Daspit AS, Kirkiles-Smith NC, Al-Lamki R, Thiru S, Bradley JA, Saeb-Parsy K, Bradley JR, Nicholson ML, Saltzman WM, Pober JS. Sci Transl Med. 2017 Nov 29. PMID: 29187644.
- Molecular and cellular reorganization of neural circuits in the human lineage.Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N. Science. 2017 Nov 24. PMID: 29170230.
- Integrin alpha 11 in the regulation of the myofibroblast phenotype: implications for fibrotic diseases.Bansal R, Nakagawa S, Yazdani S, van Baarlen J, Venkatesh A, Koh AP, Song WM, Goossens N, Watanabe H, Beasley MB, Powell CA, Storm G, Kaminski N, van Goor H, Friedman SL, Hoshida Y, Prakash J. Exp Mol Med. 2017 Nov 17; 2017 Nov 17. PMID: 29147013.
- Structural basis of bacterial transcription activation.Liu B, Hong C, Huang RK, Yu Z, Steitz TA. Science. 2017 Nov 17. PMID: 29146813.
- Successful amplification of DNA aboard the International Space Station.Boguraev AS, Christensen HC, Bonneau AR, Pezza JA, Nichols NM, Giraldez AJ, Gray MM, Wagner BM, Aken JT, Foley KD, Copeland DS, Kraves S, Alvarez Saavedra E. NPJ Microgravity. 2017; 2017 Nov 16. PMID: 29167819.
- A cell-penetrating antibody inhibits human RAD51 via direct binding.Turchick A, Hegan DC, Jensen RB, Glazer PM. Nucleic Acids Res. 2017 Nov 16. PMID: 29036688.
- Serum Matrix Metalloproteinase-7, Respiratory Symptoms, and Mortality in Community-Dwelling Adults. MESA (Multi-Ethnic Study of Atherosclerosis).Armstrong HF, Podolanczuk AJ, Barr RG, Oelsner EC, Kawut SM, Hoffman EA, Tracy R, Kaminski N, McClelland RL, Lederer DJ. Am J Respir Crit Care Med. 2017 Nov 15. PMID: 28570100.
- Eph-B4 regulates adaptive venous remodeling to improve arteriovenous fistula patency.Protack CD, Foster TR, Hashimoto T, Yamamoto K, Lee MY, Kraehling JR, Bai H, Hu H, Isaji T, Santana JM, Wang M, Sessa WC, Dardik A. Sci Rep. 2017 Nov 13; 2017 Nov 13. PMID: 29133876.
- Alk and Ltk ligands are essential for iridophore development in zebrafish mediated by the receptor tyrosine kinase Ltk.Mo ES, Cheng Q, Reshetnyak AV, Schlessinger J, Nicoli S. Proc Natl Acad Sci U S A. 2017 Nov 7; 2017 Oct 23. PMID: 29078341.
- Humanized mouse model supports development, function, and tissue residency of human natural killer cells.Herndler-Brandstetter D, Shan L, Yao Y, Stecher C, Plajer V, Lietzenmayer M, Strowig T, de Zoete MR, Palm NW, Chen J, Blish CA, Frleta D, Gurer C, Macdonald LE, Murphy AJ, Yancopoulos GD, Montgomery RR, Flavell RA. Proc Natl Acad Sci U S A. 2017 Nov 7; 2017 Oct 25. PMID: 29078283.
- Isolation of mutants with abnormal petal epidermal cell morphology.Saffer AM, Irish VF. Plant Signal Behav. 2017 Nov 2; 2017 Oct 26. PMID: 29072548.
- Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers.Lünse CE, Weinberg Z, Breaker RR. RNA Biol. 2017 Nov 2; 2017 Nov 3. PMID: 27858507.
- The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H. Neuron. 2017 Nov 1. PMID: 29096072.
- Zika virus targets blood monocytes.Jurado KA, Iwasaki A. Nat Microbiol. 2017 Nov. PMID: 29070824.
- The cellular endosomal protein stannin inhibits intracellular trafficking of human papillomavirus during virus entry.Lipovsky A, Erden A, Kanaya E, Zhang W, Crite M, Bradfield C, MacMicking J, DiMaio D, Schoggins JW, Iwasaki A. J Gen Virol. 2017 Nov; 2017 Oct 23. PMID: 29058661.
- Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study.Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N. Lancet Respir Med. 2017 Nov; 2017 Sep 21. PMID: 28942086.
- B cells require Type 1 interferon to produce alloantibodies to transfused KEL-expressing red blood cells in mice.Gibb DR, Liu J, Santhanakrishnan M, Natarajan P, Madrid DJ, Patel S, Eisenbarth SC, Tormey CA, Stowell SR, Iwasaki A, Hendrickson JE. Transfusion. 2017 Nov; 2017 Aug 23. PMID: 28836263.
- Degradable bioadhesive nanoparticles for prolonged intravaginal delivery and retention of elvitegravir.Mohideen M, Quijano E, Song E, Deng Y, Panse G, Zhang W, Clark MR, Saltzman WM. Biomaterials. 2017 Nov; 2017 Aug 15. PMID: 28829952.
- LungMAP: The Molecular Atlas of Lung Development Program.Ardini-Poleske ME, Clark RF, Ansong C, Carson JP, Corley RA, Deutsch GH, Hagood JS, Kaminski N, Mariani TJ, Potter SS, Pryhuber GS, Warburton D, Whitsett JA, Palmer SM, Ambalavanan N. Am J Physiol Lung Cell Mol Physiol. 2017 Nov 1; 2017 Aug 10. PMID: 28798251.
- The central role of tRNA in genetic code expansion.Reynolds NM, Vargas-Rodriguez O, Söll D, Crnković A. Biochim Biophys Acta Gen Subj. 2017 Nov; 2017 Mar 18. PMID: 28323071.
- A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNA(His) pair.Englert M, Vargas-Rodriguez O, Reynolds NM, Wang YS, Söll D, Umehara T. Biochim Biophys Acta Gen Subj. 2017 Nov; 2017 Mar 10. PMID: 28288813.
- Genetic Dissection of the Impact of miR-33a and miR-33b during the Progression of Atherosclerosis.Price NL, Rotllan N, Canfrán-Duque A, Zhang X, Pati P, Arias N, Moen J, Mayr M, Ford DA, Baldán Á, Suárez Y, Fernández-Hernando C. Cell Rep. 2017 Oct 31. PMID: 29091769.
- Membrane dynamics and organelle biogenesis-lipid pipelines and vesicular carriers.Stefan CJ, Trimble WS, Grinstein S, Drin G, Reinisch K, De Camilli P, Cohen S, Valm AM, Lippincott-Schwartz J, Levine TP, Iaea DB, Maxfield FR, Futter CE, Eden ER, Judith D, van Vliet AR, Agostinis P, Tooze SA, Sugiura A, McBride HM. BMC Biol. 2017 Oct 31; 2017 Oct 31. PMID: 29089042.
- The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei.Chikne V, Gupta SK, Doniger T, K SR, Cohen-Chalamish S, Waldman Ben-Asher H, Kolet L, Yahia NH, Unger R, Ullu E, Kolev NG, Tschudi C, Michaeli S. J Mol Biol. 2017 Oct 27; 2017 Apr 26. PMID: 28456523.
- Distinct Microbial Communities Trigger Colitis Development upon Intestinal Barrier Damage via Innate or Adaptive Immune Cells.Roy U, Gálvez EJC, Iljazovic A, Lesker TR, Błażejewski AJ, Pils MC, Heise U, Huber S, Flavell RA, Strowig T. Cell Rep. 2017 Oct 24. PMID: 29069606.
- A conserved C-terminal RXG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity.Grabińska KA, Edani BH, Park EJ, Kraehling JR, Sessa WC. J Biol Chem. 2017 Oct 20; 2017 Aug 23. PMID: 28842490.
- Health Care Use by Older Adults With Acute Myeloid Leukemia at the End of Life.Wang R, Zeidan AM, Halene S, Xu X, Davidoff AJ, Huntington SF, Podoltsev NA, Gross CP, Gore SD, Ma X. J Clin Oncol. 2017 Oct 20; 2017 Aug 7. PMID: 28783450.
- Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4(+) T Cells Permissive for Latent HIV-1 Infection.Shan L, Deng K, Gao H, Xing S, Capoferri AA, Durand CM, Rabi SA, Laird GM, Kim M, Hosmane NN, Yang HC, Zhang H, Margolick JB, Li L, Cai W, Ke R, Flavell RA, Siliciano JD, Siliciano RF. Immunity. 2017 Oct 17. PMID: 29045905.
- Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.Li S, Breaker RR. BMC Genomics. 2017 Oct 13; 2017 Oct 13. PMID: 29029611.
- Fractionation iCLIP detects persistent SR protein binding to conserved, retained introns in chromatin, nucleoplasm and cytoplasm.Brugiolo M, Botti V, Liu N, Müller-McNicoll M, Neugebauer KM. Nucleic Acids Res. 2017 Oct 13. PMID: 28977534.
- Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions.Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR, Sherlock ME, Breaker RR. Nucleic Acids Res. 2017 Oct 13. PMID: 28977401.
- Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling.Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM. Nat Commun. 2017 Oct 9; 2017 Oct 9. PMID: 28993621.
- Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli.D'Lima NG, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. J Proteome Res. 2017 Oct 6; 2017 Sep 19. PMID: 28861998.
- Comparative analysis reveals genomic features of stress-induced transcriptional readthrough.Vilborg A, Sabath N, Wiesel Y, Nathans J, Levy-Adam F, Yario TA, Steitz JA, Shalgi R. Proc Natl Acad Sci U S A. 2017 Oct 3; 2017 Sep 19. PMID: 28928151.
- Critical role of caveolin-1 in ocular neovascularization and multitargeted antiangiogenic effects of cavtratin via JNK.Jiang Y, Lin X, Tang Z, Lee C, Tian G, Du Y, Yin X, Ren X, Huang L, Ye Z, Chen W, Zhang F, Mi J, Gao Z, Wang S, Chen Q, Xing L, Wang B, Cao Y, Sessa WC, Ju R, Liu Y, Li X. Proc Natl Acad Sci U S A. 2017 Oct 3; 2017 Sep 18. PMID: 28923916.
- Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL.Zhang F, May A, Irish VF. Trends Plant Sci. 2017 Oct; 2017 Sep 5. PMID: 28886911.
- Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet. 2017 Oct; 2017 Sep 4. PMID: 28869592.
- AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma.Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, Platt RJ, Chen S. Nat Neurosci. 2017 Oct; 2017 Aug 14. PMID: 28805815.
- Splicing and transcription touch base: co-transcriptional spliceosome assembly and function.Herzel L, Ottoz DSM, Alpert T, Neugebauer KM. Nat Rev Mol Cell Biol. 2017 Oct; 2017 Aug 9. PMID: 28792005.
- The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion.Christiano R, Kolev NG, Shi H, Ullu E, Walther TC, Tschudi C. Mol Microbiol. 2017 Oct; 2017 Aug 4. PMID: 28742275.
- A Dirichlet process mixture model for clustering longitudinal gene expression data.Sun J, Herazo-Maya JD, Kaminski N, Zhao H, Warren JL. Stat Med. 2017 Sep 30; 2017 Jun 15. PMID: 28620908.
- Intestinal type 1 regulatory T cells migrate to periphery to suppress diabetogenic T cells and prevent diabetes development.Yu H, Gagliani N, Ishigame H, Huber S, Zhu S, Esplugues E, Herold KC, Wen L, Flavell RA. Proc Natl Acad Sci U S A. 2017 Sep 26; 2017 Sep 11. PMID: 28894001.
- A Protein Scaffold Coordinates SRC-Mediated JNK Activation in Response to Metabolic Stress.Kant S, Standen CL, Morel C, Jung DY, Kim JK, Swat W, Flavell RA, Davis RJ. Cell Rep. 2017 Sep 19. PMID: 28930674.
- Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA.Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. Immunity. 2017 Sep 19. PMID: 28930659.
- Selective degradation of PU.1 during autophagy represses the differentiation and antitumour activity of T(H)9 cells.Rivera Vargas T, Cai Z, Shen Y, Dosset M, Benoit-Lizon I, Martin T, Roussey A, Flavell RA, Ghiringhelli F, Apetoh L. Nat Commun. 2017 Sep 15; 2017 Sep 15. PMID: 28916785.
- Not just Salk.Greider C, Hopkins N, Steitz J, Amon A, Asai D, Barres B, Bass B, Bassler B, Birgeneau R, Bjorkman P, Botchan M, Brugge J, Cech T, Colwell R, Craig N, deLange T, Eisen M, Gottesman S, Green R, Handelsman J, Kimble J, King MC, Lehmann R, Marder E, Mullins D, O'Shea E, Schmid S, Seydoux G, Spradling A, Storz G, Szostak J, Telesnitsky A, Tilghman S, Tjian R, Vale R, Wolberger C, Zakian V. Science. 2017 Sep 15. PMID: 28912235.
- No Oxygen? No Glucose? No Problem: Fatty Acid Catabolism Enhances Effector CD8(+) TILs.Bailis W, Shyer JA, Chiorazzi M, Flavell RA. Cancer Cell. 2017 Sep 11. PMID: 28898693.
- The ABC model of floral development.Irish V. Curr Biol. 2017 Sep 11. PMID: 28898659.
- Rewriting the Genetic Code.Mukai T, Lajoie MJ, Englert M, Söll D. Annu Rev Microbiol. 2017 Sep 8; 2017 Jul 11. PMID: 28697669.
- Ezrin links CFTR to TLR4 signaling to orchestrate anti-bacterial immune response in macrophages.Di Pietro C, Zhang PX, O'Rourke TK, Murray TS, Wang L, Britto CJ, Koff JL, Krause DS, Egan ME, Bruscia EM. Sci Rep. 2017 Sep 7; 2017 Sep 7. PMID: 28883468.
- Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA.Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD. Biochemistry. 2017 Sep 5; 2017 Aug 18. PMID: 28820243.
- Single methyl groups can act as toggle switches to specify transmembrane Protein-protein interactions.He L, Steinocher H, Shelar A, Cohen EB, Heim EN, Kragelund BB, Grigoryan G, DiMaio D. Elife. 2017 Sep 4; 2017 Sep 4. PMID: 28869036.
- Crystal Structure of the C-terminal Domain of Human eIF2D and Its Implications on Eukaryotic Translation Initiation.Vaidya AT, Lomakin IB, Joseph NN, Dmitriev SE, Steitz TA. J Mol Biol. 2017 Sep 1; 2017 Jul 21. PMID: 28736176.
- Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites.Kolev NG, Günzl A, Tschudi C. Mol Biochem Parasitol. 2017 Sep; 2017 Jul 14. PMID: 28716719.
- Macrophage deficiency of miR-21 promotes apoptosis, plaque necrosis, and vascular inflammation during atherogenesis.Canfrán-Duque A, Rotllan N, Zhang X, Fernández-Fuertes M, Ramírez-Hidalgo C, Araldi E, Daimiel L, Busto R, Fernández-Hernando C, Suárez Y. EMBO Mol Med. 2017 Sep. PMID: 28674080.
- Structural basis for ligand binding to the guanidine-II riboswitch.Reiss CW, Strobel SA. RNA. 2017 Sep; 2017 Jun 9. PMID: 28600356.
- Transcriptome profiles in sarcoidosis and their potential role in disease prediction.Schupp JC, Vukmirovic M, Kaminski N, Prasse A. Curr Opin Pulm Med. 2017 Sep. PMID: 28590292.
- Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.Balasubramanian S, Fu Y, Pawashe M, McGillivray P, Jin M, Liu J, Karczewski KJ, MacArthur DG, Gerstein M. Nat Commun. 2017 Aug 29; 2017 Aug 29. PMID: 28851873.
- Activation of master virulence regulator PhoP in acidic pH requires the Salmonella-specific protein UgtL.Choi J, Groisman EA. Sci Signal. 2017 Aug 29; 2017 Aug 29. PMID: 28851823.
- Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation.Karabadzhak AG, Petti LM, Barrera FN, Edwards APB, Moya-Rodríguez A, Polikanov YS, Freites JA, Tobias DJ, Engelman DM, DiMaio D. Proc Natl Acad Sci U S A. 2017 Aug 29; 2017 Aug 14. PMID: 28808001.
- m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways.Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA. Nature. 2017 Aug 17; 2017 Aug 9. PMID: 28792938.
- The DNA Methylcytosine Dioxygenase Tet2 Sustains Immunosuppressive Function of Tumor-Infiltrating Myeloid Cells to Promote Melanoma Progression.Pan W, Zhu S, Qu K, Meeth K, Cheng J, He K, Ma H, Liao Y, Wen X, Roden C, Tobiasova Z, Wei Z, Zhao J, Liu J, Zheng J, Guo B, Khan SA, Bosenberg M, Flavell RA, Lu J. Immunity. 2017 Aug 15. PMID: 28813659.
- Analysis of RNA-protein interactions in vertebrate embryos using UV crosslinking approaches.Despic V, Dejung M, Butter F, Neugebauer KM. Methods. 2017 Aug 15; 2017 Jul 19. PMID: 28734934.
- Rhamnose-Containing Cell Wall Polymers Suppress Helical Plant Growth Independently of Microtubule Orientation.Saffer AM, Carpita NC, Irish VF. Curr Biol. 2017 Aug 7; 2017 Jul 20. PMID: 28736166.
- Evidence for regulated expression of Telomeric Repeat-containing RNAs (TERRA) in parasitic trypanosomatids.Damasceno JD, Silva G, Tschudi C, Tosi LR. Mem Inst Oswaldo Cruz. 2017 Aug. PMID: 28767983.
- Aging Impairs Alveolar Macrophage Phagocytosis and Increases Influenza-Induced Mortality in Mice.Wong CK, Smith CA, Sakamoto K, Kaminski N, Koff JL, Goldstein DR. J Immunol. 2017 Aug 1; 2017 Jun 23. PMID: 28646038.
- Type I IFN Is Necessary and Sufficient for Inflammation-Induced Red Blood Cell Alloimmunization in Mice.Gibb DR, Liu J, Natarajan P, Santhanakrishnan M, Madrid DJ, Eisenbarth SC, Zimring JC, Iwasaki A, Hendrickson JE. J Immunol. 2017 Aug 1; 2017 Jun 19. PMID: 28630094.
- Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense.Sasai M, Sakaguchi N, Ma JS, Nakamura S, Kawabata T, Bando H, Lee Y, Saitoh T, Akira S, Iwasaki A, Standley DM, Yoshimori T, Yamamoto M. Nat Immunol. 2017 Aug; 2017 Jun 12. PMID: 28604719.
- Local DNA Repair Inhibition for Sustained Radiosensitization of High-Grade Gliomas.King AR, Corso CD, Chen EM, Song E, Bongiorni P, Chen Z, Sundaram RK, Bindra RS, Saltzman WM. Mol Cancer Ther. 2017 Aug; 2017 May 31. PMID: 28566437.
- Mast cell-derived prostaglandin D(2) attenuates anaphylactic reactions in mice.Nakamura T, Fujiwara Y, Yamada R, Fujii W, Hamabata T, Lee MY, Maeda S, Aritake K, Roers A, Sessa WC, Nakamura M, Urade Y, Murata T. J Allergy Clin Immunol. 2017 Aug; 2017 Apr 27. PMID: 28457595.
- Quantitative microscopy-based measurements of circulating nanoparticle concentration using microliter blood volumes.Tietjen GT, DiRito J, Pober JS, Saltzman WM. Nanomedicine. 2017 Aug; 2017 Apr 13. PMID: 28412144.
- mRNA length-sensing in eukaryotic translation: reconsidering the "closed loop" and its implications for translational control.Thompson MK, Gilbert WV. Curr Genet. 2017 Aug; 2016 Dec 27. PMID: 28028558.
- Control of species-dependent cortico-motoneuronal connections underlying manual dexterity.Gu Z, Kalambogias J, Yoshioka S, Han W, Li Z, Kawasawa YI, Pochareddy S, Li Z, Liu F, Xu X, Wijeratne HRS, Ueno M, Blatz E, Salomone J, Kumanogoh A, Rasin MR, Gebelein B, Weirauch MT, Sestan N, Martin JH, Yoshida Y. Science. 2017 Jul 28. PMID: 28751609.
- AIM2 Engages Active but Unprocessed Caspase-1 to Induce Noncanonical Activation of the NLRP3 Inflammasome.Cunha LD, Silva ALN, Ribeiro JM, Mascarenhas DPA, Quirino GFS, Santos LL, Flavell RA, Zamboni DS. Cell Rep. 2017 Jul 25. PMID: 28746866.
- Opportunities and Challenges in RNA Structural Modeling and Design.Schlick T, Pyle AM. Biophys J. 2017 Jul 25; 2017 Feb 2. PMID: 28162235.
- MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.Yan KK, Lou S, Gerstein M. PLoS Comput Biol. 2017 Jul; 2017 Jul 24. PMID: 28742097.
- Sensing Self and Foreign Circular RNAs by Intron Identity.Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY. Mol Cell. 2017 Jul 20; 2017 Jun 15. PMID: 28625551.
- Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.Lomakin IB, Stolboushkina EA, Vaidya AT, Zhao C, Garber MB, Dmitriev SE, Steitz TA. Cell Rep. 2017 Jul 18. PMID: 28723557.
- HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M. Bioinformatics. 2017 Jul 15. PMID: 28369339.
- Extreme Trait Whole-Genome Sequencing Identifies PTPRO as a Novel Candidate Gene in Emphysema with Severe Airflow Obstruction.Radder JE, Zhang Y, Gregory AD, Yu S, Kelly NJ, Leader JK, Kaminski N, Sciurba FC, Shapiro SD. Am J Respir Crit Care Med. 2017 Jul 15. PMID: 28199135.
- Microbes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis.Huang Y, Ma SF, Espindola MS, Vij R, Oldham JM, Huffnagle GB, Erb-Downward JR, Flaherty KR, Moore BB, White ES, Zhou T, Li J, Lussier YA, Han MK, Kaminski N, Garcia JGN, Hogaboam CM, Martinez FJ, Noth I. Am J Respir Crit Care Med. 2017 Jul 15. PMID: 28157391.
- Evolution of the Human Nervous System Function, Structure, and Development.Sousa AMM, Meyer KA, Santpere G, Gulden FO, Sestan N. Cell. 2017 Jul 13. PMID: 28708995.
- Whole-exome sequencing in evaluation of patients with venous thromboembolism.Lee EJ, Dykas DJ, Leavitt AD, Camire RM, Ebberink E, García de Frutos P, Gnanasambandan K, Gu SX, Huntington JA, Lentz SR, Mertens K, Parish CR, Rezaie AR, Sayeski PP, Cromwell C, Bar N, Halene S, Neparidze N, Parker TL, Burns AJ, Dumont A, Yao X, Chaar CIO, Connors JM, Bale AE, Lee AI. Blood Adv. 2017 Jul 11; 2017 Jun 29. PMID: 29296762.
- RAB15 empowers dendritic cells to drive antiviral immunity.Wong P, Iwasaki A. Sci Immunol. 2017 Jul 7. PMID: 28783705.
- Cancer genomics: Less is more in the hunt for driver mutations.Kumar S, Gerstein M. Nature. 2017 Jul 6; 2017 Jun 28. PMID: 28658210.
- Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. Nat Commun. 2017 Jul 5; 2017 Jul 5. PMID: 28680106.
- The fate and lifespan of human monocyte subsets in steady state and systemic inflammation.Patel AA, Zhang Y, Fullerton JN, Boelen L, Rongvaux A, Maini AA, Bigley V, Flavell RA, Gilroy DW, Asquith B, Macallan D, Yona S. J Exp Med. 2017 Jul 3; 2017 Jun 12. PMID: 28606987.
- Cellular differentiation state modulates the mRNA export activity of SR proteins.Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. J Cell Biol. 2017 Jul 3; 2017 Jun 7. PMID: 28592444.
- Post-transcriptional regulation of mouse neurogenesis by Pumilio proteins.Zhang M, Chen D, Xia J, Han W, Cui X, Neuenkirchen N, Hermes G, Sestan N, Lin H. Genes Dev. 2017 Jul 1; 2017 Aug 9. PMID: 28794184.
- Riboswitch diversity and distribution.McCown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR. RNA. 2017 Jul; 2017 Apr 10. PMID: 28396576.
- Modified mesenchymal stem cells using miRNA transduction alter lung injury in a bleomycin model.Huleihel L, Sellares J, Cardenes N, Álvarez D, Faner R, Sakamoto K, Yu G, Kapetanaki MG, Kaminski N, Rojas M. Am J Physiol Lung Cell Mol Physiol. 2017 Jul 1; 2017 Apr 6. PMID: 28385811.
- Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM. Genome Res. 2017 Jul; 2017 Apr 5. PMID: 28381614.
- Landscape and variation of novel retroduplications in 26 human populations.Zhang Y, Li S, Abyzov A, Gerstein MB. PLoS Comput Biol. 2017 Jun; 2017 Jun 29. PMID: 28662076.
- Nlrp9b inflammasome restricts rotavirus infection in intestinal epithelial cells.Zhu S, Ding S, Wang P, Wei Z, Pan W, Palm NW, Yang Y, Yu H, Li HB, Wang G, Lei X, de Zoete MR, Zhao J, Zheng Y, Chen H, Zhao Y, Jurado KA, Feng N, Shan L, Kluger Y, Lu J, Abraham C, Fikrig E, Greenberg HB, Flavell RA. Nature. 2017 Jun 29; 2017 Jun 21. PMID: 28636595.
- Lanosterol Modulates TLR4-Mediated Innate Immune Responses in Macrophages.Araldi E, Fernández-Fuertes M, Canfrán-Duque A, Tang W, Cline GW, Madrigal-Matute J, Pober JS, Lasunción MA, Wu D, Fernández-Hernando C, Suárez Y. Cell Rep. 2017 Jun 27. PMID: 28658622.
- Long-term consumption of caffeine-free high sucrose cola beverages aggravates the pathogenesis of EAE in mice.Cao G, Wang Q, Huang W, Tong J, Ye D, He Y, Liu Z, Tang X, Cheng H, Wen Q, Li D, Chau HT, Wen Y, Zhong H, Meng Z, Liu H, Wu Z, Zhao L, Flavell RA, Zhou H, Xu A, Yang H, Yin Z. Cell Discov. 2017; 2017 Jun 20. PMID: 28670480.
- An Exportin-1-dependent microRNA biogenesis pathway during human cell quiescence.Martinez I, Hayes KE, Barr JA, Harold AD, Xie M, Bukhari SIA, Vasudevan S, Steitz JA, DiMaio D. Proc Natl Acad Sci U S A. 2017 Jun 20; 2017 Jun 5. PMID: 28584122.
- Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease.Thiemann S, Smit N, Roy U, Lesker TR, Gálvez EJC, Helmecke J, Basic M, Bleich A, Goodman AL, Kalinke U, Flavell RA, Erhardt M, Strowig T. Cell Host Microbe. 2017 Jun 14. PMID: 28618267.
- Microbiota Normalization Reveals that Canonical Caspase-1 Activation Exacerbates Chemically Induced Intestinal Inflammation.Błażejewski AJ, Thiemann S, Schenk A, Pils MC, Gálvez EJC, Roy U, Heise U, de Zoete MR, Flavell RA, Strowig T. Cell Rep. 2017 Jun 13. PMID: 28614717.
- The lost language of the RNA World.Nelson JW, Breaker RR. Sci Signal. 2017 Jun 13; 2017 Jun 13. PMID: 28611182.
- Macrophage function in tissue repair and remodeling requires IL-4 or IL-13 with apoptotic cells.Bosurgi L, Cao YG, Cabeza-Cabrerizo M, Tucci A, Hughes LD, Kong Y, Weinstein JS, Licona-Limon P, Schmid ET, Pelorosso F, Gagliani N, Craft JE, Flavell RA, Ghosh S, Rothlin CV. Science. 2017 Jun 9; 2017 May 11. PMID: 28495875.
- Rusty neutrophils in β-thalassemia: no traction!Gaines P, Halene S. Blood. 2017 Jun 8. PMID: 28596437.
- IRE1α promotes viral infection by conferring resistance to apoptosis.Fink SL, Jayewickreme TR, Molony RD, Iwawaki T, Landis CS, Lindenbach BD, Iwasaki A. Sci Signal. 2017 Jun 6; 2017 Jun 6. PMID: 28588082.
- Special focus on the Cajal Body.Neugebauer KM. RNA Biol. 2017 Jun 3. PMID: 28486008.
- Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos.Heyn P, Salmonowicz H, Rodenfels J, Neugebauer KM. RNA Biol. 2017 Jun 3; 2016 Nov 18. PMID: 27858508.
- Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma.Boyden LM, Vincent NG, Zhou J, Hu R, Craiglow BG, Bayliss SJ, Rosman IS, Lucky AW, Diaz LA, Goldsmith LA, Paller AS, Lifton RP, Baserga SJ, Choate KA. Am J Hum Genet. 2017 Jun 1. PMID: 28575652.
- Functional RNA structures throughout the Hepatitis C Virus genome.Adams RL, Pirakitikulr N, Pyle AM. Curr Opin Virol. 2017 Jun; 2017 May 13. PMID: 28511116.
- Fetal Growth Restriction Caused by Sexual Transmission of Zika Virus in Mice.Uraki R, Jurado KA, Hwang J, Szigeti-Buck K, Horvath TL, Iwasaki A, Fikrig E. J Infect Dis. 2017 Jun 1. PMID: 28472297.
- Nickel induces transcriptional down-regulation of DNA repair pathways in tumorigenic and non-tumorigenic lung cells.Scanlon SE, Scanlon CD, Hegan DC, Sulkowski PL, Glazer PM. Carcinogenesis. 2017 Jun 1. PMID: 28472268.
- Akt1 Controls the Timing and Amplitude of Vascular Circadian Gene Expression.Luciano AK, Santana JM, Velazquez H, Sessa WC. J Biol Rhythms. 2017 Jun; 2017 Apr 28. PMID: 28452287.
- Structural Insights into the Mechanism of Group II Intron Splicing.Zhao C, Pyle AM. Trends Biochem Sci. 2017 Jun; 2017 Apr 21. PMID: 28438387.
- Corrigendum to "Epicutaneous immunization with phosphorylcholine conjugated to bovine serum albumin (PC-BSA) and TLR9 ligand CpG alleviates pneumococcal pneumonia in mice" [Pharmacol. Rep. 66 (2014) 570-575].Majewska-Szczepanik M, Yamamoto N, Askenase PW, Szczepanik M. Pharmacol Rep. 2017 Jun; 2017 Mar 29. PMID: 28365257.
- Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease.Modena BD, Bleecker ER, Busse WW, Erzurum SC, Gaston BM, Jarjour NN, Meyers DA, Milosevic J, Tedrow JR, Wu W, Kaminski N, Wenzel SE. Am J Respir Crit Care Med. 2017 Jun 1. PMID: 27984699.
- A novel community driven software for functional enrichment analysis of extracellular vesicles data.Pathan M, Keerthikumar S, Chisanga D, Alessandro R, Ang CS, Askenase P, Batagov AO, Benito-Martin A, Camussi G, Clayton A, Collino F, Di Vizio D, Falcon-Perez JM, Fonseca P, Fonseka P, Fontana S, Gho YS, Hendrix A, Hoen EN, Iraci N, Kastaniegaard K, Kislinger T, Kowal J, Kurochkin IV, Leonardi T, Liang Y, Llorente A, Lunavat TR, Maji S, Monteleone F, Øverbye A, Panaretakis T, Patel T, Peinado H, Pluchino S, Principe S, Ronquist G, Royo F, Sahoo S, Spinelli C, Stensballe A, Théry C, van Herwijnen MJC, Wauben M, Welton JL, Zhao K, Mathivanan S. J Extracell Vesicles. 2017; 2017 May 26. PMID: 28717418.
- SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume.Zou S, Teixeira AM, Kostadima M, Astle WJ, Radhakrishnan A, Simon LM, Truman L, Fang JS, Hwa J, Zhang PX, van der Harst P, Bray PF, Ouwehand WH, Frontini M, Krause DS. PLoS One. 2017; 2017 May 23. PMID: 28542600.
- Surface chemistry governs cellular tropism of nanoparticles in the brain.Song E, Gaudin A, King AR, Seo YE, Suh HW, Deng Y, Cui J, Tietjen GT, Huttner A, Saltzman WM. Nat Commun. 2017 May 19; 2017 May 19. PMID: 28524852.
- Corrigendum.Li J, Wang Y, Zhang Y, Wang W, Irish VF, Huang T. J Exp Bot. 2017 May 17. PMID: 28207071.
- Settling the m(6)A debate: methylation of mature mRNA is not dynamic but accelerates turnover.Rosa-Mercado NA, Withers JB, Steitz JA. Genes Dev. 2017 May 15. PMID: 28637691.
- A Systematic RNAi Screen Reveals a Novel Role of a Spindle Assembly Checkpoint Protein BuGZ in Synaptic Transmission in C. elegans.Han M, Zou W, Chang H, Yu Y, Zhang H, Li S, Cheng H, Wei G, Chen Y, Reinke V, Xu T, Kang L. Front Mol Neurosci. 2017; 2017 May 11. PMID: 28553202.
- mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4.Park Y, Reyna-Neyra A, Philippe L, Thoreen CC. Cell Rep. 2017 May 9. PMID: 28494858.
- RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea.Mukai T, Crnković A, Umehara T, Ivanova NN, Kyrpides NC, Söll D. mBio. 2017 May 9; 2017 May 9. PMID: 28487430.
- Mycofumigation through production of the volatile DNA-methylating agent N-methyl-N-nitrosoisobutyramide by fungi in the genus Muscodor.Hutchings ML, Alpha-Cobb CJ, Hiller DA, Berro J, Strobel SA. J Biol Chem. 2017 May 5; 2017 Mar 10. PMID: 28283571.
- Ribosomes Need Straight A's to Sleep.Sondalle SB, Baserga SJ. Cell. 2017 May 4. PMID: 28475888.
- Fluoride export (FEX) proteins from fungi, plants and animals are 'single barreled' channels containing one functional and one vestigial ion pore.Berbasova T, Nallur S, Sells T, Smith KD, Gordon PB, Tausta SL, Strobel SA. PLoS One. 2017; 2017 May 4. PMID: 28472134.
- How do messenger RNA splicing alterations drive myelodysplasia?Joshi P, Halene S, Abdel-Wahab O. Blood. 2017 May 4; 2017 Mar 27. PMID: 28348147.
- Readthrough transcription: How are DoGs made and what do they do?Vilborg A, Steitz JA. RNA Biol. 2017 May 4; 2016 Feb 9. PMID: 26861889.
- Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.Dhingra P, Fu Y, Gerstein M, Khurana E. Curr Protoc Bioinformatics. 2017 May 2; 2017 May 2. PMID: 28463398.
- The cationic small molecule GW4869 is cytotoxic to high phosphatidylserine-expressing myeloma cells.Vuckovic S, Vandyke K, Rickards DA, McCauley Winter P, Brown SHJ, Mitchell TW, Liu J, Lu J, Askenase PW, Yuriev E, Capuano B, Ramsland PA, Hill GR, Zannettino ACW, Hutchinson AT. Br J Haematol. 2017 May; 2017 Feb 17. PMID: 28211573.
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Meyer KA, Marques-Bonet T, Sestan N. Mol Biol Evol. 2017 May 1. PMID: 28204568.
- An endoplasmic reticulum protein, Nogo-B, facilitates alcoholic liver disease through regulation of kupffer cell polarization.Park JK, Shao M, Kim MY, Baik SK, Cho MY, Utsumi T, Satoh A, Ouyang X, Chung C, Iwakiri Y. Hepatology. 2017 May; 2017 Mar 22. PMID: 28090670.
- Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins.Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ, Kelleher NL, Jewett MC. Biotechnol Bioeng. 2017 May; 2017 Feb 2. PMID: 27987323.
- Mechanistic Debris Generated by Twister Ribozymes.Breaker RR. ACS Chem Biol. 2017 Apr 21; 2017 Feb 21. PMID: 28191925.
- Sequestration from Protease Adaptor Confers Differential Stability to Protease Substrate.Yeom J, Wayne KJ, Groisman EA. Mol Cell. 2017 Apr 20. PMID: 28431231.
- TAM Receptors Are Not Required for Zika Virus Infection in Mice.Hastings AK, Yockey LJ, Jagger BW, Hwang J, Uraki R, Gaitsch HF, Parnell LA, Cao B, Mysorekar IU, Rothlin CV, Fikrig E, Diamond MS, Iwasaki A. Cell Rep. 2017 Apr 18. PMID: 28423319.
- Lipid Droplet Biogenesis and Function in the Endothelium.Kuo A, Lee MY, Sessa WC. Circ Res. 2017 Apr 14; 2017 Jan 24. PMID: 28119423.
- Hematopoiesis Lineage Tree Uprooted: Every Cell Is a Rainbow.Hirschi KK, Nicoli S, Walsh K. Dev Cell. 2017 Apr 10. PMID: 28399402.
- Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson O. Nucleic Acids Res. 2017 Apr 7. PMID: 28175342.
- Structuring supplemental materials in support of reproducibility.Greenbaum D, Rozowsky J, Stodden V, Gerstein M. Genome Biol. 2017 Apr 5; 2017 Apr 5. PMID: 28381262.
- Finally, Progress in Pulmonary Hypertension Associated with Heart Failure with Preserved Ejection Fraction.Fares WH, Kaminski N. Am J Respir Cell Mol Biol. 2017 Apr. PMID: 28362152.
- Stroke and Circulating Extracellular RNAs.Mick E, Shah R, Tanriverdi K, Murthy V, Gerstein M, Rozowsky J, Kitchen R, Larson MG, Levy D, Freedman JE. Stroke. 2017 Apr; 2017 Mar 13. PMID: 28289238.
- One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM. Genome Res. 2017 Apr; 2017 Feb 24. PMID: 28235832.
- Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change.Morley VJ, Turner PE. Evolution. 2017 Apr; 2017 Feb 14. PMID: 28121018.
- Climate change and lung health: the challenge for a new president.Hopkinson NS, Hart N, Jenkins G, Kaminski N, Rosenfeld M, Smyth A, Wilkinson A. Thorax. 2017 Apr; 2017 Jan 19. PMID: 28104829.
- Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron.Schwalm ND 3rd, Townsend GE 2nd, Groisman EA. Mol Microbiol. 2017 Apr; 2017 Feb 3. PMID: 28009067.
- Validation of the prognostic value of MMP-7 in idiopathic pulmonary fibrosis.Tzouvelekis A, Herazo-Maya JD, Slade M, Chu JH, Deiuliis G, Ryu C, Li Q, Sakamoto K, Ibarra G, Pan H, Gulati M, Antin-Ozerkis D, Herzog EL, Kaminski N. Respirology. 2017 Apr; 2016 Oct 19. PMID: 27761978.
- Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen.Brechbuhl HM, Finlay-Schultz J, Yamamoto TM, Gillen AE, Cittelly DM, Tan AC, Sams SB, Pillai MM, Elias AD, Robinson WA, Sartorius CA, Kabos P. Clin Cancer Res. 2017 Apr 1; 2016 Oct 4. PMID: 27702820.
- Contemporary Approaches to Modulating the Nitric Oxide-cGMP Pathway in Cardiovascular Disease.Kraehling JR, Sessa WC. Circ Res. 2017 Mar 31. PMID: 28360348.
- Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.Li S, Shuch BM, Gerstein MB. PLoS Genet. 2017 Mar; 2017 Mar 30. PMID: 28358873.
- MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.Kasper DM, Moro A, Ristori E, Narayanan A, Hill-Teran G, Fleming E, Moreno-Mateos M, Vejnar CE, Zhang J, Lee D, Gu M, Gerstein M, Giraldez A, Nicoli S. Dev Cell. 2017 Mar 27. PMID: 28350988.
- miR-181b regulates vascular stiffness age dependently in part by regulating TGF-β signaling.Hori D, Dunkerly-Eyring B, Nomura Y, Biswas D, Steppan J, Henao-Mejia J, Adachi H, Santhanam L, Berkowitz DE, Steenbergen C, Flavell RA, Das S. PLoS One. 2017; 2017 Mar 21. PMID: 28323879.
- Perspectives on the ribosome.Steitz TA, Moore PB. Philos Trans R Soc Lond B Biol Sci. 2017 Mar 19. PMID: 28138074.
- Transfer RNAs with novel cloverleaf structures.Mukai T, Vargas-Rodriguez O, Englert M, Tripp HJ, Ivanova NN, Rubin EM, Kyrpides NC, Söll D. Nucleic Acids Res. 2017 Mar 17. PMID: 28076288.
- Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation.Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EA. Mol Cell. 2017 Mar 16. PMID: 28306505.
- Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.Naghdi MR, Smail K, Wang JX, Wade F, Breaker RR, Perreault J. Methods. 2017 Mar 15; 2017 Mar 6. PMID: 28279853.
- Loss of Twist1 in the Mesenchymal Compartment Promotes Increased Fibrosis in Experimental Lung Injury by Enhanced Expression of CXCL12.Tan J, Tedrow JR, Nouraie M, Dutta JA, Miller DT, Li X, Yu S, Chu Y, Juan-Guardela B, Kaminski N, Ramani K, Biswas PS, Zhang Y, Kass DJ. J Immunol. 2017 Mar 15; 2017 Feb 8. PMID: 28179498.
- Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity.Weinberg Z, Nelson JW, Lünse CE, Sherlock ME, Breaker RR. Proc Natl Acad Sci U S A. 2017 Mar 14; 2017 Mar 6. PMID: 28265071.
- RNA Methylation Clears the Way.Kontur C, Giraldez A. Dev Cell. 2017 Mar 13. PMID: 28292421.
- Bile acids initiate cholestatic liver injury by triggering a hepatocyte-specific inflammatory response.Cai SY, Ouyang X, Chen Y, Soroka CJ, Wang J, Mennone A, Wang Y, Mehal WZ, Jain D, Boyer JL. JCI Insight. 2017 Mar 9; 2017 Mar 9. PMID: 28289714.
- Disruptions in asymmetric centrosome inheritance and WDR62-Aurora kinase B interactions in primary microcephaly.Sgourdou P, Mishra-Gorur K, Saotome I, Henagariu O, Tuysuz B, Campos C, Ishigame K, Giannikou K, Quon JL, Sestan N, Caglayan AO, Gunel M, Louvi A. Sci Rep. 2017 Mar 8; 2017 Mar 8. PMID: 28272472.
- A Ribosomopathy Reveals Decoding Defective Ribosomes Driving Human Dysmorphism.Paolini NA, Attwood M, Sondalle SB, Vieira CMDS, van Adrichem AM, di Summa FM, O'Donohue MF, Gleizes PE, Rachuri S, Briggs JW, Fischer R, Ratcliffe PJ, Wlodarski MW, Houtkooper RH, von Lindern M, Kuijpers TW, Dinman JD, Baserga SJ, Cockman ME, MacInnes AW. Am J Hum Genet. 2017 Mar 2. PMID: 28257692.
- Immune Regulation of Antibody Access to Neuronal Tissues.Iwasaki A. Trends Mol Med. 2017 Mar; 2017 Feb 7. PMID: 28185790.
- Pediatric non-Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes.de Rooij JD, Branstetter C, Ma J, Li Y, Walsh MP, Cheng J, Obulkasim A, Dang J, Easton J, Verboon LJ, Mulder HL, Zimmermann M, Koss C, Gupta P, Edmonson M, Rusch M, Lim JY, Reinhardt K, Pigazzi M, Song G, Yeoh AE, Shih LY, Liang DC, Halene S, Krause DS, Zhang J, Downing JR, Locatelli F, Reinhardt D, van den Heuvel-Eibrink MM, Zwaan CM, Fornerod M, Gruber TA. Nat Genet. 2017 Mar; 2017 Jan 23. PMID: 28112737.
- DNA Polymerase Beta Germline Variant Confers Cellular Response to Cisplatin Therapy.Nemec AA, Abriola L, Merkel JS, de Stanchina E, DeVeaux M, Zelterman D, Glazer PM, Sweasy JB. Mol Cancer Res. 2017 Mar; 2017 Jan 10. PMID: 28074003.
- Visualizing the secondary and tertiary architectural domains of lncRNA RepA.Liu F, Somarowthu S, Pyle AM. Nat Chem Biol. 2017 Mar; 2017 Jan 9. PMID: 28068310.
- Perfect timing: splicing and transcription rates in living cells.Alpert T, Herzel L, Neugebauer KM. Wiley Interdiscip Rev RNA. 2017 Mar; 2016 Nov 21. PMID: 27873472.
- β-Hydroxybutyrate Deactivates Neutrophil NLRP3 Inflammasome to Relieve Gout Flares.Goldberg EL, Asher JL, Molony RD, Shaw AC, Zeiss CJ, Wang C, Morozova-Roche LA, Herzog RI, Iwasaki A, Dixit VD. Cell Rep. 2017 Feb 28. PMID: 28249154.
- Divergent Effects of miR-181 Family Members on Myocardial Function Through Protective Cytosolic and Detrimental Mitochondrial microRNA Targets.Das S, Kohr M, Dunkerly-Eyring B, Lee DI, Bedja D, Kent OA, Leung AK, Henao-Mejia J, Flavell RA, Steenbergen C. J Am Heart Assoc. 2017 Feb 27; 2017 Feb 27. PMID: 28242633.
- A novel humanized mouse model with significant improvement of class-switched, antigen-specific antibody production.Yu H, Borsotti C, Schickel JN, Zhu S, Strowig T, Eynon EE, Frleta D, Gurer C, Murphy AJ, Yancopoulos GD, Meffre E, Manz MG, Flavell RA. Blood. 2017 Feb 23; 2017 Jan 11. PMID: 28077418.
- Zika virus causes testicular atrophy.Uraki R, Hwang J, Jurado KA, Householder S, Yockey LJ, Hastings AK, Homer RJ, Iwasaki A, Fikrig E. Sci Adv. 2017 Feb; 2017 Feb 22. PMID: 28261663.
- Bioinformatic Analysis Reveals Archaeal tRNA(Tyr) and tRNA(Trp) Identities in Bacteria.Mukai T, Reynolds NM, Crnković A, Söll D. Life (Basel). 2017 Feb 21; 2017 Feb 21. PMID: 28230768.
- Lipid transport by TMEM24 at ER-plasma membrane contacts regulates pulsatile insulin secretion.Lees JA, Messa M, Sun EW, Wheeler H, Torta F, Wenk MR, De Camilli P, Reinisch KM. Science. 2017 Feb 17. PMID: 28209843.
- Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding.Fitzgerald ME, Rawling DC, Potapova O, Ren X, Kohlway A, Pyle AM. Nucleic Acids Res. 2017 Feb 17. PMID: 28180316.
- Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors.Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Nucleic Acids Res. 2017 Feb 17. PMID: 28003475.
- Legionella pneumophila Strain 130b Evades Macrophage Cell Death Independent of the Effector SidF in the Absence of Flagellin.Speir M, Vogrin A, Seidi A, Abraham G, Hunot S, Han Q, Dorn GW 2nd, Masters SL, Flavell RA, Vince JE, Naderer T. Front Cell Infect Microbiol. 2017; 2017 Feb 16. PMID: 28261564.
- SH2 Domain-Containing Phosphatase-2 Is a Novel Antifibrotic Regulator in Pulmonary Fibrosis.Tzouvelekis A, Yu G, Lino Cardenas CL, Herazo-Maya JD, Wang R, Woolard T, Zhang Y, Sakamoto K, Lee H, Yi JS, DeIuliis G, Xylourgidis N, Ahangari F, Lee PJ, Aidinis V, Herzog EL, Homer R, Bennett AM, Kaminski N. Am J Respir Crit Care Med. 2017 Feb 15. PMID: 27736153.
- The molecular basis of mTORC1-regulated translation.Thoreen CC. Biochem Soc Trans. 2017 Feb 8. PMID: 28202675.
- Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats.Chen J, Wang B, Regan L, Gerstein M. J Mol Biol. 2017 Feb 3; 2016 Dec 7. PMID: 27939289.
- 2-Hydroxyglutarate produced by neomorphic IDH mutations suppresses homologous recombination and induces PARP inhibitor sensitivity.Sulkowski PL, Corso CD, Robinson ND, Scanlon SE, Purshouse KR, Bai H, Liu Y, Sundaram RK, Hegan DC, Fons NR, Breuer GA, Song Y, Mishra-Gorur K, De Feyter HM, de Graaf RA, Surovtseva YV, Kachman M, Halene S, Günel M, Glazer PM, Bindra RS. Sci Transl Med. 2017 Feb 1. PMID: 28148839.
- RESA identifies mRNA-regulatory sequences at high resolution.Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. Nat Methods. 2017 Feb; 2016 Dec 26. PMID: 28024160.
- IL-10 Receptor Signaling Is Essential for TR1 Cell Function In Vivo.Brockmann L, Gagliani N, Steglich B, Giannou AD, Kempski J, Pelczar P, Geffken M, Mfarrej B, Huber F, Herkel J, Wan YY, Esplugues E, Battaglia M, Krebs CF, Flavell RA, Huber S. J Immunol. 2017 Feb 1; 2016 Dec 21. PMID: 28003377.
- Dual-Targeting Nanoparticles for In Vivo Delivery of Suicide Genes to Chemotherapy-Resistant Ovarian Cancer Cells.Cocco E, Deng Y, Shapiro EM, Bortolomai I, Lopez S, Lin K, Bellone S, Cui J, Menderes G, Black JD, Schwab CL, Bonazzoli E, Yang F, Predolini F, Zammataro L, Altwerger G, de Haydu C, Clark M, Alvarenga J, Ratner E, Azodi M, Silasi DA, Schwartz PE, Litkouhi B, Saltzman WM, Santin AD. Mol Cancer Ther. 2017 Feb; 2016 Dec 12. PMID: 27956521.
- A human microprotein that interacts with the mRNA decapping complex.D'Lima NG, Ma J, Winkler L, Chu Q, Loh KH, Corpuz EO, Budnik BA, Lykke-Andersen J, Saghatelian A, Slavoff SA. Nat Chem Biol. 2017 Feb; 2016 Dec 5. PMID: 27918561.
- Rac2 Modulates Atherosclerotic Calcification by Regulating Macrophage Interleukin-1β Production.Ceneri N, Zhao L, Young BD, Healy A, Coskun S, Vasavada H, Yarovinsky TO, Ike K, Pardi R, Qin L, Qin L, Tellides G, Hirschi K, Meadows J, Soufer R, Chun HJ, Sadeghi MM, Bender JR, Morrison AR. Arterioscler Thromb Vasc Biol. 2017 Feb; 2016 Nov 10. PMID: 27834690.
- The Steroidogenic Acute Regulatory Protein (StAR) Is Regulated by the H19/let-7 Axis.Men Y, Fan Y, Shen Y, Lu L, Kallen AN. Endocrinology. 2017 Feb 1. PMID: 27813675.
- Time to share: lessons from post hoc analyses of IPF trials.Kass DJ, Kaminski N. Thorax. 2017 Feb; 2016 Oct 27. PMID: 27789650.
- Crystal structure of Pistol, a class of self-cleaving ribozyme.Nguyen LA, Wang J, Steitz TA. Proc Natl Acad Sci U S A. 2017 Jan 31; 2017 Jan 17. PMID: 28096403.
- The Stromal Intervention: Regulation of Immunity and Inflammation at the Epithelial-Mesenchymal Barrier.Nowarski R, Jackson R, Flavell RA. Cell. 2017 Jan 26. PMID: 28129537.
- Selecting the most appropriate time points to profile in high-throughput studies.Kleyman M, Sefer E, Nicola T, Espinoza C, Chhabra D, Hagood JS, Kaminski N, Ambalavanan N, Bar-Joseph Z. Elife. 2017 Jan 26; 2017 Jan 26. PMID: 28124972.
- RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader.Kriner MA, Groisman EA. Nucleic Acids Res. 2017 Jan 25; 2016 Oct 5. PMID: 28123036.
- Structural insights into NusG regulating transcription elongation.Liu B, Steitz TA. Nucleic Acids Res. 2017 Jan 25; 2016 Nov 29. PMID: 27899640.
- Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class.Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR. Mol Cell. 2017 Jan 19; 2016 Dec 15. PMID: 27989440.
- The Biology of Free Guanidine As Revealed by Riboswitches.Breaker RR, Atilho RM, Malkowski SN, Nelson JW, Sherlock ME. Biochemistry. 2017 Jan 17; 2017 Jan 6. PMID: 28060483.
- Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria.Sherlock ME, Breaker RR. Biochemistry. 2017 Jan 17; 2017 Jan 6. PMID: 28001372.
- Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria.Sherlock ME, Malkowski SN, Breaker RR. Biochemistry. 2017 Jan 17; 2017 Jan 6. PMID: 28001368.
- Toward Precision Medicine of Symptom Control in Asthma.Gomez JL, Kaminski N. Am J Respir Crit Care Med. 2017 Jan 15. PMID: 28084831.
- Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis.Vukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, Stefanovic B, Kaminski N. BMC Pulm Med. 2017 Jan 12; 2017 Jan 12. PMID: 28081703.
- Fluorescence Amplification Method for Forward Genetic Discovery of Factors in Human mRNA Degradation.Alexandrov A, Shu MD, Steitz JA. Mol Cell. 2017 Jan 5; 2016 Dec 22. PMID: 28017590.
- Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.Reiss CW, Xiong Y, Strobel SA. Structure. 2017 Jan 3; 2016 Dec 22. PMID: 28017522.
- Local and Systemic CD4(+) T Cell Exhaustion Reverses with Clinical Resolution of Pulmonary Sarcoidosis.Hawkins C, Shaginurova G, Shelton DA, Herazo-Maya JD, Oswald-Richter KA, Rotsinger JE, Young A, Celada LJ, Kaminski N, Sevin C, Drake WP. J Immunol Res. 2017; 2017 Nov 6. PMID: 29234685.
- Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos.Heyn P, Neugebauer KM. Methods Mol Biol. 2017. PMID: 28456961.
- Axonal ribosomes and mRNAs associate with fragile X granules in adult rodent and human brains.Akins MR, Berk-Rauch HE, Kwan KY, Mitchell ME, Shepard KA, Korsak LI, Stackpole EE, Warner-Schmidt JL, Sestan N, Cameron HA, Fallon JR. Hum Mol Genet. 2017 Jan 1. PMID: 28082376.
- Early local immune defences in the respiratory tract.Iwasaki A, Foxman EF, Molony RD. Nat Rev Immunol. 2017 Jan; 2016 Nov 28. PMID: 27890913.
- Multiparameter Single Cell Profiling of Airway Inflammatory Cells.Yao Y, Welp T, Liu Q, Niu N, Wang X, Britto CJ, Krishnaswamy S, Chupp GL, Montgomery RR. Cytometry B Clin Cytom. 2017 Jan. PMID: 27807928.
- Interleukin-17A Promotes CD8+ T Cell Cytotoxicity To Facilitate West Nile Virus Clearance.Acharya D, Wang P, Paul AM, Dai J, Gate D, Lowery JE, Stokic DS, Leis AA, Flavell RA, Town T, Fikrig E, Bai F. J Virol. 2017 Jan 1; 2016 Dec 16. PMID: 27795421.
- E2F-2 Promotes Nuclear Condensation and Enucleation of Terminally Differentiated Erythroblasts.Swartz KL, Wood SN, Murthy T, Ramirez O, Qin G, Pillai MM, Rao S, Minella AC. Mol Cell Biol. 2017 Jan 1; 2016 Dec 19. PMID: 27795297.
- A structure-based kinetic model of transcription.Zuo Y, Steitz TA. Transcription. 2017 Jan; 2016 Sep 22. PMID: 27656764.
- Axon regeneration in C. elegans: Worming our way to mechanisms of axon regeneration.Byrne AB, Hammarlund M. Exp Neurol. 2017 Jan; 2016 Aug 26. PMID: 27569538.
2016
- Inhibition of Poly-ADP-Ribosylation Fails to Increase Axonal Regeneration or Improve Functional Recovery after Adult Mammalian CNS Injury.Wang X, Sekine Y, Byrne AB, Cafferty WB, Hammarlund M, Strittmatter SM. eNeuro. 2016 Nov-Dec; 2016 Dec 26. PMID: 28032120.
- Mitochondria Localize to Injured Axons to Support Regeneration.Han SM, Baig HS, Hammarlund M. Neuron. 2016 Dec 21. PMID: 28009276.
- Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans.Savage AF, Kolev NG, Franklin JB, Vigneron A, Aksoy S, Tschudi C. PLoS One. 2016; 2016 Dec 21. PMID: 28002435.
- Simultaneous dimension reduction and adjustment for confounding variation.Lin Z, Yang C, Zhu Y, Duchi J, Fu Y, Wang Y, Jiang B, Zamanighomi M, Xu X, Li M, Sestan N, Zhao H, Wong WH. Proc Natl Acad Sci U S A. 2016 Dec 20; 2016 Dec 7. PMID: 27930330.
- Hematopoietic Stem Cell Niches Produce Lineage-Instructive Signals to Control Multipotent Progenitor Differentiation.Cordeiro Gomes A, Hara T, Lim VY, Herndler-Brandstetter D, Nevius E, Sugiyama T, Tani-Ichi S, Schlenner S, Richie E, Rodewald HR, Flavell RA, Nagasawa T, Ikuta K, Pereira JP. Immunity. 2016 Dec 20; 2016 Nov 29. PMID: 27913094.
- Enriching s(4) U-RNA Using Methane Thiosulfonate (MTS) Chemistry.Duffy EE, Simon MD. Curr Protoc Chem Biol. 2016 Dec 7; 2016 Dec 7. PMID: 27925666.
- Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA.Brown JA, Kinzig CG, DeGregorio SJ, Steitz JA. Proc Natl Acad Sci U S A. 2016 Dec 6; 2016 Nov 21. PMID: 27872311.
- Localized structural frustration for evaluating the impact of sequence variants.Kumar S, Clarke D, Gerstein M. Nucleic Acids Res. 2016 Dec 1; 2016 Oct 18. PMID: 27915290.
- Novel Developments in Leukopenia and Pancytopenia.Onuoha C, Arshad J, Astle J, Xu M, Halene S. Prim Care. 2016 Dec. PMID: 27866577.
- RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis.Li J, Wang Y, Zhang Y, Wang W, Irish VF, Huang T. J Exp Bot. 2016 Dec; 2016 Nov 12. PMID: 27838638.
- TLR8 Couples SOCS-1 and Restrains TLR7-Mediated Antiviral Immunity, Exacerbating West Nile Virus Infection in Mice.Paul AM, Acharya D, Le L, Wang P, Stokic DS, Leis AA, Alexopoulou L, Town T, Flavell RA, Fikrig E, Bai F. J Immunol. 2016 Dec 1; 2016 Oct 21. PMID: 27798161.
- Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis.Peng X, Moore M, Mathur A, Zhou Y, Sun H, Gan Y, Herazo-Maya JD, Kaminski N, Hu X, Pan H, Ryu C, Osafo-Addo A, Homer RJ, Feghali-Bostwick C, Fares WH, Gulati M, Hu B, Lee CG, Elias JA, Herzog EL. FASEB J. 2016 Dec; 2016 Sep 8. PMID: 27609773.
- Preface to: "microRNAs in lipid/energy metabolism and cardiometabolic disease".Suárez Y, Fernández-Hernando C. Biochim Biophys Acta. 2016 Dec; 2016 Jul 7. PMID: 27396679.
- Expression of RXFP1 Is Decreased in Idiopathic Pulmonary Fibrosis. Implications for Relaxin-based Therapies.Tan J, Tedrow JR, Dutta JA, Juan-Guardela B, Nouraie M, Chu Y, Trejo Bittar H, Ramani K, Biswas PS, Veraldi KL, Kaminski N, Zhang Y, Kass DJ. Am J Respir Crit Care Med. 2016 Dec 1. PMID: 27310652.
- MicroRNAs as regulators of endothelial cell functions in cardiometabolic diseases.Araldi E, Suárez Y. Biochim Biophys Acta. 2016 Dec; 2016 Jan 26. PMID: 26825686.
- PI3 kinase inhibition improves vascular malformations in mouse models of hereditary haemorrhagic telangiectasia.Ola R, Dubrac A, Han J, Zhang F, Fang JS, Larrivée B, Lee M, Urarte AA, Kraehling JR, Genet G, Hirschi KK, Sessa WC, Canals FV, Graupera M, Yan M, Young LH, Oh PS, Eichmann A. Nat Commun. 2016 Nov 29; 2016 Nov 29. PMID: 27897192.
- Genome-wide RNAi screen reveals ALK1 mediates LDL uptake and transcytosis in endothelial cells.Kraehling JR, Chidlow JH, Rajagopal C, Sugiyama MG, Fowler JW, Lee MY, Zhang X, Ramírez CM, Park EJ, Tao B, Chen K, Kuruvilla L, Larriveé B, Folta-Stogniew E, Ola R, Rotllan N, Zhou W, Nagle MW, Herz J, Williams KJ, Eichmann A, Lee WL, Fernández-Hernando C, Sessa WC. Nat Commun. 2016 Nov 21; 2016 Nov 21. PMID: 27869117.
- Multifunctional Poly(amine-co-ester-co-ortho ester) for Efficient and Safe Gene Delivery.Zhang J, Cui J, Deng Y, Jiang Z, Saltzman WM. ACS Biomater Sci Eng. 2016 Nov 14; 2016 Sep 26. PMID: 28649641.
- The DNA-sensing AIM2 inflammasome controls radiation-induced cell death and tissue injury.Hu B, Jin C, Li HB, Tong J, Ouyang X, Cetinbas NM, Zhu S, Strowig T, Lam FC, Zhao C, Henao-Mejia J, Yilmaz O, Fitzgerald KA, Eisenbarth SC, Elinav E, Flavell RA. Science. 2016 Nov 11. PMID: 27846608.
- Evolution of Osteocrin as an activity-regulated factor in the primate brain.Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME. Nature. 2016 Nov 10. PMID: 27830782.
- CD301b+ dendritic cells stimulate tissue-resident memory CD8+ T cells to protect against genital HSV-2.Shin H, Kumamoto Y, Gopinath S, Iwasaki A. Nat Commun. 2016 Nov 9; 2016 Nov 9. PMID: 27827367.
- A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes.Liu Y, Vinyard DJ, Reesbeck ME, Suzuki T, Manakongtreecheep K, Holland PL, Brudvig GW, Söll D. Proc Natl Acad Sci U S A. 2016 Nov 8; 2016 Oct 24. PMID: 27791189.
- A chemical biology route to site-specific authentic protein modifications.Yang A, Ha S, Ahn J, Kim R, Kim S, Lee Y, Kim J, Söll D, Lee HY, Park HS. Science. 2016 Nov 4; 2016 Sep 29. PMID: 27708052.
- Reducing Ribosome Biosynthesis Promotes Translation during Low Mg(2+) Stress.Pontes MH, Yeom J, Groisman EA. Mol Cell. 2016 Nov 3; 2016 Oct 13. PMID: 27746019.
- Hepatitis C Virus Proteins Interact with the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery via Ubiquitination To Facilitate Viral Envelopment.Barouch-Bentov R, Neveu G, Xiao F, Beer M, Bekerman E, Schor S, Campbell J, Boonyaratanakornkit J, Lindenbach B, Lu A, Jacob Y, Einav S. mBio. 2016 Nov 1; 2016 Nov 1. PMID: 27803188.
- Microenvironment-dependent growth of preneoplastic and malignant plasma cells in humanized mice.Das R, Strowig T, Verma R, Koduru S, Hafemann A, Hopf S, Kocoglu MH, Borsotti C, Zhang L, Branagan A, Eynon E, Manz MG, Flavell RA, Dhodapkar MV. Nat Med. 2016 Nov; 2016 Oct 10. PMID: 27723723.
- TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons.Caubit X, Gubellini P, Andrieux J, Roubertoux PL, Metwaly M, Jacq B, Fatmi A, Had-Aissouni L, Kwan KY, Salin P, Carlier M, Liedén A, Rudd E, Shinawi M, Vincent-Delorme C, Cuisset JM, Lemaitre MP, Abderrehamane F, Duban B, Lemaitre JF, Woolf AS, Bockenhauer D, Severac D, Dubois E, Zhu Y, Sestan N, Garratt AN, Lydia Kerkerian-Le Goff, Fasano L. Nat Genet. 2016 Nov; 2016 Sep 26. PMID: 27668656.
- Singlet glycine riboswitches bind ligand as well as tandem riboswitches.Ruff KM, Muhammad A, McCown PJ, Breaker RR, Strobel SA. RNA. 2016 Nov; 2016 Sep 22. PMID: 27659053.
- A proximity-dependent assay for specific RNA-protein interactions in intact cells.Zhang W, Xie M, Shu MD, Steitz JA, DiMaio D. RNA. 2016 Nov; 2016 Sep 22. PMID: 27659050.
- A renaissance in plant development.Chitwood DH, Irish VF. Dev Biol. 2016 Nov 1; 2016 Sep 13. PMID: 27637462.
- Glioma-induced inhibition of caspase-3 in microglia promotes a tumor-supportive phenotype.Shen X, Burguillos MA, Osman AM, Frijhoff J, Carrillo-Jiménez A, Kanatani S, Augsten M, Saidi D, Rodhe J, Kavanagh E, Rongvaux A, Rraklli V, Nyman U, Holmberg J, Östman A, Flavell RA, Barragan A, Venero JL, Blomgren K, Joseph B. Nat Immunol. 2016 Nov; 2016 Sep 12. PMID: 27618552.
- HSV-2 enhances ZIKV infection of the placenta and induces apoptosis in first-trimester trophoblast cells.Aldo P, You Y, Szigeti K, Horvath TL, Lindenbach B, Mor G. Am J Reprod Immunol. 2016 Nov; 2016 Sep 10. PMID: 27613665.
- Comprehensive cellular-resolution atlas of the adult human brain.Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BA, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Wright M, Zöllei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, Lein ES. J Comp Neurol. 2016 Nov 1. PMID: 27418273.
- Nanotechnology for delivery of peptide nucleic acids (PNAs).Gupta A, Bahal R, Gupta M, Glazer PM, Saltzman WM. J Control Release. 2016 Oct 28; 2016 Jan 8. PMID: 26776051.
- inv(16) and NPM1mut AMLs engraft human cytokine knock-in mice.Ellegast JM, Rauch PJ, Kovtonyuk LV, Müller R, Wagner U, Saito Y, Wildner-Verhey van Wijk N, Fritz C, Rafiei A, Lysenko V, Dudkiewicz E, Theocharides AP, Soldini D, Goede JS, Flavell RA, Manz MG. Blood. 2016 Oct 27; 2016 Aug 31. PMID: 27581357.
- Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis.Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. BMC Dev Biol. 2016 Oct 26; 2016 Oct 26. PMID: 27784267.
- In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery.Bahal R, Ali McNeer N, Quijano E, Liu Y, Sulkowski P, Turchick A, Lu YC, Bhunia DC, Manna A, Greiner DL, Brehm MA, Cheng CJ, López-Giráldez F, Ricciardi A, Beloor J, Krause DS, Kumar P, Gallagher PG, Braddock DT, Mark Saltzman W, Ly DH, Glazer PM. Nat Commun. 2016 Oct 26; 2016 Oct 26. PMID: 27782131.
- A pathogenic role for T cell-derived IL-22BP in inflammatory bowel disease.Pelczar P, Witkowski M, Perez LG, Kempski J, Hammel AG, Brockmann L, Kleinschmidt D, Wende S, Haueis C, Bedke T, Witkowski M, Krasemann S, Steurer S, Booth CJ, Busch P, König A, Rauch U, Benten D, Izbicki JR, Rösch T, Lohse AW, Strowig T, Gagliani N, Flavell RA, Huber S. Science. 2016 Oct 21. PMID: 27846573.
- Platelet WDR1 suppresses platelet activity and is associated with cardiovascular disease.Montenont E, Echagarruga C, Allen N, Araldi E, Suarez Y, Berger JS. Blood. 2016 Oct 20; 2016 Sep 8. PMID: 27609643.
- DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.Wang D, He F, Maslov S, Gerstein M. PLoS Comput Biol. 2016 Oct; 2016 Oct 19. PMID: 27760135.
- Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis.Kusko RL, Brothers JF 2nd, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, Geraci M, Yang I, Schwartz DA, Beane J, Spira A, Kaminski N. Am J Respir Crit Care Med. 2016 Oct 15. PMID: 27104832.
- Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.Yip WS, Shigematsu H, Taylor DW, Baserga SJ. Nucleic Acids Res. 2016 Oct 14; 2016 Jun 24. PMID: 27342279.
- Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron.Schwalm ND 3rd, Townsend GE 2nd, Groisman EA. mBio. 2016 Oct 11; 2016 Oct 11. PMID: 27729509.
- Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA.Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TM. Nat Commun. 2016 Oct 11; 2016 Oct 11. PMID: 27725644.
- Improved i.p. drug delivery with bioadhesive nanoparticles.Deng Y, Yang F, Cocco E, Song E, Zhang J, Cui J, Mohideen M, Bellone S, Santin AD, Saltzman WM. Proc Natl Acad Sci U S A. 2016 Oct 11; 2016 Sep 23. PMID: 27663731.
- Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.Dobosz-Bartoszek M, Pinkerton MH, Otwinowski Z, Chakravarthy S, Söll D, Copeland PR, Simonović M. Nat Commun. 2016 Oct 6; 2016 Oct 6. PMID: 27708257.
- Peripheral blood CD34(+) cells efficiently engraft human cytokine knock-in mice.Saito Y, Ellegast JM, Rafiei A, Song Y, Kull D, Heikenwalder M, Rongvaux A, Halene S, Flavell RA, Manz MG. Blood. 2016 Oct 6; 2016 Aug 19. PMID: 27543436.
- Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil.Donald CL, Brennan B, Cumberworth SL, Rezelj VV, Clark JJ, Cordeiro MT, Freitas de Oliveira França R, Pena LJ, Wilkie GS, Da Silva Filipe A, Davis C, Hughes J, Varjak M, Selinger M, Zuvanov L, Owsianka AM, Patel AH, McLauchlan J, Lindenbach BD, Fall G, Sall AA, Biek R, Rehwinkel J, Schnettler E, Kohl A. PLoS Negl Trop Dis. 2016 Oct; 2016 Oct 5. PMID: 27706161.
- Inhibiting poly(ADP-ribosylation) improves axon regeneration.Byrne AB, McWhirter RD, Sekine Y, Strittmatter SM, Miller DM, Hammarlund M. Elife. 2016 Oct 4; 2016 Oct 4. PMID: 27697151.
- Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. EMBO J. 2016 Oct 4; 2016 Jul 19. PMID: 27436874.
- Optimization Strategies for the CRISPR-Cas9 Genome-Editing System.Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Cold Spring Harb Protoc. 2016 Oct 3; 2016 Oct 3. PMID: 27698246.
- Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish.Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Cold Spring Harb Protoc. 2016 Oct 3; 2016 Oct 3. PMID: 27698232.
- TFH cells progressively differentiate to regulate the germinal center response.Weinstein JS, Herman EI, Lainez B, Licona-Limón P, Esplugues E, Flavell R, Craft J. Nat Immunol. 2016 Oct; 2016 Aug 29. PMID: 27573866.
- The time-resolved transcriptome of C. elegans.Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH. Genome Res. 2016 Oct; 2016 Aug 16. PMID: 27531719.
- PEGylated squalenoyl-gemcitabine nanoparticles for the treatment of glioblastoma.Gaudin A, Song E, King AR, Saucier-Sawyer JK, Bindra R, Desmaële D, Couvreur P, Saltzman WM. Biomaterials. 2016 Oct; 2016 Aug 4. PMID: 27521616.
- A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans.Weicksel SE, Mahadav A, Moyle M, Cipriani PG, Kudron M, Pincus Z, Bahmanyar S, Abriola L, Merkel J, Gutwein M, Fernandez AG, Piano F, Gunsalus KC, Reinke V. Development. 2016 Oct 1; 2016 Aug 10. PMID: 27510972.
- Pangolin genomes and the evolution of mammalian scales and immunity.Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ. Genome Res. 2016 Oct; 2016 Aug 10. PMID: 27510566.
- Expression of asthma susceptibility genes in bronchial epithelial cells and bronchial alveolar lavage in the Severe Asthma Research Program (SARP) cohort.Li X, Hawkins GA, Moore WC, Hastie AT, Ampleford EJ, Milosevic J, Li H, Busse WW, Erzurum SC, Kaminski N, Wenzel SE, Bleecker ER, Meyers DA. J Asthma. 2016 Oct; 2016 Apr 6. PMID: 27050946.
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- Viral Spread to Enteric Neurons Links Genital HSV-1 Infection to Toxic Megacolon and Lethality.Khoury-Hanold W, Yordy B, Kong P, Kong Y, Ge W, Szigeti-Buck K, Ralevski A, Horvath TL, Iwasaki A. Cell Host Microbe. 2016 Jun 8. PMID: 27281569.
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- Akt-mediated foxo1 inhibition is required for liver regeneration.Pauta M, Rotllan N, Fernández-Hernando A, Langhi C, Ribera J, Lu M, Boix L, Bruix J, Jimenez W, Suárez Y, Ford DA, Baldán A, Birnbaum MJ, Morales-Ruiz M, Fernández-Hernando C. Hepatology. 2016 May; 2015 Dec 18. PMID: 26473496.
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- In Vivo Biosynthesis of a β-Amino Acid-Containing Protein.Melo Czekster C, Robertson WE, Walker AS, Söll D, Schepartz A. J Am Chem Soc. 2016 Apr 27; 2016 Apr 18. PMID: 27086674.
- Diverse human extracellular RNAs are widely detected in human plasma.Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova-Zamor M, Mikhalev E, Tanriverdi K. Nat Commun. 2016 Apr 26; 2016 Apr 26. PMID: 27112789.
- Mx1 reveals innate pathways to antiviral resistance and lethal influenza disease.Pillai PS, Molony RD, Martinod K, Dong H, Pang IK, Tal MC, Solis AG, Bielecki P, Mohanty S, Trentalange M, Homer RJ, Flavell RA, Wagner DD, Montgomery RR, Shaw AC, Staeheli P, Iwasaki A. Science. 2016 Apr 22. PMID: 27102485.
- Configuration-dependent Presentation of Multivalent IL-15:IL-15Rα Enhances the Antigen-specific T Cell Response and Anti-tumor Immunity.Hong E, Usiskin IM, Bergamaschi C, Hanlon DJ, Edelson RL, Justesen S, Pavlakis GN, Flavell RA, Fahmy TM. J Biol Chem. 2016 Apr 22; 2015 Dec 30. PMID: 26719339.
- PD-1 marks dysfunctional regulatory T cells in malignant gliomas.Lowther DE, Goods BA, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA. JCI Insight. 2016 Apr 21. PMID: 27182555.
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- A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. Nat Commun. 2016 Apr 18; 2016 Apr 18. PMID: 27089393.
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- Increased susceptibility of Cftr-/- mice to LPS-induced lung remodeling.Bruscia EM, Zhang PX, Barone C, Scholte BJ, Homer R, Krause DS, Egan ME. Am J Physiol Lung Cell Mol Physiol. 2016 Apr 15; 2016 Feb 5. PMID: 26851259.
- The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome.McCann KL, Teramoto T, Zhang J, Tanaka Hall TM, Baserga SJ. Elife. 2016 Apr 14; 2016 Apr 14. PMID: 27077951.
- Extending gene ontology in the context of extracellular RNA and vesicle communication.Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. J Biomed Semantics. 2016; 2016 Apr 12. PMID: 27076901.
- Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism.Liu B, Zuo Y, Steitz TA. Proc Natl Acad Sci U S A. 2016 Apr 12; 2016 Mar 28. PMID: 27035955.
- Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.Oesterreich FC, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM. Cell. 2016 Apr 7; 2016 Mar 24. PMID: 27020755.
- The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures.Pirakitikulr N, Kohlway A, Lindenbach BD, Pyle AM. Mol Cell. 2016 Apr 7; 2016 Feb 25. PMID: 26924328.
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- The TAM family receptor tyrosine kinase TYRO3 is a negative regulator of type 2 immunity.Chan PY, Carrera Silva EA, De Kouchkovsky D, Joannas LD, Hao L, Hu D, Huntsman S, Eng C, Licona-Limón P, Weinstein JS, Herbert DR, Craft JE, Flavell RA, Repetto S, Correale J, Burchard EG, Torgerson DG, Ghosh S, Rothlin CV. Science. 2016 Apr 1. PMID: 27034374.
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- miR-155 Overexpression Promotes Genomic Instability by Reducing High-fidelity Polymerase Delta Expression and Activating Error-Prone DSB Repair.Czochor JR, Sulkowski P, Glazer PM. Mol Cancer Res. 2016 Apr; 2016 Feb 5. PMID: 26850462.
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- Repeatable Population Dynamics among Vesicular Stomatitis Virus Lineages Evolved under High Co-infection.Williams ES, Morales NM, Wasik BR, Brusic V, Whelan SP, Turner PE. Front Microbiol. 2016; 2016 Mar 31. PMID: 27065953.
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- Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M. Cell Syst. 2016 Mar 23. PMID: 27047991.
- The real cost of sequencing: scaling computation to keep pace with data generation.Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. Genome Biol. 2016 Mar 23; 2016 Mar 23. PMID: 27009100.
- Interaction between Simian Virus 40 Major Capsid Protein VP1 and Cell Surface Ganglioside GM1 Triggers Vacuole Formation.Luo Y, Motamedi N, Magaldi TG, Gee GV, Atwood WJ, DiMaio D. mBio. 2016 Mar 22; 2016 Mar 22. PMID: 27006465.
- EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression.Lee N, Yario TA, Gao JS, Steitz JA. Proc Natl Acad Sci U S A. 2016 Mar 22; 2016 Mar 7. PMID: 26951683.
- Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition.Gagnon MG, Roy RN, Lomakin IB, Florin T, Mankin AS, Steitz TA. Nucleic Acids Res. 2016 Mar 18; 2016 Jan 24. PMID: 26809677.
- An oxidase road to platelet adhesion.Krause DS. Blood. 2016 Mar 17. PMID: 26989190.
- Down Syndrome Developmental Brain Transcriptome Reveals Defective Oligodendrocyte Differentiation and Myelination.Olmos-Serrano JL, Kang HJ, Tyler WA, Silbereis JC, Cheng F, Zhu Y, Pletikos M, Jankovic-Rapan L, Cramer NP, Galdzicki Z, Goodliffe J, Peters A, Sethares C, Delalle I, Golden JA, Haydar TF, Sestan N. Neuron. 2016 Mar 16; 2016 Feb 25. PMID: 26924435.
- [Dual genetic encoding of acetyl-lysine and non-deacetylatablethioacetyl-lysine mediated by flexizyme].Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Angew Chem Weinheim Bergstr Ger. 2016 Mar 14; 2016 Feb 23. PMID: 27330229.
- Dual Genetic Encoding of Acetyl-lysine and Non-deacetylatable Thioacetyl-lysine Mediated by Flexizyme.Xiong H, Reynolds NM, Fan C, Englert M, Hoyer D, Miller SJ, Söll D. Angew Chem Int Ed Engl. 2016 Mar 14; 2016 Feb 23. PMID: 26914285.
- CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS.Chen M, Lin H, Zhao H. Ann Appl Stat. 2016 Mar; 2016 Mar 25. PMID: 27231496.
- SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export.Müller-McNicoll M, Botti V, de Jesus Domingues AM, Brandl H, Schwich OD, Steiner MC, Curk T, Poser I, Zarnack K, Neugebauer KM. Genes Dev. 2016 Mar 1. PMID: 26944680.
- Quantification of private information leakage from phenotype-genotype data: linking attacks.Harmanci A, Gerstein M. Nat Methods. 2016 Mar; 2016 Feb 1. PMID: 26828419.
- Smooth Muscle Hypoxia-Inducible Factor 1α Links Intravascular Pressure and Atherosclerosis--Brief Report.Liu D, Lei L, Desir M, Huang Y, Cleman J, Jiang W, Fernandez-Hernando C, Di Lorenzo A, Sessa WC, Giordano FJ. Arterioscler Thromb Vasc Biol. 2016 Mar; 2016 Jan 21. PMID: 26800562.
- Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins.Peng JC, Valouev A, Liu N, Lin H. Nat Genet. 2016 Mar; 2016 Jan 18. PMID: 26780607.
- The molecular actions of oestrogen in the regulation of vascular health.Usselman CW, Stachenfeld NS, Bender JR. Exp Physiol. 2016 Mar. PMID: 26778523.
- Regulation of alveolar septation by microRNA-489.Olave N, Lal CV, Halloran B, Pandit K, Cuna AC, Faye-Petersen OM, Kelly DR, Nicola T, Benos PV, Kaminski N, Ambalavanan N. Am J Physiol Lung Cell Mol Physiol. 2016 Mar 1; 2015 Dec 30. PMID: 26719145.
- Transcriptome Analysis of the Human Striatum in Tourette Syndrome.Lennington JB, Coppola G, Kataoka-Sasaki Y, Fernandez TV, Palejev D, Li Y, Huttner A, Pletikos M, Sestan N, Leckman JF, Vaccarino FM. Biol Psychiatry. 2016 Mar 1; 2014 Jul 24. PMID: 25199956.
- Isolation and Culture of Adult Zebrafish Brain-derived Neurospheres.Lopez-Ramirez MA, Calvo CF, Ristori E, Thomas JL, Nicoli S. J Vis Exp. 2016 Feb 29; 2016 Feb 29. PMID: 26967835.
- Challenges in RNA Structural Modeling and Design.Pyle AM, Schlick T. J Mol Biol. 2016 Feb 27; 2016 Feb 12. PMID: 26876599.
- Excitatory transmission onto AgRP neurons is regulated by cJun NH2-terminal kinase 3 in response to metabolic stress.Vernia S, Morel C, Madara JC, Cavanagh-Kyros J, Barrett T, Chase K, Kennedy NJ, Jung DY, Kim JK, Aronin N, Flavell RA, Lowell BB, Davis RJ. Elife. 2016 Feb 24; 2016 Feb 24. PMID: 26910012.
- YY1 inhibits differentiation and function of regulatory T cells by blocking Foxp3 expression and activity.Hwang SS, Jang SW, Kim MK, Kim LK, Kim BS, Kim HS, Kim K, Lee W, Flavell RA, Lee GR. Nat Commun. 2016 Feb 19; 2016 Feb 19. PMID: 26892542.
- Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2.Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJ. Neuron. 2016 Feb 17; 2016 Jan 28. PMID: 26833134.
- The Wnt Antagonist Dickkopf-1 Promotes Pathological Type 2 Cell-Mediated Inflammation.Chae WJ, Ehrlich AK, Chan PY, Teixeira AM, Henegariu O, Hao L, Shin JH, Park JH, Tang WH, Kim ST, Maher SE, Goldsmith-Pestana K, Shan P, Hwa J, Lee PJ, Krause DS, Rothlin CV, McMahon-Pratt D, Bothwell AL. Immunity. 2016 Feb 16; 2016 Feb 9. PMID: 26872695.
- Understanding genome structural variations.Abyzov A, Li S, Gerstein MB. Oncotarget. 2016 Feb 16. PMID: 26657727.
- miR-34a Silences c-SRC to Attenuate Tumor Growth in Triple-Negative Breast Cancer.Adams BD, Wali VB, Cheng CJ, Inukai S, Booth CJ, Agarwal S, Rimm DL, Győrffy B, Santarpia L, Pusztai L, Saltzman WM, Slack FJ. Cancer Res. 2016 Feb 15; 2015 Dec 16. PMID: 26676753.
- Editorial overview: Nucleic acids and their protein complexes.Lilley DM, Pyle AM. Curr Opin Struct Biol. 2016 Feb; 2016 Mar 2. PMID: 26948825.
- Generalized selection to overcome innate immunity selects for host breadth in an RNA virus.Wasik BR, Muñoz-Rojas AR, Okamoto KW, Miller-Jensen K, Turner PE. Evolution. 2016 Feb; 2016 Jan 20. PMID: 26882316.
- Editing the Mouse Genome Using the CRISPR-Cas9 System.Williams A, Henao-Mejia J, Flavell RA. Cold Spring Harb Protoc. 2016 Feb 1; 2016 Feb 1. PMID: 26832693.
- Generation of Genetically Modified Mice Using the CRISPR-Cas9 Genome-Editing System.Henao-Mejia J, Williams A, Rongvaux A, Stein J, Hughes C, Flavell RA. Cold Spring Harb Protoc. 2016 Feb 1; 2016 Feb 1. PMID: 26832688.
- SREBP-1c/MicroRNA 33b Genomic Loci Control Adipocyte Differentiation.Price NL, Holtrup B, Kwei SL, Wabitsch M, Rodeheffer M, Bianchini L, Suárez Y, Fernández-Hernando C. Mol Cell Biol. 2016 Feb 1; 2016 Feb 1. PMID: 26830228.
- O-linked sugars sound the alarm.Gopinath S, Kumamoto Y, Iwasaki A. Nat Immunol. 2016 Feb. PMID: 26784258.
- Role of non-coding sequence variants in cancer.Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M. Nat Rev Genet. 2016 Feb; 2016 Jan 19. PMID: 26781813.
- NgBR is essential for endothelial cell glycosylation and vascular development.Park EJ, Grabińska KA, Guan Z, Sessa WC. EMBO Rep. 2016 Feb; 2016 Jan 11. PMID: 26755743.
- The Protein Acyl Transferase ZDHHC21 Modulates α1 Adrenergic Receptor Function and Regulates Hemodynamics.Marin EP, Jozsef L, Di Lorenzo A, Held KF, Luciano AK, Melendez J, Milstone LM, Velazquez H, Sessa WC. Arterioscler Thromb Vasc Biol. 2016 Feb; 2015 Dec 29. PMID: 26715683.
- Engineering an allosteric transcription factor to respond to new ligands.Taylor ND, Garruss AS, Moretti R, Chan S, Arbing MA, Cascio D, Rogers JK, Isaacs FJ, Kosuri S, Baker D, Fields S, Church GM, Raman S. Nat Methods. 2016 Feb; 2015 Dec 21. PMID: 26689263.
- A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting.Herbert KM, Sarkar SK, Mills M, Delgado De la Herran HC, Neuman KC, Steitz JA. RNA. 2016 Feb; 2015 Dec 18. PMID: 26683315.
- Stromal Expression of miR-143/145 Promotes Neoangiogenesis in Lung Cancer Development.Dimitrova N, Gocheva V, Bhutkar A, Resnick R, Jong RM, Miller KM, Bendor J, Jacks T. Cancer Discov. 2016 Feb; 2015 Nov 19. PMID: 26586766.
- T Cell Receptor Mediated Calcium Entry Requires Alternatively Spliced Cav1.1 Channels.Matza D, Badou A, Klemic KG, Stein J, Govindarajulu U, Nadler MJ, Kinet JP, Peled A, Shapira OM, Kaczmarek LK, Flavell RA. PLoS One. 2016; 2016 Jan 27. PMID: 26815481.
- Tudor-SN Interacts with Piwi Antagonistically in Regulating Spermatogenesis but Synergistically in Silencing Transposons in Drosophila.Ku HY, Gangaraju VK, Qi H, Liu N, Lin H. PLoS Genet. 2016 Jan; 2016 Jan 25. PMID: 26808625.
- Evolution in spatially mixed host environments increases divergence for evolved fitness and intrapopulation genetic diversity in RNA viruses.Morley VJ, Sistrom M, Usme-Ciro JA, Remold SK, Turner PE. Virus Evol. 2016 Jan; 2016 Jan 20. PMID: 27774292.
- The Cellular and Molecular Landscapes of the Developing Human Central Nervous System.Silbereis JC, Pochareddy S, Zhu Y, Li M, Sestan N. Neuron. 2016 Jan 20. PMID: 26796689.
- miR-430 regulates oriented cell division during neural tube development in zebrafish.Takacs CM, Giraldez AJ. Dev Biol. 2016 Jan 15; 2015 Nov 30. PMID: 26658217.
- Adding insult to injury: autoimmune haemolytic anaemia complicated by pulmonary embolism.Woodson KA, Lee Y, Gopalratnam K, Halene S. BMJ Case Rep. 2016 Jan 14; 2016 Jan 14. PMID: 26768839.
- Thank You, Edward. Merci, Louis.DiMaio D. PLoS Pathog. 2016 Jan; 2016 Jan 14. PMID: 26766042.
- Autophagy Snuffs a Macrophage's Inner Fire.Khoury-Hanold W, Iwasaki A. Cell Host Microbe. 2016 Jan 13. PMID: 26764592.
- Uncoupling Caveolae From Intracellular Signaling In Vivo.Kraehling JR, Hao Z, Lee MY, Vinyard DJ, Velazquez H, Liu X, Stan RV, Brudvig GW, Sessa WC. Circ Res. 2016 Jan 8; 2015 Nov 24. PMID: 26602865.
- VEGF-Induced Expression of miR-17-92 Cluster in Endothelial Cells Is Mediated by ERK/ELK1 Activation and Regulates Angiogenesis.Chamorro-Jorganes A, Lee MY, Araldi E, Landskroner-Eiger S, Fernández-Fuertes M, Sahraei M, Quiles Del Rey M, van Solingen C, Yu J, Fernández-Hernando C, Sessa WC, Suárez Y. Circ Res. 2016 Jan 8; 2015 Oct 15. PMID: 26472816.
- Gatekeeper role of brain antigen-presenting CD11c+ cells in neuroinflammation.Paterka M, Siffrin V, Voss JO, Werr J, Hoppmann N, Gollan R, Belikan P, Bruttger J, Birkenstock J, Jung S, Esplugues E, Yogev N, Flavell RA, Bopp T, Zipp F. EMBO J. 2016 Jan 4; 2015 Nov 26. PMID: 26612827.
- Calcium signaling and transcription: elongation, DoGs, and eRNAs.Vilborg A, Passarelli MC, Steitz JA. Receptors Clin Investig. 2016; 2016 Feb 1. PMID: 29147672.
- The SGLT-2 Inhibitor Dapagliflozin Has a Therapeutic Effect on Atherosclerosis in Diabetic ApoE(-/-) Mice.Leng W, Ouyang X, Lei X, Wu M, Chen L, Wu Q, Deng W, Liang Z. Mediators Inflamm. 2016; 2016 Dec 26. PMID: 28104929.
- PTPN22 inhibition resets defective human central B cell tolerance.Schickel JN, Kuhny M, Baldo A, Bannock JM, Massad C, Wang H, Katz N, Oe T, Menard L, Soulas-Sprauel P, Strowig T, Flavell R, Meffre E. Sci Immunol. 2016; 2016 Jul 22. PMID: 27917411.
- Post-GWAS Prioritization Through Data Integration Provides Novel Insights on Chronic Obstructive Pulmonary Disease.Lu Q, Jin C, Sun J, Bowler R, Kechris K, Kaminski N, Zhao H. Stat Biosci. 2016; 2016 Jun 13. PMID: 27812370.
- Capture Hybridization Analysis of DNA Targets.Sexton AN, Machyna M, Simon MD. Methods Mol Biol. 2016. PMID: 27659977.
- Signal Transduction and Regulation: Insights into Evolution.Yi S, Chen S, Zhang L, Sahni N. Biomed Res Int. 2016; 2016 Jul 20. PMID: 27525280.
- Intronless β-Globin Reporter: A Tool for Studying Nuclear RNA Stability Elements.Brown JA, Steitz JA. Methods Mol Biol. 2016. PMID: 27236793.
- Blocking MHC class II on human endothelium mitigates acute rejection.Abrahimi P, Qin L, Chang WG, Bothwell AL, Tellides G, Saltzman WM, Pober JS. JCI Insight. 2016; 2016 Jan 21. PMID: 26900601.
- Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM, Ait-Si-Ali S, Akematsu T, Akporiaye ET, Al-Rubeai M, Albaiceta GM, Albanese C, Albani D, Albert ML, Aldudo J, Algül H, Alirezaei M, Alloza I, Almasan A, Almonte-Beceril M, Alnemri ES, Alonso C, Altan-Bonnet N, Altieri DC, Alvarez S, Alvarez-Erviti L, Alves S, Amadoro G, Amano A, Amantini C, Ambrosio S, Amelio I, Amer AO, Amessou M, Amon A, An Z, Anania FA, Andersen SU, Andley UP, Andreadi CK, Andrieu-Abadie N, Anel A, Ann DK, Anoopkumar-Dukie S, Antonioli M, Aoki H, Apostolova N, Aquila S, Aquilano K, Araki K, Arama E, Aranda A, Araya J, Arcaro A, Arias E, Arimoto H, Ariosa AR, Armstrong JL, Arnould T, Arsov I, Asanuma K, Askanas V, Asselin E, Atarashi R, Atherton SS, Atkin JD, Attardi LD, Auberger P, Auburger G, Aurelian L, Autelli R, Avagliano L, Avantaggiati ML, Avrahami L, Awale S, Azad N, Bachetti T, Backer JM, Bae DH, Bae JS, Bae ON, Bae SH, Baehrecke EH, Baek SH, Baghdiguian S, Bagniewska-Zadworna A, Bai H, Bai J, Bai XY, Bailly Y, Balaji KN, Balduini W, Ballabio A, Balzan R, Banerjee R, Bánhegyi G, Bao H, Barbeau B, Barrachina MD, Barreiro E, Bartel B, Bartolomé A, Bassham DC, Bassi MT, Bast RC Jr, Basu A, Batista MT, Batoko H, Battino M, Bauckman K, Baumgarner BL, Bayer KU, Beale R, Beaulieu JF, Beck GR Jr, Becker C, Beckham JD, Bédard PA, Bednarski PJ, Begley TJ, Behl C, Behrends C, Behrens GM, Behrns KE, Bejarano E, Belaid A, Belleudi F, Bénard G, Berchem G, Bergamaschi D, Bergami M, Berkhout B, Berliocchi L, Bernard A, Bernard M, Bernassola F, Bertolotti A, Bess AS, Besteiro S, Bettuzzi S, Bhalla S, Bhattacharyya S, Bhutia SK, Biagosch C, Bianchi MW, Biard-Piechaczyk M, Billes V, Bincoletto C, Bingol B, Bird SW, Bitoun M, Bjedov I, 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Yin XM, Yip CK, Yoo YM, Yoo YH, Yoon SY, Yoshida K, Yoshimori T, Young KH, Yu H, Yu JJ, Yu JT, Yu J, Yu L, Yu WH, Yu XF, Yu Z, Yuan J, Yuan ZM, Yue BY, Yue J, Yue Z, Zacks DN, Zacksenhaus E, Zaffaroni N, Zaglia T, Zakeri Z, Zecchini V, Zeng J, Zeng M, Zeng Q, Zervos AS, Zhang DD, Zhang F, Zhang G, Zhang GC, Zhang H, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang J, Zhang JP, Zhang L, Zhang L, Zhang L, Zhang L, Zhang MY, Zhang X, Zhang XD, Zhang Y, Zhang Y, Zhang Y, Zhang Y, Zhang Y, Zhao M, Zhao WL, Zhao X, Zhao YG, Zhao Y, Zhao Y, Zhao YX, Zhao Z, Zhao ZJ, Zheng D, Zheng XL, Zheng X, Zhivotovsky B, Zhong Q, Zhou GZ, Zhou G, Zhou H, Zhou SF, Zhou XJ, Zhu H, Zhu H, Zhu WG, Zhu W, Zhu XF, Zhu Y, Zhuang SM, Zhuang X, Ziparo E, Zois CE, Zoladek T, Zong WX, Zorzano A, Zughaier SM. 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- Humanized hemato-lymphoid system mice.Theocharides AP, Rongvaux A, Fritsch K, Flavell RA, Manz MG. Haematologica. 2016 Jan. PMID: 26721800.
- Cell penetrating peptide-modified poly(lactic-co-glycolic acid) nanoparticles with enhanced cell internalization.Steinbach JM, Seo YE, Saltzman WM. Acta Biomater. 2016 Jan; 2015 Nov 18. PMID: 26602822.
- The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane.Baskin JM, Wu X, Christiano R, Oh MS, Schauder CM, Gazzerro E, Messa M, Baldassari S, Assereto S, Biancheri R, Zara F, Minetti C, Raimondi A, Simons M, Walther TC, Reinisch KM, De Camilli P. Nat Cell Biol. 2016 Jan; 2015 Nov 16. PMID: 26571211.
- Expression of activation-induced cytidine deaminase enhances the clearance of pneumococcal pneumonia: evidence of a subpopulation of protective anti-pneumococcal B1a cells.Yamamoto N, Kerfoot SM, Hutchinson AT, Dela Cruz CS, Nakazawa N, Szczepanik M, Majewska-Szczepanik M, Nazimek K, Ohana N, Bryniarski K, Mori T, Muramatsu M, Kanemitsu K, Askenase PW. Immunology. 2016 Jan. PMID: 26456931.
- Gene networks controlling petal organogenesis.Huang T, Irish VF. J Exp Bot. 2016 Jan; 2015 Oct 1. PMID: 26428062.
- Insight into lncRNA biology using hybridization capture analyses.Simon MD. Biochim Biophys Acta. 2016 Jan; 2015 Sep 14. PMID: 26381323.
- IL-10-producing forkhead box protein 3-negative regulatory T cells inhibit B-cell responses and are involved in systemic lupus erythematosus.Facciotti F, Gagliani N, Häringer B, Alfen JS, Penatti A, Maglie S, Paroni M, Iseppon A, Moro M, Crosti MC, Stölzel K, Romagnani C, Moroni G, Ingegnoli F, Torretta S, Pignataro L, Annoni A, Russo F, Pagani M, Abrignani S, Meroni P, Flavell R, Geginat J. J Allergy Clin Immunol. 2016 Jan; 2015 Aug 25. PMID: 26318071.
2015
- Stelliosphaerols A and B, Sesquiterpene-Polyol Conjugates from an Ecuadorian Fungal Endophyte.Forcina GC, Castro A, Bokesch HR, Spakowicz DJ, Legaspi ME, Kucera K, Villota S, Narváez-Trujillo A, McMahon JB, Gustafson KR, Strobel SA. J Nat Prod. 2015 Dec 24; 2015 Dec 14. PMID: 26651879.
- Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola.Sistrom M, Park D, O'Brien HE, Wang Z, Guttman DS, Townsend JP, Turner PE. PLoS One. 2015; 2015 Dec 15. PMID: 26670219.
- An RNA motif advances transcription by preventing Rho-dependent termination.Sevostyanova A, Groisman EA. Proc Natl Acad Sci U S A. 2015 Dec 15; 2015 Nov 16. PMID: 26630006.
- Probing the active site tryptophan of Staphylococcus aureus thioredoxin with an analog.Englert M, Nakamura A, Wang YS, Eiler D, Söll D, Guo LT. Nucleic Acids Res. 2015 Dec 15; 2015 Nov 17. PMID: 26582921.
- Rationally evolving tRNAPyl for efficient incorporation of noncanonical amino acids.Fan C, Xiong H, Reynolds NM, Söll D. Nucleic Acids Res. 2015 Dec 15; 2015 Aug 6. PMID: 26250114.
- Probing Xist RNA Structure in Cells Using Targeted Structure-Seq.Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. PLoS Genet. 2015 Dec; 2015 Dec 8. PMID: 26646615.
- The Bacterial Transcription Termination Factor Rho Coordinates Mg(2+) Homeostasis with Translational Signals.Kriner MA, Groisman EA. J Mol Biol. 2015 Dec 4; 2015 Oct 30. PMID: 26523680.
- Epithelial IL-18 Equilibrium Controls Barrier Function in Colitis.Nowarski R, Jackson R, Gagliani N, de Zoete MR, Palm NW, Bailis W, Low JS, Harman CC, Graham M, Elinav E, Flavell RA. Cell. 2015 Dec 3. PMID: 26638073.
- Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling.Levy M, Thaiss CA, Zeevi D, Dohnalová L, Zilberman-Schapira G, Mahdi JA, David E, Savidor A, Korem T, Herzig Y, Pevsner-Fischer M, Shapiro H, Christ A, Harmelin A, Halpern Z, Latz E, Flavell RA, Amit I, Segal E, Elinav E. Cell. 2015 Dec 3. PMID: 26638072.
- The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador.Rundell SM, Spakowicz DJ, Narváez-Trujillo A, Strobel SA. J Fungi (Basel). 2015 Dec 2; 2015 Dec 2. PMID: 29376917.
- Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms.D'Gama AM, Pochareddy S, Li M, Jamuar SS, Reiff RE, Lam AN, Sestan N, Walsh CA. Neuron. 2015 Dec 2. PMID: 26637798.
- Reads meet rotamers: structural biology in the age of deep sequencing.Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Curr Opin Struct Biol. 2015 Dec; 2015 Dec 1. PMID: 26658741.
- Enhancing potency of siRNA targeting fusion genes by optimization outside of target sequence.Gavrilov K, Seo YE, Tietjen GT, Cui J, Cheng CJ, Saltzman WM. Proc Natl Acad Sci U S A. 2015 Dec 1; 2015 Nov 16. PMID: 26627251.
- The PsychENCODE project.Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. Nat Neurosci. 2015 Dec. PMID: 26605881.
- Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids.Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, Isaacs FJ. Nat Biotechnol. 2015 Dec; 2015 Nov 16. PMID: 26571098.
- Transition State Charge Stabilization and Acid-Base Catalysis of mRNA Cleavage by the Endoribonuclease RelE.Dunican BF, Hiller DA, Strobel SA. Biochemistry. 2015 Dec 1; 2015 Nov 12. PMID: 26535789.
- miR-27b inhibits LDLR and ABCA1 expression but does not influence plasma and hepatic lipid levels in mice.Goedeke L, Rotllan N, Ramírez CM, Aranda JF, Canfrán-Duque A, Araldi E, Fernández-Hernando A, Langhi C, de Cabo R, Baldán Á, Suárez Y, Fernández-Hernando C. Atherosclerosis. 2015 Dec. PMID: 26520906.
- Crystal structure of group II intron domain 1 reveals a template for RNA assembly.Zhao C, Rajashankar KR, Marcia M, Pyle AM. Nat Chem Biol. 2015 Dec; 2015 Oct 26. PMID: 26502156.
- Guanylate binding proteins enable rapid activation of canonical and noncanonical inflammasomes in Chlamydia-infected macrophages.Finethy R, Jorgensen I, Haldar AK, de Zoete MR, Strowig T, Flavell RA, Yamamoto M, Nagarajan UM, Miao EA, Coers J. Infect Immun. 2015 Dec; 2015 Sep 28. PMID: 26416908.
- A sunblock based on bioadhesive nanoparticles.Deng Y, Ediriwickrema A, Yang F, Lewis J, Girardi M, Saltzman WM. Nat Mater. 2015 Dec; 2015 Sep 28. PMID: 26413985.
- VCAM-1 is a TGF-β1 inducible gene upregulated in idiopathic pulmonary fibrosis.Agassandian M, Tedrow JR, Sembrat J, Kass DJ, Zhang Y, Goncharova EA, Kaminski N, Mallampalli RK, Vuga LJ. Cell Signal. 2015 Dec; 2015 Sep 18. PMID: 26386411.
- In silico discovery and modeling of non-coding RNA structure in viruses.Moss WN, Steitz JA. Methods. 2015 Dec; 2015 Jun 23. PMID: 26116541.
- Clostridium perfringens enterotoxin C-terminal domain labeled to fluorescent dyes for in vivo visualization of micrometastatic chemotherapy-resistant ovarian cancer.Cocco E, Shapiro EM, Gasparrini S, Lopez S, Schwab CL, Bellone S, Bortolomai I, Sumi NJ, Bonazzoli E, Nicoletti R, Deng Y, Saltzman WM, Zeiss CJ, Centritto F, Black JD, Silasi DA, Ratner E, Azodi M, Rutherford TJ, Schwartz PE, Pecorelli S, Santin AD. Int J Cancer. 2015 Dec 1; 2015 Aug 18. PMID: 26060989.
- A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis.Huang Y, Ma SF, Vij R, Oldham JM, Herazo-Maya J, Broderick SM, Strek ME, White SR, Hogarth DK, Sandbo NK, Lussier YA, Gibson KF, Kaminski N, Garcia JG, Noth I. BMC Pulm Med. 2015 Nov 21; 2015 Nov 21. PMID: 26589497.
- Nanomedicine gets personal.Tietjen GT, Saltzman WM. Sci Transl Med. 2015 Nov 18. PMID: 26582895.
- High-order neural networks and kernel methods for peptide-MHC binding prediction.Kuksa PP, Min MR, Dugar R, Gerstein M. Bioinformatics. 2015 Nov 15; 2015 Jul 23. PMID: 26206306.
- Nlrp6 regulates intestinal antiviral innate immunity.Wang P, Zhu S, Yang L, Cui S, Pan W, Jackson R, Zheng Y, Rongvaux A, Sun Q, Yang G, Gao S, Lin R, You F, Flavell R, Fikrig E. Science. 2015 Nov 13; 2015 Oct 22. PMID: 26494172.
- Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes.Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N. BMC Genomics. 2015 Nov 11; 2015 Nov 11. PMID: 26560100.
- Survival of Hepatitis C Virus in Syringes Is Dependent on the Design of the Syringe-Needle and Dead Space Volume.Binka M, Paintsil E, Patel A, Lindenbach BD, Heimer R. PLoS One. 2015; 2015 Nov 4. PMID: 26536599.
- Neuregulin-activated ERBB4 induces the SREBP-2 cholesterol biosynthetic pathway and increases low-density lipoprotein uptake.Haskins JW, Zhang S, Means RE, Kelleher JK, Cline GW, Canfrán-Duque A, Suárez Y, Stern DF. Sci Signal. 2015 Nov 3; 2015 Nov 3. PMID: 26535009.
- Reply: the bleomycin model: in pursuit of relevant biomakers.Bauer Y, Nayler O, Kaminski N. Am J Respir Cell Mol Biol. 2015 Nov. PMID: 26517754.
- MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels.Goedeke L, Rotllan N, Canfrán-Duque A, Aranda JF, Ramírez CM, Araldi E, Lin CS, Anderson NN, Wagschal A, de Cabo R, Horton JD, Lasunción MA, Näär AM, Suárez Y, Fernández-Hernando C. Nat Med. 2015 Nov; 2015 Oct 5. PMID: 26437365.
- Tissue-Engineered Microvasculature to Reperfuse Isolated Renal Glomeruli.Chang WG, Fornoni A, Tietjen G, Mendez JJ, Niklason LE, Saltzman WM, Pober JS. Tissue Eng Part A. 2015 Nov; 2015 Oct 1. PMID: 26414101.
- Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology.Ling J, O'Donoghue P, Söll D. Nat Rev Microbiol. 2015 Nov; 2015 Sep 22. PMID: 26411296.
- Biochemical analysis of hatchet self-cleaving ribozymes.Li S, Lünse CE, Harris KA, Breaker RR. RNA. 2015 Nov; 2015 Sep 18. PMID: 26385510.
- Biochemical analysis of pistol self-cleaving ribozymes.Harris KA, Lünse CE, Li S, Brewer KI, Breaker RR. RNA. 2015 Nov; 2015 Sep 18. PMID: 26385507.
- Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators.Guo YE, Oei T, Steitz JA. J Virol. 2015 Nov; 2015 Aug 19. PMID: 26292323.
- Essential roles for Cavβ2 and Cav1 channels in thymocyte development and T cell homeostasis.Jha A, Singh AK, Weissgerber P, Freichel M, Flockerzi V, Flavell RA, Jha MK. Sci Signal. 2015 Oct 20; 2015 Oct 20. PMID: 26486172.
- Endothelial miR-17∼92 cluster negatively regulates arteriogenesis via miRNA-19 repression of WNT signaling.Landskroner-Eiger S, Qiu C, Perrotta P, Siragusa M, Lee MY, Ulrich V, Luciano AK, Zhuang ZW, Corti F, Simons M, Montgomery RL, Wu D, Yu J, Sessa WC. Proc Natl Acad Sci U S A. 2015 Oct 13; 2015 Sep 28. PMID: 26417068.
- Mesenchymal stem cells use extracellular vesicles to outsource mitophagy and shuttle microRNAs.Phinney DG, Di Giuseppe M, Njah J, Sala E, Shiva S, St Croix CM, Stolz DB, Watkins SC, Di YP, Leikauf GD, Kolls J, Riches DW, Deiuliis G, Kaminski N, Boregowda SV, McKenna DH, Ortiz LA. Nat Commun. 2015 Oct 7; 2015 Oct 7. PMID: 26442449.
- An integrated map of structural variation in 2,504 human genomes.Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Nature. 2015 Oct 1. PMID: 26432246.
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. Nat Methods. 2015 Oct; 2015 Aug 31. PMID: 26322839.
- Identification of a novel de novo GATA3 mutation in a patient with HDR syndrome.Chen L, Chen B, Leng W, Lui X, Wu Q, Ouyang X, Liang Z. J Int Med Res. 2015 Oct; 2015 Aug 12. PMID: 26268891.
- Prenatal acetaminophen affects maternal immune and endocrine adaptation to pregnancy, induces placental damage, and impairs fetal development in mice.Thiele K, Solano ME, Huber S, Flavell RA, Kessler T, Barikbin R, Jung R, Karimi K, Tiegs G, Arck PC. Am J Pathol. 2015 Oct; 2015 Aug 5. PMID: 26254283.
- Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol.Moller DR, Koth LL, Maier LA, Morris A, Drake W, Rossman M, Leader JK, Collman RG, Hamzeh N, Sweiss NJ, Zhang Y, O'Neal S, Senior RM, Becich M, Hochheiser HS, Kaminski N, Wisniewski SR, Gibson KF. Ann Am Thorac Soc. 2015 Oct. PMID: 26193069.
- Repurposing the translation apparatus for synthetic biology.Soye BJD, Patel JR, Isaacs FJ, Jewett MC. Curr Opin Chem Biol. 2015 Oct; 2015 Jul 15. PMID: 26186264.
- Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol.Strange C, Senior RM, Sciurba F, O'Neal S, Morris A, Wisniewski SR, Bowler R, Hochheiser HS, Becich MJ, Zhang Y, Leader JK, Methé BA, Kaminski N, Sandhaus RA. Ann Am Thorac Soc. 2015 Oct. PMID: 26153726.
- YU238259 Is a Novel Inhibitor of Homology-Dependent DNA Repair That Exhibits Synthetic Lethality and Radiosensitization in Repair-Deficient Tumors.Stachelek GC, Peterson-Roth E, Liu Y, Fernandez RJ 3rd, Pike LR, Qian JM, Abriola L, Hoyer D, Hungerford W, Merkel J, Glazer PM. Mol Cancer Res. 2015 Oct; 2015 Jun 26. PMID: 26116172.
- Na(+) /H(+) exchanger regulatory factor 1 knockout mice have an attenuated hepatic inflammatory response and are protected from cholestatic liver injury.Li M, Mennone A, Soroka CJ, Hagey LR, Ouyang X, Weinman EJ, Boyer JL. Hepatology. 2015 Oct; 2015 Aug 22. PMID: 26108984.
- From Mysterious Supernatant Entity to miRNA-150 in Antigen-Specific Exosomes: a History of Hapten-Specific T Suppressor Factor.Ptak W, Nazimek K, Askenase PW, Bryniarski K. Arch Immunol Ther Exp (Warsz). 2015 Oct; 2015 Feb 18. PMID: 25690461.
- LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M. Nucleic Acids Res. 2015 Sep 30; 2015 Aug 24. PMID: 26304545.
- Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.Mu JC, Tootoonchi Afshar P, Mohiyuddin M, Chen X, Li J, Bani Asadi N, Gerstein MB, Wong WH, Lam HY. Sci Rep. 2015 Sep 28; 2015 Sep 28. PMID: 26412485.
- An ensemble approach to accurately detect somatic mutations using SomaticSeq.Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY. Genome Biol. 2015 Sep 17; 2015 Sep 17. PMID: 26381235.
- Solving the Conundrum: Immunogenetics of Sarcoidosis.Kaminski N, Drake WP. Am J Respir Crit Care Med. 2015 Sep 15. PMID: 26371809.
- Establishing the role of ATP for the function of the RIG-I innate immune sensor.Rawling DC, Fitzgerald ME, Pyle AM. Elife. 2015 Sep 15; 2015 Sep 15. PMID: 26371557.
- The Legionella Anti-autophagy Effector RavZ Targets the Autophagosome via PI3P- and Curvature-Sensing Motifs.Horenkamp FA, Kauffman KJ, Kohler LJ, Sherwood RK, Krueger KP, Shteyn V, Roy CR, Melia TJ, Reinisch KM. Dev Cell. 2015 Sep 14; 2015 Sep 3. PMID: 26343456.
- Robust production of recombinant phosphoproteins using cell-free protein synthesis.Oza JP, Aerni HR, Pirman NL, Barber KW, Ter Haar CM, Rogulina S, Amrofell MB, Isaacs FJ, Rinehart J, Jewett MC. Nat Commun. 2015 Sep 9; 2015 Sep 9. PMID: 26350765.
- A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation.Pirman NL, Barber KW, Aerni HR, Ma NJ, Haimovich AD, Rogulina S, Isaacs FJ, Rinehart J. Nat Commun. 2015 Sep 9; 2015 Sep 9. PMID: 26350500.
- NLRP3 deficiency protects from type 1 diabetes through the regulation of chemotaxis into the pancreatic islets.Hu C, Ding H, Li Y, Pearson JA, Zhang X, Flavell RA, Wong FS, Wen L. Proc Natl Acad Sci U S A. 2015 Sep 8; 2015 Aug 24. PMID: 26305961.
- Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Mol Cell. 2015 Sep 3. PMID: 26340425.
- Menopause and the Heart.Nkonde-Price C, Bender JR. Endocrinol Metab Clin North Am. 2015 Sep; 2015 Jun 22. PMID: 26316243.
- Tissue instruction for migration and retention of TRM cells.Iijima N, Iwasaki A. Trends Immunol. 2015 Sep; 2015 Aug 14. PMID: 26282885.
- Genomes by design.Haimovich AD, Muir P, Isaacs FJ. Nat Rev Genet. 2015 Sep; 2015 Aug 11. PMID: 26260262.
- Noncoding RNA-guided recruitment of transcription factors: A prevalent but undocumented mechanism?Lee N, Steitz JA. Bioessays. 2015 Sep; 2015 Jul 22. PMID: 26200477.
- Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora.Blount KF, Megyola C, Plummer M, Osterman D, O'Connell T, Aristoff P, Quinn C, Chrusciel RA, Poel TJ, Schostarez HJ, Stewart CA, Walker DP, Wuts PG, Breaker RR. Antimicrob Agents Chemother. 2015 Sep; 2015 Jul 13. PMID: 26169403.
- The miR-199-dynamin regulatory axis controls receptor-mediated endocytosis.Aranda JF, Canfrán-Duque A, Goedeke L, Suárez Y, Fernández-Hernando C. J Cell Sci. 2015 Sep 1; 2015 Jul 10. PMID: 26163491.
- Disruption of the mevalonate pathway induces dNTP depletion and DNA damage.Martín Sánchez C, Pérez Martín JM, Jin JS, Dávalos A, Zhang W, de la Peña G, Martínez-Botas J, Rodríguez-Acebes S, Suárez Y, Hazen MJ, Gómez-Coronado D, Busto R, Cheng YC, Lasunción MA. Biochim Biophys Acta. 2015 Sep; 2015 Jun 5. PMID: 26055626.
- Quantification of co-transcriptional splicing from RNA-Seq data.Herzel L, Neugebauer KM. Methods. 2015 Sep 1; 2015 Apr 27. PMID: 25929182.
- Toll-like receptor 9 trafficking and signaling for type I interferons requires PIKfyve activity.Hayashi K, Sasai M, Iwasaki A. Int Immunol. 2015 Sep; 2015 Apr 29. PMID: 25925170.
- Macrophages play an essential role in antigen-specific immune suppression mediated by T CD8⁺ cell-derived exosomes.Nazimek K, Ptak W, Nowak B, Ptak M, Askenase PW, Bryniarski K. Immunology. 2015 Sep; 2015 Apr 27. PMID: 25808106.
- Determinants of mammalian nucleolar architecture.Farley KI, Surovtseva Y, Merkel J, Baserga SJ. Chromosoma. 2015 Sep; 2015 Feb 12. PMID: 25670395.
- Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A. J Extracell Vesicles. 2015; 2015 Aug 28. PMID: 26320941.
- Biologically active LIL proteins built with minimal chemical diversity.Heim EN, Marston JL, Federman RS, Edwards AP, Karabadzhak AG, Petti LM, Engelman DM, DiMaio D. Proc Natl Acad Sci U S A. 2015 Aug 25; 2015 Aug 10. PMID: 26261320.
- Rate of novel host invasion affects adaptability of evolving RNA virus lineages.Morley VJ, Mendiola SY, Turner PE. Proc Biol Sci. 2015 Aug 22. PMID: 26246544.
- Riding the R Train into the Cell.DiMaio D, Burd CG, Goodner K. PLoS Pathog. 2015 Aug; 2015 Aug 20. PMID: 26291450.
- Stromal cell-derived factor 2 is critical for Hsp90-dependent eNOS activation.Siragusa M, Fröhlich F, Park EJ, Schleicher M, Walther TC, Sessa WC. Sci Signal. 2015 Aug 18; 2015 Aug 18. PMID: 26286023.
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- Antimicrobial peptides targeting bacterial ribosome.Lomakin IB, Gagnon MG, Steitz TA. Oncotarget. 2015 Aug 7. PMID: 26300053.
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- Production of IL-10 by CD4(+) regulatory T cells during the resolution of infection promotes the maturation of memory CD8(+) T cells.Laidlaw BJ, Cui W, Amezquita RA, Gray SM, Guan T, Lu Y, Kobayashi Y, Flavell RA, Kleinstein SH, Craft J, Kaech SM. Nat Immunol. 2015 Aug; 2015 Jul 6. PMID: 26147684.
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- Fusaric acid induces a notochord malformation in zebrafish via copper chelation.Yin ES, Rakhmankulova M, Kucera K, de Sena Filho JG, Portero CE, Narváez-Trujillo A, Holley SA, Strobel SA. Biometals. 2015 Aug; 2015 Apr 26. PMID: 25913293.
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- Selenoprotein biosynthesis defect causes progressive encephalopathy with elevated lactate.Anttonen AK, Hilander T, Linnankivi T, Isohanni P, French RL, Liu Y, Simonović M, Söll D, Somer M, Muth-Pawlak D, Corthals GL, Laari A, Ylikallio E, Lähde M, Valanne L, Lönnqvist T, Pihko H, Paetau A, Lehesjoki AE, Suomalainen A, Tyynismaa H. Neurology. 2015 Jul 28; 2015 Jun 26. PMID: 26115735.
- Regulation of actin polymerization by tropomodulin-3 controls megakaryocyte actin organization and platelet biogenesis.Sui Z, Nowak RB, Sanada C, Halene S, Krause DS, Fowler VM. Blood. 2015 Jul 23; 2015 May 11. PMID: 25964668.
- Codon Bias as a Means to Fine-Tune Gene Expression.Quax TE, Claassens NJ, Söll D, van der Oost J. Mol Cell. 2015 Jul 16. PMID: 26186290.
- FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM. Cell. 2015 Jul 16. PMID: 26186191.
- The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3' ends.Xie M, Zhang W, Shu MD, Xu A, Lenis DA, DiMaio D, Steitz JA. Genes Dev. 2015 Jul 15. PMID: 26220997.
- DNA-dependent targeting of cell nuclei by a lupus autoantibody.Weisbart RH, Chan G, Jordaan G, Noble PW, Liu Y, Glazer PM, Nishimura RN, Hansen JE. Sci Rep. 2015 Jul 9; 2015 Jul 9. PMID: 26156563.
- Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation.Gagliani N, Amezcua Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, Cotton MJ, Drier Y, Bernstein B, Geginat J, Stockinger B, Esplugues E, Huber S, Flavell RA. Nature. 2015 Jul 9; 2015 Apr 29. PMID: 25924064.
- Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis.Gonzalez J, Qi H, Liu N, Lin H. Cell Rep. 2015 Jul 7; 2015 Jun 25. PMID: 26119740.
- RNA ligation in neurons by RtcB inhibits axon regeneration.Kosmaczewski SG, Han SM, Han B, Irving Meyer B, Baig HS, Athar W, Lin-Moore AT, Koelle MR, Hammarlund M. Proc Natl Acad Sci U S A. 2015 Jul 7; 2015 Jun 22. PMID: 26100902.
- Efficient gene disruption in cultured primary human endothelial cells by CRISPR/Cas9.Abrahimi P, Chang WG, Kluger MS, Qyang Y, Tellides G, Saltzman WM, Pober JS. Circ Res. 2015 Jul 3; 2015 May 4. PMID: 25940550.
- Crystal Structure of Human Profilaggrin S100 Domain and Identification of Target Proteins Annexin II, Stratifin, and HSP27.Bunick CG, Presland RB, Lawrence OT, Pearton DJ, Milstone LM, Steitz TA. J Invest Dermatol. 2015 Jul; 2015 Mar 11. PMID: 25760235.
- Alterations in gene expression and DNA methylation during murine and human lung alveolar septation.Cuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman DK, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani TJ, Ambalavanan N. Am J Respir Cell Mol Biol. 2015 Jul. PMID: 25387348.
- Executioner Caspase-3 and 7 Deficiency Reduces Myocyte Number in the Developing Mouse Heart.Cardona M, López JA, Serafín A, Rongvaux A, Inserte J, García-Dorado D, Flavell R, Llovera M, Cañas X, Vázquez J, Sanchis D. PLoS One. 2015; 2015 Jun 29. PMID: 26121671.
- Proteomics and Transcriptomics of BJAB Cells Expressing the Epstein-Barr Virus Noncoding RNAs EBER1 and EBER2.Pimienta G, Fok V, Haslip M, Nagy M, Takyar S, Steitz JA. PLoS One. 2015; 2015 Jun 29. PMID: 26121143.
- Temporal Control of Plant Organ Growth by TCP Transcription Factors.Huang T, Irish VF. Curr Biol. 2015 Jun 29; 2015 Jun 11. PMID: 26073137.
- Vascular Mural Cells Promote Noradrenergic Differentiation of Embryonic Sympathetic Neurons.Fortuna V, Pardanaud L, Brunet I, Ola R, Ristori E, Santoro MM, Nicoli S, Eichmann A. Cell Rep. 2015 Jun 23; 2015 Jun 11. PMID: 26074079.
- Regulation of Adipose Tissue Inflammation and Insulin Resistance by MAPK Phosphatase 5.Zhang Y, Nguyen T, Tang P, Kennedy NJ, Jiao H, Zhang M, Reynolds JM, Jaeschke A, Martin-Orozco N, Chung Y, He WM, Wang C, Jia W, Ge B, Davis RJ, Flavell RA, Dong C. J Biol Chem. 2015 Jun 12; 2015 Apr 28. PMID: 25922079.
- Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A.Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS, Lu W, Burnett BJ, Dinos G, Reynolds KA, Blanchard SC, Steitz TA, Wilson DN. Mol Cell. 2015 Jun 4; 2015 May 28. PMID: 26028538.
- AMCase is a crucial regulator of type 2 immune responses to inhaled house dust mites.Kim LK, Morita R, Kobayashi Y, Eisenbarth SC, Lee CG, Elias J, Eynon EE, Flavell RA. Proc Natl Acad Sci U S A. 2015 Jun 2; 2015 May 18. PMID: 26038565.
- Nuns, warts, viruses, and cancer.DiMaio D. Yale J Biol Med. 2015 Jun; 2015 Jun 1. PMID: 26029011.
- Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB. Nat Commun. 2015 Jun 1; 2015 Jun 1. PMID: 26028266.
- The mechanism of inhibition of protein synthesis by the proline-rich peptide oncocin.Roy RN, Lomakin IB, Gagnon MG, Steitz TA. Nat Struct Mol Biol. 2015 Jun; 2015 May 18. PMID: 25984972.
- Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential.Spakowicz DJ, Strobel SA. Appl Microbiol Biotechnol. 2015 Jun; 2015 May 10. PMID: 25957494.
- Poor ovarian response in women undergoing in vitro fertilization is associated with altered microRNA expression in cumulus cells.Karakaya C, Guzeloglu-Kayisli O, Uyar A, Kallen AN, Babayev E, Bozkurt N, Unsal E, Karabacak O, Seli E. Fertil Steril. 2015 Jun; 2015 Apr 22. PMID: 25910568.
- The Greater Affinity of JC Polyomavirus Capsid for α2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.Ströh LJ, Maginnis MS, Blaum BS, Nelson CD, Neu U, Gee GV, O'Hara BA, Motamedi N, DiMaio D, Atwood WJ, Stehle T. J Virol. 2015 Jun; 2015 Apr 8. PMID: 25855729.
- Genetic Evidence Supports a Major Role for Akt1 in VSMCs During Atherogenesis.Rotllan N, Wanschel AC, Fernández-Hernando A, Salerno AG, Offermanns S, Sessa WC, Fernández-Hernando C. Circ Res. 2015 May 22; 2015 Apr 13. PMID: 25868464.
- Cervicovaginal microbiota: simple is better.Gopinath S, Iwasaki A. Immunity. 2015 May 19. PMID: 25992855.
- Phosphorylation of GATA-6 is required for vascular smooth muscle cell differentiation after mTORC1 inhibition.Xie Y, Jin Y, Merenick BL, Ding M, Fetalvero KM, Wagner RJ, Mai A, Gleim S, Tucker DF, Birnbaum MJ, Ballif BA, Luciano AK, Sessa WC, Rzucidlo EM, Powell RJ, Hou L, Zhao H, Hwa J, Yu J, Martin KA. Sci Signal. 2015 May 12; 2015 May 12. PMID: 25969542.
- MiR-125a targets effector programs to stabilize Treg-mediated immune homeostasis.Pan W, Zhu S, Dai D, Liu Z, Li D, Li B, Gagliani N, Zheng Y, Tang Y, Weirauch MT, Chen X, Zhu W, Wang Y, Chen B, Qian Y, Chen Y, Fang J, Herbst R, Richman L, Jallal B, Harley JB, Flavell RA, Yao Y, Shen N. Nat Commun. 2015 May 12; 2015 May 12. PMID: 25963922.
- SRSF2 Mutations Contribute to Myelodysplasia by Mutant-Specific Effects on Exon Recognition.Kim E, Ilagan JO, Liang Y, Daubner GM, Lee SC, Ramakrishnan A, Li Y, Chung YR, Micol JB, Murphy ME, Cho H, Kim MK, Zebari AS, Aumann S, Park CY, Buonamici S, Smith PG, Deeg HJ, Lobry C, Aifantis I, Modis Y, Allain FH, Halene S, Bradley RK, Abdel-Wahab O. Cancer Cell. 2015 May 11. PMID: 25965569.
- Crystal structures of the E. coli transcription initiation complexes with a complete bubble.Zuo Y, Steitz TA. Mol Cell. 2015 May 7; 2015 Apr 9. PMID: 25866247.
- Mechanism of action studies of lomaiviticin A and the monomeric lomaiviticin aglycon. Selective and potent activity toward DNA double-strand break repair-deficient cell lines.Colis LC, Hegan DC, Kaneko M, Glazer PM, Herzon SB. J Am Chem Soc. 2015 May 6; 2015 Apr 22. PMID: 25849366.
- Retraction for Theivanthiran et al., NOD2 signaling contributes to host defense in the lungs against Escherichia coli infection.Theivanthiran B, Batra S, Balamayooran G, Cai S, Kobayashi K, Flavell RA, Jeyaseelan S. Infect Immun. 2015 May. PMID: 25878164.
- Species-specific dynamic responses of gut bacteria to a mammalian glycan.Raghavan V, Groisman EA. J Bacteriol. 2015 May; 2015 Feb 17. PMID: 25691527.
- Can oncology recapitulate paleontology? Lessons from species extinctions.Walther V, Hiley CT, Shibata D, Swanton C, Turner PE, Maley CC. Nat Rev Clin Oncol. 2015 May; 2015 Feb 17. PMID: 25687908.
- Oral immunotherapy with type V collagen in idiopathic pulmonary fibrosis.Wilkes DS, Chew T, Flaherty KR, Frye S, Gibson KF, Kaminski N, Klemsz MJ, Lange W, Noth I, Rothhaar K. Eur Respir J. 2015 May; 2015 Jan 22. PMID: 25614165.
- VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. Bioinformatics. 2015 May 1; 2014 Dec 17. PMID: 25524895.
- Free Extracellular miRNA Functionally Targets Cells by Transfecting Exosomes from Their Companion Cells.Bryniarski K, Ptak W, Martin E, Nazimek K, Szczepanik M, Sanak M, Askenase PW. PLoS One. 2015; 2015 Apr 29. PMID: 25923429.
- Control of bacterial exoelectrogenesis by c-AMP-GMP.Nelson JW, Sudarsan N, Phillips GE, Stav S, Lünse CE, McCown PJ, Breaker RR. Proc Natl Acad Sci U S A. 2015 Apr 28; 2015 Apr 6. PMID: 25848023.
- Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium.McNeer NA, Anandalingam K, Fields RJ, Caputo C, Kopic S, Gupta A, Quijano E, Polikoff L, Kong Y, Bahal R, Geibel JP, Glazer PM, Saltzman WM, Egan ME. Nat Commun. 2015 Apr 27; 2015 Apr 27. PMID: 25914116.
- Small molecule fluoride toxicity agonists.Nelson JW, Plummer MS, Blount KF, Ames TD, Breaker RR. Chem Biol. 2015 Apr 23. PMID: 25910244.
- Mitochondrial DNA stress primes the antiviral innate immune response.West AP, Khoury-Hanold W, Staron M, Tal MC, Pineda CM, Lang SM, Bestwick M, Duguay BA, Raimundo N, MacDuff DA, Kaech SM, Smiley JR, Means RE, Iwasaki A, Shadel GS. Nature. 2015 Apr 23; 2015 Feb 2. PMID: 25642965.
- Salmonella promotes virulence by repressing cellulose production.Pontes MH, Lee EJ, Choi J, Groisman EA. Proc Natl Acad Sci U S A. 2015 Apr 21; 2015 Apr 6. PMID: 25848006.
- No viral association found in a set of differentiated vulvar intraepithelial neoplasia cases by human papillomavirus and pan-viral microarray testing.Saglam O, Samayoa E, Somasekar S, Naccache S, Iwasaki A, Chiu CY. PLoS One. 2015; 2015 Apr 20. PMID: 25894343.
- Loregic: a method to characterize the cooperative logic of regulatory factors.Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB. PLoS Comput Biol. 2015 Apr; 2015 Apr 17. PMID: 25884877.
- HOTAIR forms an intricate and modular secondary structure.Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM. Mol Cell. 2015 Apr 16; 2015 Apr 9. PMID: 25866246.
- A protein interaction map of the LSU processome.McCann KL, Charette JM, Vincent NG, Baserga SJ. Genes Dev. 2015 Apr 15; 2015 Apr 15. PMID: 25877921.
- Functional synergy between cholecystokinin receptors CCKAR and CCKBR in mammalian brain development.Nishimura S, Bilgüvar K, Ishigame K, Sestan N, Günel M, Louvi A. PLoS One. 2015; 2015 Apr 15. PMID: 25875176.
- Hepatitis C virus RNA replication depends on specific cis- and trans-acting activities of viral nonstructural proteins.Kazakov T, Yang F, Ramanathan HN, Kohlway A, Diamond MS, Lindenbach BD. PLoS Pathog. 2015 Apr; 2015 Apr 13. PMID: 25875808.
- Dynamin 2-dependent endocytosis sustains T-cell receptor signaling and drives metabolic reprogramming in T lymphocytes.Willinger T, Staron M, Ferguson SM, De Camilli P, Flavell RA. Proc Natl Acad Sci U S A. 2015 Apr 7; 2015 Mar 23. PMID: 25831514.
- Re-visiting the trans insertion model for complexin clamping.Krishnakumar SS, Li F, Coleman J, Schauder CM, Kümmel D, Pincet F, Rothman JE, Reinisch KM. Elife. 2015 Apr 2; 2015 Apr 2. PMID: 25831964.
- Genome rearrangement affects RNA virus adaptability on prostate cancer cells.Pesko K, Voigt EA, Swick A, Morley VJ, Timm C, Yin J, Turner PE. Front Genet. 2015; 2015 Apr 1. PMID: 25883601.
- Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome.Macia L, Tan J, Vieira AT, Leach K, Stanley D, Luong S, Maruya M, Ian McKenzie C, Hijikata A, Wong C, Binge L, Thorburn AN, Chevalier N, Ang C, Marino E, Robert R, Offermanns S, Teixeira MM, Moore RJ, Flavell RA, Fagarasan S, Mackay CR. Nat Commun. 2015 Apr 1; 2015 Apr 1. PMID: 25828455.
- Endothelial glucocorticoid receptor suppresses atherogenesis--brief report.Goodwin JE, Zhang X, Rotllan N, Feng Y, Zhou H, Fernández-Hernando C, Yu J, Sessa WC. Arterioscler Thromb Vasc Biol. 2015 Apr; 2015 Feb 19. PMID: 25810297.
- Control of adaptive immunity by the innate immune system.Iwasaki A, Medzhitov R. Nat Immunol. 2015 Apr. PMID: 25789684.
- A tRNA-guided research journey from synthetic chemistry to synthetic biology.Soll D. RNA. 2015 Apr. PMID: 25780217.
- Rediscovering RNA.Pyle AM. RNA. 2015 Apr. PMID: 25780205.
- RNA: master or servant?Neugebauer KM. RNA. 2015 Apr. PMID: 25780198.
- RNA-RNA base-pairing: theme and variations.Steitz J. RNA. 2015 Apr. PMID: 25780100.
- Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly.Polikanov YS, Melnikov SV, Söll D, Steitz TA. Nat Struct Mol Biol. 2015 Apr; 2015 Mar 16. PMID: 25775268.
- Controlled protein delivery in the generation of microvascular networks.Andrejecsk JW, Chang WG, Pober JS, Saltzman WM. Drug Deliv Transl Res. 2015 Apr. PMID: 25767747.
- Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H.Shaw JJ, Spakowicz DJ, Dalal RS, Davis JH, Lehr NA, Dunican BF, Orellana EA, Narváez-Trujillo A, Strobel SA. Appl Microbiol Biotechnol. 2015 Apr; 2015 Feb 12. PMID: 25672844.
- Epigenetics in idiopathic pulmonary fibrosis.Tzouvelekis A, Kaminski N. Biochem Cell Biol. 2015 Apr; 2015 Jan 13. PMID: 25659821.
- Zombies in TCGA.DiMaio D. J Virol. 2015 Apr; 2015 Jan 28. PMID: 25631081.
- A holistic approach to targeting disease with polymeric nanoparticles.Cheng CJ, Tietjen GT, Saucier-Sawyer JK, Saltzman WM. Nat Rev Drug Discov. 2015 Apr; 2015 Jan 19. PMID: 25598505.
- Endothelial cilia are essential for developmental vascular integrity in zebrafish.Kallakuri S, Yu JA, Li J, Li Y, Weinstein BM, Nicoli S, Sun Z. J Am Soc Nephrol. 2015 Apr; 2014 Sep 11. PMID: 25214579.
- An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M. Genome Biol. 2015 Mar 31; 2015 Mar 31. PMID: 25880651.
- Myosin VI regulates gene pairing and transcriptional pause release in T cells.Zorca CE, Kim LK, Kim YJ, Krause MR, Zenklusen D, Spilianakis CG, Flavell RA. Proc Natl Acad Sci U S A. 2015 Mar 31; 2015 Mar 13. PMID: 25770220.
- Spatial proximity of homologous alleles and long noncoding RNAs regulate a switch in allelic gene expression.Stratigi K, Kapsetaki M, Aivaliotis M, Town T, Flavell RA, Spilianakis CG. Proc Natl Acad Sci U S A. 2015 Mar 31; 2015 Mar 13. PMID: 25770217.
- Identification of a fungal 1,8-cineole synthase from Hypoxylon sp. with specificity determinants in common with the plant synthases.Shaw JJ, Berbasova T, Sasaki T, Jefferson-George K, Spakowicz DJ, Dunican BF, Portero CE, Narváez-Trujillo A, Strobel SA. J Biol Chem. 2015 Mar 27; 2015 Feb 3. PMID: 25648891.
- Spatially heterogeneous choroid plexus transcriptomes encode positional identity and contribute to regional CSF production.Lun MP, Johnson MB, Broadbelt KG, Watanabe M, Kang YJ, Chau KF, Springel MW, Malesz A, Sousa AM, Pletikos M, Adelita T, Calicchio ML, Zhang Y, Holtzman MJ, Lidov HG, Sestan N, Steen H, Monuki ES, Lehtinen MK. J Neurosci. 2015 Mar 25. PMID: 25810521.
- Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Dev Cell. 2015 Mar 23. PMID: 25805139.
- Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Mol Cell. 2015 Mar 19. PMID: 25794617.
- MAPK Phosphatase 5 Expression Induced by Influenza and Other RNA Virus Infection Negatively Regulates IRF3 Activation and Type I Interferon Response.James SJ, Jiao H, Teh HY, Takahashi H, Png CW, Phoon MC, Suzuki Y, Sawasaki T, Xiao H, Chow VTK, Yamamoto N, Reynolds JM, Flavell RA, Dong C, Zhang Y. Cell Rep. 2015 Mar 17; 2015 Mar 12. PMID: 25772359.
- A conserved NS3 surface patch orchestrates NS2 protease stimulation, NS5A hyperphosphorylation and HCV genome replication.Isken O, Langerwisch U, Jirasko V, Rehders D, Redecke L, Ramanathan H, Lindenbach BD, Bartenschlager R, Tautz N. PLoS Pathog. 2015 Mar; 2015 Mar 16. PMID: 25774920.
- Viral noncoding RNAs: more surprises.Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, Xie M, Steitz JA. Genes Dev. 2015 Mar 15. PMID: 25792595.
- Matrix metalloproteinase (MMP)-19-deficient fibroblasts display a profibrotic phenotype.Jara P, Calyeca J, Romero Y, Plácido L, Yu G, Kaminski N, Maldonado V, Cisneros J, Selman M, Pardo A. Am J Physiol Lung Cell Mol Physiol. 2015 Mar 15; 2015 Jan 9. PMID: 25575513.
- The ribosome biogenesis factor Nol11 is required for optimal rDNA transcription and craniofacial development in Xenopus.Griffin JN, Sondalle SB, Del Viso F, Baserga SJ, Khokha MK. PLoS Genet. 2015 Mar; 2015 Mar 10. PMID: 25756904.
- The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. Nat Commun. 2015 Mar 10; 2015 Mar 10. PMID: 25752243.
- Coincidental loss of DOCK8 function in NLRP10-deficient and C3H/HeJ mice results in defective dendritic cell migration.Krishnaswamy JK, Singh A, Gowthaman U, Wu R, Gorrepati P, Sales Nascimento M, Gallman A, Liu D, Rhebergen AM, Calabro S, Xu L, Ranney P, Srivastava A, Ranson M, Gorham JD, McCaw Z, Kleeberger SR, Heinz LX, Müller AC, Bennett KL, Superti-Furga G, Henao-Mejia J, Sutterwala FS, Williams A, Flavell RA, Eisenbarth SC. Proc Natl Acad Sci U S A. 2015 Mar 10; 2015 Feb 23. PMID: 25713392.
- A Dicer-miR-107 Interaction Regulates Biogenesis of Specific miRNAs Crucial for Neurogenesis.Ristori E, Lopez-Ramirez MA, Narayanan A, Hill-Teran G, Moro A, Calvo CF, Thomas JL, Nicoli S. Dev Cell. 2015 Mar 9; 2015 Feb 5. PMID: 25662174.
- Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. Science. 2015 Mar 6. PMID: 25745175.
- A MARKOV RANDOM FIELD-BASED APPROACH TO CHARACTERIZING HUMAN BRAIN DEVELOPMENT USING SPATIAL-TEMPORAL TRANSCRIPTOME DATA.Lin Z, Sanders SJ, Li M, Sestan N, State MW, Zhao H. Ann Appl Stat. 2015 Mar. PMID: 26877824.
- Synchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei.Ramey-Butler K, Ullu E, Kolev NG, Tschudi C. Mol Biochem Parasitol. 2015 Mar-Apr; 2015 Apr 18. PMID: 25896436.
- Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline.Watanabe T, Cheng EC, Zhong M, Lin H. Genome Res. 2015 Mar; 2014 Dec 5. PMID: 25480952.
- Oxaliplatin-related acute disseminated intravascular coagulation syndrome in a patient with metastatic colon cancer.Malkhasyan K, Halene S, Lacy J. Clin Colorectal Cancer. 2015 Mar; 2014 Oct 2. PMID: 25446051.
- Disinfection of syringes contaminated with hepatitis C virus by rinsing with household products.Binka M, Paintsil E, Patel A, Lindenbach BD, Heimer R. Open Forum Infect Dis. 2015 Jan; 2015 Feb 23. PMID: 26034767.
- Direct binding of retromer to human papillomavirus type 16 minor capsid protein L2 mediates endosome exit during viral infection.Popa A, Zhang W, Harrison MS, Goodner K, Kazakov T, Goodwin EC, Lipovsky A, Burd CG, DiMaio D. PLoS Pathog. 2015 Feb; 2015 Feb 18. PMID: 25693203.
- Multilayered genetic safeguards limit growth of microorganisms to defined environments.Gallagher RR, Patel JR, Interiano AL, Rovner AJ, Isaacs FJ. Nucleic Acids Res. 2015 Feb 18; 2015 Jan 7. PMID: 25567985.
- Modified poly(lactic-co-glycolic acid) nanoparticles for enhanced cellular uptake and gene editing in the lung.Fields RJ, Quijano E, McNeer NA, Caputo C, Bahal R, Anandalingam K, Egan ME, Glazer PM, Saltzman WM. Adv Healthc Mater. 2015 Feb 18; 2014 Aug 25. PMID: 25156908.
- Candida albicans morphology and dendritic cell subsets determine T helper cell differentiation.Kashem SW, Igyarto BZ, Gerami-Nejad M, Kumamoto Y, Mohammed JA, Jarrett E, Drummond RA, Zurawski SM, Zurawski G, Berman J, Iwasaki A, Brown GD, Kaplan DH. Immunity. 2015 Feb 17; 2015 Feb 10. PMID: 25680275.
- Structural basis for transcription reactivation by RapA.Liu B, Zuo Y, Steitz TA. Proc Natl Acad Sci U S A. 2015 Feb 17; 2015 Feb 2. PMID: 25646438.
- IRAK-M promotes alternative macrophage activation and fibroproliferation in bleomycin-induced lung injury.Ballinger MN, Newstead MW, Zeng X, Bhan U, Mo XM, Kunkel SL, Moore BB, Flavell R, Christman JW, Standiford TJ. J Immunol. 2015 Feb 15; 2015 Jan 16. PMID: 25595781.
- EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA.Lee N, Moss WN, Yario TA, Steitz JA. Cell. 2015 Feb 12; 2015 Feb 5. PMID: 25662012.
- Pharmacological modulation of the AKT/microRNA-199a-5p/CAV1 pathway ameliorates cystic fibrosis lung hyper-inflammation.Zhang PX, Cheng J, Zou S, D'Souza AD, Koff JL, Lu J, Lee PJ, Krause DS, Egan ME, Bruscia EM. Nat Commun. 2015 Feb 10; 2015 Feb 10. PMID: 25665524.
- Flagella-independent surface motility in Salmonella enterica serovar Typhimurium.Park SY, Pontes MH, Groisman EA. Proc Natl Acad Sci U S A. 2015 Feb 10; 2015 Jan 26. PMID: 25624475.
- Nanotherapy for Cancer: Targeting and Multifunctionality in the Future of Cancer Therapies.Ediriwickrema A, Saltzman WM. ACS Biomater Sci Eng. 2015 Feb 9; 2015 Jan 13. PMID: 25984571.
- Stem cell maintenance: aMPLe splicing choices.Halene S, Krause DS. Blood. 2015 Feb 5. PMID: 25655452.
- Recoded organisms engineered to depend on synthetic amino acids.Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW, Gassaway BM, Amiram M, Patel JR, Gallagher RR, Rinehart J, Isaacs FJ. Nature. 2015 Feb 5; 2015 Jan 21. PMID: 25607356.
- MicroRNA silencing for cancer therapy targeted to the tumour microenvironment.Cheng CJ, Bahal R, Babar IA, Pincus Z, Barrera F, Liu C, Svoronos A, Braddock DT, Glazer PM, Engelman DM, Saltzman WM, Slack FJ. Nature. 2015 Feb 5; 2014 Nov 17. PMID: 25409146.
- Vascular remodeling is governed by a VEGFR3-dependent fluid shear stress set point.Baeyens N, Nicoli S, Coon BG, Ross TD, Van den Dries K, Han J, Lauridsen HM, Mejean CO, Eichmann A, Thomas JL, Humphrey JD, Schwartz MA. Elife. 2015 Feb 2; 2015 Feb 2. PMID: 25643397.
- From trans to cis: transcriptional regulatory networks in neocortical development.Shibata M, Gulden FO, Sestan N. Trends Genet. 2015 Feb; 2015 Jan 24. PMID: 25624274.
- Mycofumigation by the volatile organic compound-producing Fungus Muscodor albus induces bacterial cell death through DNA damage.Alpha CJ, Campos M, Jacobs-Wagner C, Strobel SA. Appl Environ Microbiol. 2015 Feb; 2014 Dec 1. PMID: 25452287.
- Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging.Ouyang A, Jeon T, Sunkin SM, Pletikos M, Sedmak G, Sestan N, Lein ES, Huang H. Methods. 2015 Feb; 2014 Nov 6. PMID: 25448302.
- Imaging the delivery of brain-penetrating PLGA nanoparticles in the brain using magnetic resonance.Strohbehn G, Coman D, Han L, Ragheb RR, Fahmy TM, Huttner AJ, Hyder F, Piepmeier JM, Saltzman WM, Zhou J. J Neurooncol. 2015 Feb; 2014 Nov 18. PMID: 25403507.
- Hematopoietic Akt2 deficiency attenuates the progression of atherosclerosis.Rotllan N, Chamorro-Jorganes A, Araldi E, Wanschel AC, Aryal B, Aranda JF, Goedeke L, Salerno AG, Ramírez CM, Sessa WC, Suárez Y, Fernández-Hernando C. FASEB J. 2015 Feb; 2014 Nov 12. PMID: 25392271.
- Palliative care and location of death in decedents with idiopathic pulmonary fibrosis.Lindell KO, Liang Z, Hoffman LA, Rosenzweig MQ, Saul MI, Pilewski JM, Gibson KF, Kaminski N. Chest. 2015 Feb. PMID: 25187973.
- Homozygous loss of DIAPH1 is a novel cause of microcephaly in humans.Ercan-Sencicek AG, Jambi S, Franjic D, Nishimura S, Li M, El-Fishawy P, Morgan TM, Sanders SJ, Bilguvar K, Suri M, Johnson MH, Gupta AR, Yuksel Z, Mane S, Grigorenko E, Picciotto M, Alberts AS, Gunel M, Šestan N, State MW. Eur J Hum Genet. 2015 Feb; 2014 Apr 30. PMID: 24781755.
- An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.Kim PB, Nelson JW, Breaker RR. Mol Cell. 2015 Jan 22. PMID: 25616067.
- Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells.Foxman EF, Storer JA, Fitzgerald ME, Wasik BR, Hou L, Zhao H, Turner PE, Pyle AM, Iwasaki A. Proc Natl Acad Sci U S A. 2015 Jan 20; 2015 Jan 5. PMID: 25561542.
- Conformational changes of elongation factor G on the ribosome during tRNA translocation.Lin J, Gagnon MG, Bulkley D, Steitz TA. Cell. 2015 Jan 15. PMID: 25594181.
- Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Ghiaur G, Lai J, McHugh HL, Hao H, Zhang H, Margolick JB, Gurer C, Murphy AJ, Valenzuela DM, Yancopoulos GD, Deeks SG, Strowig T, Kumar P, Siliciano JD, Salzberg SL, Flavell RA, Shan L, Siliciano RF. Nature. 2015 Jan 15; 2015 Jan 7. PMID: 25561180.
- Glucocorticoids suppress inflammation via the upregulation of negative regulator IRAK-M.Miyata M, Lee JY, Susuki-Miyata S, Wang WY, Xu H, Kai H, Kobayashi KS, Flavell RA, Li JD. Nat Commun. 2015 Jan 14; 2015 Jan 14. PMID: 25585690.
- Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat Commun. 2015 Jan 13; 2015 Jan 13. PMID: 25582907.
- Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis.Suzuki T, Nakamura A, Kato K, Söll D, Tanaka I, Sheppard K, Yao M. Proc Natl Acad Sci U S A. 2015 Jan 13; 2014 Dec 29. PMID: 25548166.
- Up-regulation of thrombospondin-2 in Akt1-null mice contributes to compromised tissue repair due to abnormalities in fibroblast function.Bancroft T, Bouaouina M, Roberts S, Lee M, Calderwood DA, Schwartz M, Simons M, Sessa WC, Kyriakides TR. J Biol Chem. 2015 Jan 2; 2014 Nov 11. PMID: 25389299.
- EOLA1 Inhibits Lipopolysaccharide-Induced Vascular Cell Adhesion Molecule-1 Expression by Association with MT2A in ECV304 Cells.Leng W, Lei X, Meng H, Ouyang X, Liang Z. Int J Inflam. 2015; 2015 Dec 31. PMID: 26881174.
- Systemic delivery of blood-brain barrier-targeted polymeric nanoparticles enhances delivery to brain tissue.Saucier-Sawyer JK, Deng Y, Seo YE, Cheng CJ, Zhang J, Quijano E, Saltzman WM. J Drug Target. 2015. PMID: 26453169.
- The Maternal-to-Zygotic Transition During Vertebrate Development: A Model for Reprogramming.Yartseva V, Giraldez AJ. Curr Top Dev Biol. 2015; 2015 Aug 13. PMID: 26358874.
- Native Purification and Analysis of Long RNAs.Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM. Methods Enzymol. 2015; 2015 Feb 27. PMID: 26068736.
- Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.Eliaz D, Doniger T, Tkacz ID, Biswas VK, Gupta SK, Kolev NG, Unger R, Ullu E, Tschudi C, Michaeli S. RNA Biol. 2015; 2015 May 13. PMID: 25970223.
- Coilin: The first 25 years.Machyna M, Neugebauer KM, Staněk D. RNA Biol. 2015. PMID: 25970135.
- Application of the proximity-dependent assay and fluorescence imaging approaches to study viral entry pathways.Lipovsky A, Zhang W, Iwasaki A, DiMaio D. Methods Mol Biol. 2015. PMID: 25702134.
- LKB1 preserves genome integrity by stimulating BRCA1 expression.Gupta R, Liu AY, Glazer PM, Wajapeyee N. Nucleic Acids Res. 2015 Jan; 2014 Dec 8. PMID: 25488815.
- miRNAs expression profile in zebrafish developing vessels.Ristori E, Nicoli S. Methods Mol Biol. 2015. PMID: 25468601.
- Therapeutic genome mutagenesis using synthetic donor DNA and triplex-forming molecules.Reza F, Glazer PM. Methods Mol Biol. 2015. PMID: 25408401.
- The regulatory role of serum response factor pathway in neutrophil inflammatory response.Taylor A, Halene S. Curr Opin Hematol. 2015 Jan. PMID: 25402621.
- Construction of Trypanosoma brucei Illumina RNA-Seq libraries enriched for transcript ends.Kolev NG, Ullu E, Tschudi C. Methods Mol Biol. 2015. PMID: 25388113.
2014
- A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TM. Proc Natl Acad Sci U S A. 2014 Dec 30; 2014 Dec 15. PMID: 25512524.
- Resemble and Inhibit: when RLR meets TGF-β.Zhu S, Li HB, Flavell RA. Mol Cell. 2014 Dec 18. PMID: 25526529.
- Apoptotic caspases prevent the induction of type I interferons by mitochondrial DNA.Rongvaux A, Jackson R, Harman CC, Li T, West AP, de Zoete MR, Wu Y, Yordy B, Lakhani SA, Kuan CY, Taniguchi T, Shadel GS, Chen ZJ, Iwasaki A, Flavell RA. Cell. 2014 Dec 18. PMID: 25525875.
- Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors.Mishra-Gorur K, Çağlayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüş GT, Nishimura S, Han W, Tu S, Baran B, Gümüş H, Dilber C, Zaki MS, Hossni HA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çağlar C, Çağlar Ç, Dölen D, Baranoski JF, Kumandaş S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi NC, Šestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M. Neuron. 2014 Dec 17. PMID: 25521378.
- Radiolabeling of poly(lactic-co-glycolic acid) (PLGA) nanoparticles with biotinylated F-18 prosthetic groups and imaging of their delivery to the brain with positron emission tomography.Sirianni RW, Zheng MQ, Patel TR, Shafbauer T, Zhou J, Saltzman WM, Carson RE, Huang Y. Bioconjug Chem. 2014 Dec 17; 2014 Dec 1. PMID: 25322194.
- Exposure to mitochondrial genotoxins and dopaminergic neurodegeneration in Caenorhabditis elegans.González-Hunt CP, Leung MC, Bodhicharla RK, McKeever MG, Arrant AE, Margillo KM, Ryde IT, Cyr DD, Kosmaczewski SG, Hammarlund M, Meyer JN. PLoS One. 2014; 2014 Dec 8. PMID: 25486066.
- A multi-channel device for high-density target-selective stimulation and long-term monitoring of cells and subcellular features in C. elegans.Lee H, Kim SA, Coakley S, Mugno P, Hammarlund M, Hilliard MA, Lu H. Lab Chip. 2014 Dec 7; 2014 Sep 26. PMID: 25257026.
- Adenylation of maternally inherited microRNAs by Wispy.Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN. Mol Cell. 2014 Dec 4; 2014 Nov 13. PMID: 25454948.
- Reducing the genetic code induces massive rearrangement of the proteome.O'Donoghue P, Prat L, Kucklick M, Schäfer JG, Riedel K, Rinehart J, Söll D, Heinemann IU. Proc Natl Acad Sci U S A. 2014 Dec 2; 2014 Nov 17. PMID: 25404328.
- Brain malformations associated with Knobloch syndrome--review of literature, expanding clinical spectrum, and identification of novel mutations.Caglayan AO, Baranoski JF, Aktar F, Han W, Tuysuz B, Guzel A, Guclu B, Kaymakcalan H, Aktekin B, Akgumus GT, Murray PB, Erson-Omay EZ, Caglar C, Bakircioglu M, Sakalar YB, Guzel E, Demir N, Tuncer O, Senturk S, Ekici B, Minja FJ, Šestan N, Yasuno K, Bilguvar K, Caksen H, Gunel M. Pediatr Neurol. 2014 Dec; 2014 Sep 4. PMID: 25456301.
- Producing GM-CSF: a unique T helper subset?Herndler-Brandstetter D, Flavell RA. Cell Res. 2014 Dec; 2014 Nov 21. PMID: 25412663.
- The RtcB RNA ligase is an essential component of the metazoan unfolded protein response.Kosmaczewski SG, Edwards TJ, Han SM, Eckwahl MJ, Meyer BI, Peach S, Hesselberth JR, Wolin SL, Hammarlund M. EMBO Rep. 2014 Dec; 2014 Nov 3. PMID: 25366321.
- Antibiotic resistance correlates with transmission in plasmid evolution.Turner PE, Williams ES, Okeke C, Cooper VS, Duffy S, Wertz JE. Evolution. 2014 Dec; 2014 Nov 24. PMID: 25351426.
- Inflammasome activation and metabolic disease progression.Li HB, Jin C, Chen Y, Flavell RA. Cytokine Growth Factor Rev. 2014 Dec; 2014 Aug 12. PMID: 25156419.
- Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.Guo LT, Wang YS, Nakamura A, Eiler D, Kavran JM, Wong M, Kiessling LL, Steitz TA, O'Donoghue P, Söll D. Proc Natl Acad Sci U S A. 2014 Nov 25; 2014 Nov 10. PMID: 25385624.
- Designed phosphoprotein recognition in Escherichia coli.Sawyer N, Gassaway BM, Haimovich AD, Isaacs FJ, Rinehart J, Regan L. ACS Chem Biol. 2014 Nov 21; 2014 Oct 6. PMID: 25272187.
- Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA.Polikanov YS, Szal T, Jiang F, Gupta P, Matsuda R, Shiozuka M, Steitz TA, Vázquez-Laslop N, Mankin AS. Mol Cell. 2014 Nov 20; 2014 Oct 9. PMID: 25306922.
- Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.Polikanov YS, Osterman IA, Szal T, Tashlitsky VN, Serebryakova MV, Kusochek P, Bulkley D, Malanicheva IA, Efimenko TA, Efremenkova OV, Konevega AL, Shaw KJ, Bogdanov AA, Rodnina MV, Dontsova OA, Mankin AS, Steitz TA, Sergiev PV. Mol Cell. 2014 Nov 20; 2014 Oct 9. PMID: 25306919.
- FLUshing in the bathroom.Amezcua C, Gagliani N, Flavell R. J Exp Med. 2014 Nov 17. PMID: 25403806.
- Neurobiology: building a bigger brain.Gulden FO, Šestan N. Nature. 2014 Nov 13. PMID: 25391958.
- The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. Mol Cell. 2014 Nov 6; 2014 Nov 6. PMID: 25514182.
- Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC. Nat Neurosci. 2014 Nov; 2014 Oct 28. PMID: 25349915.
- Inflammasome activation by Campylobacter jejuni.Bouwman LI, de Zoete MR, Bleumink-Pluym NM, Flavell RA, van Putten JP. J Immunol. 2014 Nov 1; 2014 Sep 29. PMID: 25267974.
- Ligand binding by the tandem glycine riboswitch depends on aptamer dimerization but not double ligand occupancy.Ruff KM, Strobel SA. RNA. 2014 Nov; 2014 Sep 22. PMID: 25246650.
- Multi-layered nanoparticles for combination gene and drug delivery to tumors.Ediriwickrema A, Zhou J, Deng Y, Saltzman WM. Biomaterials. 2014 Nov; 2014 Aug 8. PMID: 25112935.
- Detecting "different": Pyrin senses modified GTPases.de Zoete MR, Flavell RA. Cell Res. 2014 Nov; 2014 Aug 5. PMID: 25091449.
- Mental health. Adolescent mental health--opportunity and obligation.Lee FS, Heimer H, Giedd JN, Lein ES, Šestan N, Weinberger DR, Casey BJ. Science. 2014 Oct 31. PMID: 25359951.
- The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance.Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. Dev Cell. 2014 Oct 27. PMID: 25373775.
- Inflammation and the blood microvascular system.Pober JS, Sessa WC. Cold Spring Harb Perspect Biol. 2014 Oct 23; 2014 Oct 23. PMID: 25384307.
- Antivirulence properties of an antifreeze protein.Heisig M, Abraham NM, Liu L, Neelakanta G, Mattessich S, Sultana H, Shang Z, Ansari JM, Killiam C, Walker W, Cooley L, Flavell RA, Agaisse H, Fikrig E. Cell Rep. 2014 Oct 23; 2014 Oct 16. PMID: 25373896.
- Inflammasomes.de Zoete MR, Palm NW, Zhu S, Flavell RA. Cold Spring Harb Perspect Biol. 2014 Oct 16; 2014 Oct 16. PMID: 25324215.
- The PAR complex controls the spatiotemporal dynamics of F-actin and the MTOC in directionally migrating leukocytes.Crespo CL, Vernieri C, Keller PJ, Garrè M, Bender JR, Wittbrodt J, Pardi R. J Cell Sci. 2014 Oct 15; 2014 Sep 1. PMID: 25179599.
- Loss of the endothelial glucocorticoid receptor prevents the therapeutic protection afforded by dexamethasone after LPS.Goodwin JE, Feng Y, Velazquez H, Zhou H, Sessa WC. PLoS One. 2014; 2014 Oct 9. PMID: 25299055.
- Bacterial nucleoid-associated protein uncouples transcription levels from transcription timing.Zwir I, Yeo WS, Shin D, Latifi T, Huang H, Groisman EA. mBio. 2014 Oct 7; 2014 Oct 7. PMID: 25293763.
- T cell memory. A local macrophage chemokine network sustains protective tissue-resident memory CD4 T cells.Iijima N, Iwasaki A. Science. 2014 Oct 3; 2014 Aug 28. PMID: 25170048.
- Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs.Watanabe T, Lin H. Mol Cell. 2014 Oct 2. PMID: 25280102.
- Looking at LncRNAs with the ribozyme toolkit.Pyle AM. Mol Cell. 2014 Oct 2. PMID: 25280101.
- Matrix metalloproteinase-19 promotes metastatic behavior in vitro and is associated with increased mortality in non-small cell lung cancer.Yu G, Herazo-Maya JD, Nukui T, Romkes M, Parwani A, Juan-Guardela BM, Robertson J, Gauldie J, Siegfried JM, Kaminski N, Kass DJ. Am J Respir Crit Care Med. 2014 Oct 1. PMID: 25250855.
- MicroRNA mimicry blocks pulmonary fibrosis.Montgomery RL, Yu G, Latimer PA, Stack C, Robinson K, Dalby CM, Kaminski N, van Rooij E. EMBO Mol Med. 2014 Oct. PMID: 25239947.
- The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain.Rawling DC, Kohlway AS, Luo D, Ding SC, Pyle AM. Nucleic Acids Res. 2014 Oct; 2014 Sep 12. PMID: 25217590.
- Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA.Gallagher RR, Li Z, Lewis AO, Isaacs FJ. Nat Protoc. 2014 Oct; 2014 Sep 4. PMID: 25188632.
- Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering.Ma NJ, Moonan DW, Isaacs FJ. Nat Protoc. 2014 Oct; 2014 Sep 4. PMID: 25188631.
- Activation of N-methyl-d-aspartate receptor downregulates inflammasome activity and liver inflammation via a β-arrestin-2 pathway.Farooq A, Hoque R, Ouyang X, Farooq A, Ghani A, Ahsan K, Guerra M, Mehal WZ. Am J Physiol Gastrointest Liver Physiol. 2014 Oct 1; 2014 Aug 7. PMID: 25104498.
- The evolution of life history trade-offs in viruses.Goldhill DH, Turner PE. Curr Opin Virol. 2014 Oct; 2014 Aug 1. PMID: 25087040.
- Beyond repression of photomorphogenesis: role switching of COP/DET/FUS in light signaling.Huang X, Ouyang X, Deng XW. Curr Opin Plant Biol. 2014 Oct; 2014 Jul 25. PMID: 25061897.
- Virus meets host microRNA: the destroyer, the booster, the hijacker.Guo YE, Steitz JA. Mol Cell Biol. 2014 Oct; 2014 Jul 21. PMID: 25047834.
- Polyethyleneimine is a potent systemic adjuvant for glycoprotein antigens.Sheppard NC, Brinckmann SA, Gartlan KH, Puthia M, Svanborg C, Krashias G, Eisenbarth SC, Flavell RA, Sattentau QJ, Wegmann F. Int Immunol. 2014 Oct; 2014 May 20. PMID: 24844701.
- Controlled release for local delivery of drugs: barriers and models.Weiser JR, Saltzman WM. J Control Release. 2014 Sep 28; 2014 May 4. PMID: 24801251.
- Chemokine-coupled β2 integrin-induced macrophage Rac2-Myosin IIA interaction regulates VEGF-A mRNA stability and arteriogenesis.Morrison AR, Yarovinsky TO, Young BD, Moraes F, Ross TD, Ceneri N, Zhang J, Zhuang ZW, Sinusas AJ, Pardi R, Schwartz MA, Simons M, Bender JR. J Exp Med. 2014 Sep 22; 2014 Sep 1. PMID: 25180062.
- PIWI proteins are dispensable for mouse somatic development and reprogramming of fibroblasts into pluripotent stem cells.Cheng EC, Kang D, Wang Z, Lin H. PLoS One. 2014; 2014 Sep 19. PMID: 25238487.
- The expanding view of RNA and DNA function.Breaker RR, Joyce GF. Chem Biol. 2014 Sep 18. PMID: 25237854.
- Vesicular trafficking of incoming human papillomavirus 16 to the Golgi apparatus and endoplasmic reticulum requires γ-secretase activity.Zhang W, Kazakov T, Popa A, DiMaio D. mBio. 2014 Sep 16; 2014 Sep 16. PMID: 25227470.
- Comparative analysis of pseudogenes across three phyla.Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB. Proc Natl Acad Sci U S A. 2014 Sep 16; 2014 Aug 25. PMID: 25157146.
- Generation of transgenic Hydra by embryo microinjection.Juliano CE, Lin H, Steele RE. J Vis Exp. 2014 Sep 11; 2014 Sep 11. PMID: 25285460.
- Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.Eiler D, Wang J, Steitz TA. Proc Natl Acad Sci U S A. 2014 Sep 9; 2014 Aug 25. PMID: 25157168.
- Endothelial Akt1 mediates angiogenesis by phosphorylating multiple angiogenic substrates.Lee MY, Luciano AK, Ackah E, Rodriguez-Vita J, Bancroft TA, Eichmann A, Simons M, Kyriakides TR, Morales-Ruiz M, Sessa WC. Proc Natl Acad Sci U S A. 2014 Sep 2; 2014 Aug 18. PMID: 25136137.
- Mutation of Nogo-B receptor, a subunit of cis-prenyltransferase, causes a congenital disorder of glycosylation.Park EJ, Grabińska KA, Guan Z, Stránecký V, Hartmannová H, Hodaňová K, Barešová V, Sovová J, Jozsef L, Ondrušková N, Hansíková H, Honzík T, Zeman J, Hůlková H, Wen R, Kmoch S, Sessa WC. Cell Metab. 2014 Sep 2; 2014 Jul 24. PMID: 25066056.
- The impact of transmission mode on the evolution of benefits provided by microbial symbionts.Shapiro JW, Turner PE. Ecol Evol. 2014 Sep; 2014 Aug 6. PMID: 25535552.
- A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.Polikanov YS, Steitz TA, Innis CA. Nat Struct Mol Biol. 2014 Sep; 2014 Aug 17. PMID: 25132179.
- Structural optimization of a retrograde trafficking inhibitor that protects cells from infections by human polyoma- and papillomaviruses.Carney DW, Nelson CD, Ferris BD, Stevens JP, Lipovsky A, Kazakov T, DiMaio D, Atwood WJ, Sello JK. Bioorg Med Chem. 2014 Sep 1; 2014 Jul 10. PMID: 25087050.
- Engineering the elongation factor Tu for efficient selenoprotein synthesis.Haruna K, Alkazemi MH, Liu Y, Söll D, Englert M. Nucleic Acids Res. 2014 Sep; 2014 Jul 26. PMID: 25064855.
- Long-term therapeutic silencing of miR-33 increases circulating triglyceride levels and hepatic lipid accumulation in mice.Goedeke L, Salerno A, Ramírez CM, Guo L, Allen RM, Yin X, Langley SR, Esau C, Wanschel A, Fisher EA, Suárez Y, Baldán A, Mayr M, Fernández-Hernando C. EMBO Mol Med. 2014 Sep. PMID: 25038053.
- The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus.Kohlway A, Pirakitikulr N, Ding SC, Yang F, Luo D, Lindenbach BD, Pyle AM. J Virol. 2014 Sep; 2014 Jun 25. PMID: 24965468.
- Inflammasomes and intestinal homeostasis: regulating and connecting infection, inflammation and the microbiota.Gagliani N, Palm NW, de Zoete MR, Flavell RA. Int Immunol. 2014 Sep; 2014 Jun 19. PMID: 24948595.
- Dynamic signaling by T follicular helper cells during germinal center B cell selection.Shulman Z, Gitlin AD, Weinstein JS, Lainez B, Esplugues E, Flavell RA, Craft JE, Nussenzweig MC. Science. 2014 Aug 29. PMID: 25170154.
- Expanding the proteome of an RNA virus by phosphorylation of an intrinsically disordered viral protein.Cordek DG, Croom-Perez TJ, Hwang J, Hargittai MR, Subba-Reddy CV, Han Q, Lodeiro MF, Ning G, McCrory TS, Arnold JJ, Koc H, Lindenbach BD, Showalter SA, Cameron CE. J Biol Chem. 2014 Aug 29; 2014 Jul 16. PMID: 25031324.
- Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease.Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, Degnan PH, Hu J, Peter I, Zhang W, Ruggiero E, Cho JH, Goodman AL, Flavell RA. Cell. 2014 Aug 28. PMID: 25171403.
- Comparative analysis of regulatory information and circuits across distant species.Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Nature. 2014 Aug 28. PMID: 25164757.
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- Rare deleterious mutations of the gene EFR3A in autism spectrum disorders.Gupta AR, Pirruccello M, Cheng F, Kang HJ, Fernandez TV, Baskin JM, Choi M, Liu L, Ercan-Sencicek AG, Murdoch JD, Klei L, Neale BM, Franjic D, Daly MJ, Lifton RP, De Camilli P, Zhao H, Sestan N, State MW. Mol Autism. 2014; 2014 Apr 29. PMID: 24860643.
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- The developmental transcriptome of the human brain: implications for neurodevelopmental disorders.Tebbenkamp AT, Willsey AJ, State MW, Sestan N. Curr Opin Neurol. 2014 Apr. PMID: 24565942.
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- The emerging role of RNA-binding proteins in the life cycle of Trypanosoma brucei.Kolev NG, Ullu E, Tschudi C. Cell Microbiol. 2014 Apr; 2014 Feb 16. PMID: 24438230.
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- Piwi is required in multiple cell types to control germline stem cell lineage development in the Drosophila ovary.Ma X, Wang S, Do T, Song X, Inaba M, Nishimoto Y, Liu LP, Gao Y, Mao Y, Li H, McDowell W, Park J, Malanowski K, Peak A, Perera A, Li H, Gaudenz K, Haug J, Yamashita Y, Lin H, Ni JQ, Xie T. PLoS One. 2014; 2014 Mar 21. PMID: 24658126.
- Photoactivated UVR8-COP1 module determines photomorphogenic UV-B signaling output in Arabidopsis.Huang X, Yang P, Ouyang X, Chen L, Deng XW. PLoS Genet. 2014 Mar; 2014 Mar 20. PMID: 24651064.
- Nrf2 amplifies oxidative stress via induction of Klf9.Zucker SN, Fink EE, Bagati A, Mannava S, Bianchi-Smiraglia A, Bogner PN, Wawrzyniak JA, Foley C, Leonova KI, Grimm MJ, Moparthy K, Ionov Y, Wang J, Liu S, Sexton S, Kandel ES, Bakin AV, Zhang Y, Kaminski N, Segal BH, Nikiforov MA. Mol Cell. 2014 Mar 20; 2014 Mar 6. PMID: 24613345.
- The putative tRNA 2-thiouridine synthetase Ncs6 is an essential sulfur carrier in Methanococcus maripaludis.Liu Y, Long F, Wang L, Söll D, Whitman WB. FEBS Lett. 2014 Mar 18; 2014 Feb 11. PMID: 24530533.
- Autoregulation of glypican-1 by intronic microRNA-149 fine tunes the angiogenic response to FGF2 in human endothelial cells.Chamorro-Jorganes A, Araldi E, Rotllan N, Cirera-Salinas D, Suárez Y. J Cell Sci. 2014 Mar 15; 2014 Jan 24. PMID: 24463821.
- Let-7d microRNA affects mesenchymal phenotypic properties of lung fibroblasts.Huleihel L, Ben-Yehudah A, Milosevic J, Yu G, Pandit K, Sakamoto K, Yousef H, LeJeune M, Coon TA, Redinger CJ, Chensny L, Manor E, Schatten G, Kaminski N. Am J Physiol Lung Cell Mol Physiol. 2014 Mar 15; 2014 Jan 17. PMID: 24441869.
- Laminar and temporal expression dynamics of coding and noncoding RNAs in the mouse neocortex.Fertuzinhos S, Li M, Kawasawa YI, Ivic V, Franjic D, Singh D, Crair M, Sestan N. Cell Rep. 2014 Mar 13; 2014 Feb 20. PMID: 24561256.
- A half-zippered SNARE complex represents a functional intermediate in membrane fusion.Li F, Kümmel D, Coleman J, Reinisch KM, Rothman JE, Pincet F. J Am Chem Soc. 2014 Mar 5; 2014 Feb 18. PMID: 24533674.
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- NLRP6 inflammasome orchestrates the colonic host-microbial interface by regulating goblet cell mucus secretion.Wlodarska M, Thaiss CA, Nowarski R, Henao-Mejia J, Zhang JP, Brown EM, Frankel G, Levy M, Katz MN, Philbrick WM, Elinav E, Finlay BB, Flavell RA. Cell. 2014 Feb 27. PMID: 24581500.
- Control of a Salmonella virulence operon by proline-charged tRNA(Pro).Lee EJ, Choi J, Groisman EA. Proc Natl Acad Sci U S A. 2014 Feb 25; 2014 Feb 10. PMID: 24516160.
- On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei.Ericson M, Janes MA, Butter F, Mann M, Ullu E, Tschudi C. BMC Biol. 2014 Feb 19; 2014 Feb 19. PMID: 24552149.
- A promiscuous lipid-binding protein diversifies the subcellular sites of toll-like receptor signal transduction.Bonham KS, Orzalli MH, Hayashi K, Wolf AI, Glanemann C, Weninger W, Iwasaki A, Knipe DM, Kagan JC. Cell. 2014 Feb 13. PMID: 24529375.
- Nonstochastic reprogramming from a privileged somatic cell state.Guo S, Zi X, Schulz VP, Cheng J, Zhong M, Koochaki SH, Megyola CM, Pan X, Heydari K, Weissman SM, Gallagher PG, Krause DS, Fan R, Lu J. Cell. 2014 Feb 13; 2014 Jan 30. PMID: 24486105.
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- Insulin/IGF1 signaling inhibits age-dependent axon regeneration.Byrne AB, Walradt T, Gardner KE, Hubbert A, Reinke V, Hammarlund M. Neuron. 2014 Feb 5; 2014 Jan 16. PMID: 24440228.
- A new system for naming ribosomal proteins.Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, Lafontaine DL, Lindahl L, Liljas A, Lipton JM, McAlear MA, Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CM, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, Williamson JR, Wilson D, Yonath A, Yusupov M. Curr Opin Struct Biol. 2014 Feb; 2014 Feb 10. PMID: 24524803.
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- Sustained delivery of proangiogenic microRNA-132 by nanoparticle transfection improves endothelial cell transplantation.Devalliere J, Chang WG, Andrejecsk JW, Abrahimi P, Cheng CJ, Jane-wit D, Saltzman WM, Pober JS. FASEB J. 2014 Feb; 2013 Nov 12. PMID: 24221087.
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- Tissue specific roles for the ribosome biogenesis factor Wdr43 in zebrafish development.Zhao C, Andreeva V, Gibert Y, LaBonty M, Lattanzi V, Prabhudesai S, Zhou Y, Zon L, McCann KL, Baserga S, Yelick PC. PLoS Genet. 2014 Jan; 2014 Jan 30. PMID: 24497835.
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- The antibiotics dityromycin and GE82832 bind protein S12 and block EF-G-catalyzed translocation.Bulkley D, Brandi L, Polikanov YS, Fabbretti A, O'Connor M, Gualerzi CO, Steitz TA. Cell Rep. 2014 Jan 30; 2014 Jan 9. PMID: 24412368.
- A comparative diffusion tensor imaging study of corpus callosum subregion integrity in bipolar disorder and schizophrenia.Li J, Kale Edmiston E, Chen K, Tang Y, Ouyang X, Jiang Y, Fan G, Ren L, Liu J, Zhou Y, Jiang W, Liu Z, Xu K, Wang F. Psychiatry Res. 2014 Jan 30; 2013 Nov 7. PMID: 24300086.
- Temporal specification and bilaterality of human neocortical topographic gene expression.Pletikos M, Sousa AM, Sedmak G, Meyer KA, Zhu Y, Cheng F, Li M, Kawasawa YI, Sestan N. Neuron. 2014 Jan 22; 2013 Dec 26. PMID: 24373884.
- PIWI proteins and PIWI-interacting RNAs in the soma.Ross RJ, Weiner MM, Lin H. Nature. 2014 Jan 16. PMID: 24429634.
- Nlrp3 prevents early renal interstitial edema and vascular permeability in unilateral ureteral obstruction.Pulskens WP, Butter LM, Teske GJ, Claessen N, Dessing MC, Flavell RA, Sutterwala FS, Florquin S, Leemans JC. PLoS One. 2014; 2014 Jan 15. PMID: 24454932.
- PIWI proteins are essential for early Drosophila embryogenesis.Mani SR, Megosh H, Lin H. Dev Biol. 2014 Jan 15; 2013 Oct 31. PMID: 24184635.
- Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex.Wu X, Chi RJ, Baskin JM, Lucast L, Burd CG, De Camilli P, Reinisch KM. Dev Cell. 2014 Jan 13; 2013 Dec 19. PMID: 24360784.
- Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE. Mol Cell. 2014 Jan 9; 2013 Dec 26. PMID: 24374310.
- Axon regeneration genes identified by RNAi screening in C. elegans.Nix P, Hammarlund M, Hauth L, Lachnit M, Jorgensen EM, Bastiani M. J Neurosci. 2014 Jan 8. PMID: 24403161.
- PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells.Juliano CE, Reich A, Liu N, Götzfried J, Zhong M, Uman S, Reenan RA, Wessel GM, Steele RE, Lin H. Proc Natl Acad Sci U S A. 2014 Jan 7; 2013 Dec 23. PMID: 24367095.
- De novo selection of oncogenes.Chacón KM, Petti LM, Scheideman EH, Pirazzoli V, Politi K, DiMaio D. Proc Natl Acad Sci U S A. 2014 Jan 7; 2013 Dec 16. PMID: 24344264.
- Angiopoietin-2 secretion by endothelial cell exosomes: regulation by the phosphatidylinositol 3-kinase (PI3K)/Akt/endothelial nitric oxide synthase (eNOS) and syndecan-4/syntenin pathways.Ju R, Zhuang ZW, Zhang J, Lanahan AA, Kyriakides T, Sessa WC, Simons M. J Biol Chem. 2014 Jan 3; 2013 Nov 14. PMID: 24235146.
- ESCaping rejection: A step forward for embryonic-stem-cell-based regenerative medicine.Willinger T, Flavell RA. Cell Stem Cell. 2014 Jan 2. PMID: 24388169.
- MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.Harmanci A, Rozowsky J, Gerstein M. Genome Biol. 2014. PMID: 25292436.
- FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M. Genome Biol. 2014. PMID: 25273974.
- Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition.Bahal R, Quijano E, McNeer NA, Liu Y, Bhunia DC, Lopez-Giraldez F, Fields RJ, Saltzman WM, Ly DH, Glazer PM. Curr Gene Ther. 2014. PMID: 25174576.
- Zygotic genome activation during the maternal-to-zygotic transition.Lee MT, Bonneau AR, Giraldez AJ. Annu Rev Cell Dev Biol. 2014; 2014 Aug 11. PMID: 25150012.
- Targeted genome modification via triple helix formation.Ricciardi AS, McNeer NA, Anandalingam KK, Saltzman WM, Glazer PM. Methods Mol Biol. 2014. PMID: 25030921.
- Silver lining in the dark cloud of aneurysm disease.Chau KH, Bender JR, Elefteriades JA. Cardiology. 2014; 2014 Jun 17. PMID: 24942201.
- Versatile microRNA biogenesis in animals and their viruses.Xie M, Steitz JA. RNA Biol. 2014; 2014 May 7. PMID: 24823351.
- Viral miniproteins.DiMaio D. Annu Rev Microbiol. 2014; 2014 Apr 10. PMID: 24742054.
- Triplex-mediated genome targeting and editing.Reza F, Glazer PM. Methods Mol Biol. 2014. PMID: 24557900.
- In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP.Furukawa K, Gu H, Breaker RR. Methods Mol Biol. 2014. PMID: 24549622.
- RNA families in Epstein-Barr virus.Moss WN, Lee N, Pimienta G, Steitz JA. RNA Biol. 2014; 2013 Dec 20. PMID: 24441309.
- Epigenetic reprogramming of the type III interferon response potentiates antiviral activity and suppresses tumor growth.Ding S, Khoury-Hanold W, Iwasaki A, Robek MD. PLoS Biol. 2014 Jan; 2014 Jan 7. PMID: 24409098.
- Good cap/bad cap: how the cap-binding complex determines RNA fate.Müller-McNicoll M, Neugebauer KM. Nat Struct Mol Biol. 2014 Jan. PMID: 24389545.
- Role of miRNAs and epigenetics in neural stem cell fate determination.Lopez-Ramirez MA, Nicoli S. Epigenetics. 2014 Jan; 2013 Dec 16. PMID: 24342893.
- Peptide nucleic acid-mediated recombination for targeted genomic repair and modification.Schleifman EB, Glazer PM. Methods Mol Biol. 2014. PMID: 24297362.
- Inflammasomes and metabolic disease.Henao-Mejia J, Elinav E, Thaiss CA, Flavell RA. Annu Rev Physiol. 2014; 2013 Nov 21. PMID: 24274736.
- Signal-specific temporal response by the Salmonella PhoP/PhoQ regulatory system.Park SY, Groisman EA. Mol Microbiol. 2014 Jan; 2013 Nov 20. PMID: 24256574.
- A widespread self-cleaving ribozyme class is revealed by bioinformatics.Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. Nat Chem Biol. 2014 Jan; 2013 Nov 17. PMID: 24240507.
- Role of the Trypanosoma brucei HEN1 family methyltransferase in small interfering RNA modification.Shi H, Barnes RL, Carriero N, Atayde VD, Tschudi C, Ullu E. Eukaryot Cell. 2014 Jan; 2013 Nov 1. PMID: 24186950.
- The nanomaterial-dependent modulation of dendritic cells and its potential influence on therapeutic immunosuppression in lupus.Look M, Saltzman WM, Craft J, Fahmy TM. Biomaterials. 2014 Jan; 2013 Nov 1. PMID: 24183697.
- Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain.Kohlway A, Pirakitikulr N, Barrera FN, Potapova O, Engelman DM, Pyle AM, Lindenbach BD. J Virol. 2014 Jan; 2013 Oct 30. PMID: 24173222.
- Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs.Kasper DM, Gardner KE, Reinke V. Epigenetics. 2014 Jan; 2013 Oct 22. PMID: 24149573.
- Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria.Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF. Nucleic Acids Res. 2014 Jan; 2013 Sep 17. PMID: 24049072.
2013
- Suppression of amber codons in Caulobacter crescentus by the orthogonal Escherichia coli histidyl-tRNA synthetase/tRNAHis pair.Ko JH, Llopis PM, Heinritz J, Jacobs-Wagner C, Söll D. PLoS One. 2013; 2013 Dec 30. PMID: 24386240.
- Cartilage oligomeric matrix protein in idiopathic pulmonary fibrosis.Vuga LJ, Milosevic J, Pandit K, Ben-Yehudah A, Chu Y, Richards T, Sciurba J, Myerburg M, Zhang Y, Parwani AV, Gibson KF, Kaminski N. PLoS One. 2013; 2013 Dec 20. PMID: 24376648.
- Mammalian 5'-capped microRNA precursors that generate a single microRNA.Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Šestan N, Steitz JA. Cell. 2013 Dec 19. PMID: 24360278.
- High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. Nature. 2013 Dec 19; 2013 Oct 27. PMID: 24162848.
- Interactions between Nod-Like Receptors and Intestinal Bacteria.de Zoete MR, Flavell RA. Front Immunol. 2013 Dec 17; 2013 Dec 17. PMID: 24381573.
- eNOS-derived nitric oxide regulates endothelial barrier function through VE-cadherin and Rho GTPases.Di Lorenzo A, Lin MI, Murata T, Landskroner-Eiger S, Schleicher M, Kothiya M, Iwakiri Y, Yu J, Huang PL, Sessa WC. J Cell Sci. 2013 Dec 15; 2013 Sep 17. PMID: 24046447.
- Hypoxia and DNA repair.Glazer PM, Hegan DC, Lu Y, Czochor J, Scanlon SE. Yale J Biol Med. 2013 Dec 13; 2013 Dec 13. PMID: 24348208.
- Cortical projection neurons: sprung from the same root.Han W, Sestan N. Neuron. 2013 Dec 4. PMID: 24314721.
- Conformational dynamics of calcium-triggered activation of fusion by synaptotagmin.Krishnakumar SS, Kümmel D, Jones SJ, Radoff DT, Reinisch KM, Rothman JE. Biophys J. 2013 Dec 3. PMID: 24314081.
- Bacterial toxin RelE: a highly efficient ribonuclease with exquisite substrate specificity using atypical catalytic residues.Griffin MA, Davis JH, Strobel SA. Biochemistry. 2013 Dec 3; 2013 Nov 19. PMID: 24251350.
- ELF4 is critical for induction of type I interferon and the host antiviral response.You F, Wang P, Yang L, Yang G, Zhao YO, Qian F, Walker W, Sutton R, Montgomery R, Lin R, Iwasaki A, Fikrig E. Nat Immunol. 2013 Dec; 2013 Nov 3. PMID: 24185615.
- Riboswitches in eubacteria sense the second messenger c-di-AMP.Nelson JW, Sudarsan N, Furukawa K, Weinberg Z, Wang JX, Breaker RR. Nat Chem Biol. 2013 Dec; 2013 Oct 20. PMID: 24141192.
- Pericytes modulate endothelial sprouting.Chang WG, Andrejecsk JW, Kluger MS, Saltzman WM, Pober JS. Cardiovasc Res. 2013 Dec 1; 2013 Sep 16. PMID: 24042014.
- Very small embryonic-like stem cells from the murine bone marrow differentiate into epithelial cells of the lung.Kassmer SH, Jin H, Zhang PX, Bruscia EM, Heydari K, Lee JH, Kim CF, Kassmer SH, Krause DS. Stem Cells. 2013 Dec. PMID: 23681901.
- Phosphorylation of DGCR8 increases its intracellular stability and induces a progrowth miRNA profile.Herbert KM, Pimienta G, DeGregorio SJ, Alexandrov A, Steitz JA. Cell Rep. 2013 Nov 27; 2013 Nov 14. PMID: 24239349.
- Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW. Cell. 2013 Nov 21. PMID: 24267886.
- Coordinating the party: assembly factors and ribogenesis.Pyle AM. Mol Cell. 2013 Nov 21. PMID: 24267447.
- Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition.Lee MT, Bonneau AR, Takacs CM, Bazzini AA, DiVito KR, Fleming ES, Giraldez AJ. Nature. 2013 Nov 21; 2013 Sep 22. PMID: 24056933.
- The Nogo-B-PirB axis controls macrophage-mediated vascular remodeling.Kondo Y, Jadlowiec CC, Muto A, Yi T, Protack C, Collins MJ, Tellides G, Sessa WC, Dardik A. PLoS One. 2013; 2013 Nov 20. PMID: 24278366.
- Site-specific Genome Editing in PBMCs With PLGA Nanoparticle-delivered PNAs Confers HIV-1 Resistance in Humanized Mice.Schleifman EB, McNeer NA, Jackson A, Yamtich J, Brehm MA, Shultz LD, Greiner DL, Kumar P, Saltzman WM, Glazer PM. Mol Ther Nucleic Acids. 2013 Nov 19; 2013 Nov 19. PMID: 24253260.
- Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins.Li S, Smith KD, Davis JH, Gordon PB, Breaker RR, Strobel SA. Proc Natl Acad Sci U S A. 2013 Nov 19; 2013 Oct 30. PMID: 24173035.
- Molecular pathways: induction of polyploidy as a novel differentiation therapy for leukemia.Krause DS, Crispino JD. Clin Cancer Res. 2013 Nov 15; 2013 Aug 20. PMID: 23963861.
- Biochemistry: Metal ghosts in the splicing machine.Strobel SA. Nature. 2013 Nov 14; 2013 Nov 6. PMID: 24196709.
- Neuron-specific feeding RNAi in C. elegans and its use in a screen for essential genes required for GABA neuron function.Firnhaber C, Hammarlund M. PLoS Genet. 2013 Nov; 2013 Nov 7. PMID: 24244189.
- Solving nucleic acid structures by molecular replacement: examples from group II intron studies.Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 2013 Oct 12. PMID: 24189228.
- Reply to: "On the robustness of germ cell migration and microRNA-mediated regulation of chemokine signaling".Staton AA, Knaut H, Giraldez AJ. Nat Genet. 2013 Nov. PMID: 24165725.
- Deficient eNOS phosphorylation is a mechanism for diabetic vascular dysfunction contributing to increased stroke size.Li Q, Atochin D, Kashiwagi S, Earle J, Wang A, Mandeville E, Hayakawa K, d'Uscio LV, Lo EH, Katusic Z, Sessa W, Huang PL. Stroke. 2013 Nov; 2013 Aug 29. PMID: 23988642.
- Paracrine exchanges of molecular signals between alginate-encapsulated pericytes and freely suspended endothelial cells within a 3D protein gel.Andrejecsk JW, Cui J, Chang WG, Devalliere J, Pober JS, Saltzman WM. Biomaterials. 2013 Nov; 2013 Aug 21. PMID: 23973174.
- Hormone therapy: A to Z.Fischer C, Kallen AN, Pal L. Menopause. 2013 Nov. PMID: 23921519.
- Radiation sensitivity and sensitization in melanoma.Shahbazian D, Bindra RS, Kluger HM, Glazer PM. Pigment Cell Melanoma Res. 2013 Nov; 2013 Aug 12. PMID: 23870422.
- Nanoparticles for urothelium penetration and delivery of the histone deacetylase inhibitor belinostat for treatment of bladder cancer.Martin DT, Hoimes CJ, Kaimakliotis HZ, Cheng CJ, Zhang K, Liu J, Wheeler MA, Kelly WK, Tew GN, Saltzman WM, Weiss RM. Nanomedicine. 2013 Nov; 2013 Jun 11. PMID: 23764660.
- NALP3-mediated inflammation is a principal cause of progressive renal failure in oxalate nephropathy.Knauf F, Asplin JR, Granja I, Schmidt IM, Moeckel GW, David RJ, Flavell RA, Aronson PS. Kidney Int. 2013 Nov; 2013 Jun 5. PMID: 23739234.
- Th9 Cells Drive Host Immunity against Gastrointestinal Worm Infection.Licona-Limón P, Henao-Mejia J, Temann AU, Gagliani N, Licona-Limón I, Ishigame H, Hao L, Herbert DR, Flavell RA. Immunity. 2013 Oct 17. PMID: 24138883.
- CD301b⁺ dermal dendritic cells drive T helper 2 cell-mediated immunity.Kumamoto Y, Linehan M, Weinstein JS, Laidlaw BJ, Craft JE, Iwasaki A. Immunity. 2013 Oct 17; 2013 Sep 26. PMID: 24076051.
- Aminoacylation of tRNA 2'- or 3'-hydroxyl by phosphoseryl- and pyrrolysyl-tRNA synthetases.Englert M, Moses S, Hohn M, Ling J, O'Donoghue P, Söll D. FEBS Lett. 2013 Oct 11; 2013 Sep 8. PMID: 24021645.
- The imprinted H19 lncRNA antagonizes let-7 microRNAs.Kallen AN, Zhou XB, Xu J, Qiao C, Ma J, Yan L, Lu L, Liu C, Yi JS, Zhang H, Min W, Bennett AM, Gregory RI, Ding Y, Huang Y. Mol Cell. 2013 Oct 10; 2013 Sep 19. PMID: 24055342.
- Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B.Huang X, Ouyang X, Yang P, Lau OS, Chen L, Wei N, Deng XW. Proc Natl Acad Sci U S A. 2013 Oct 8; 2013 Sep 25. PMID: 24067658.
- Integrative annotation of variants from 1092 humans: application to cancer genomics.Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Science. 2013 Oct 4. PMID: 24092746.
- Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis.Herazo-Maya JD, Noth I, Duncan SR, Kim S, Ma SF, Tseng GC, Feingold E, Juan-Guardela BM, Richards TJ, Lussier Y, Huang Y, Vij R, Lindell KO, Xue J, Gibson KF, Shapiro SD, Garcia JG, Kaminski N. Sci Transl Med. 2013 Oct 2. PMID: 24089408.
- C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation.Doh JH, Jung Y, Reinke V, Lee MH. Worm. 2013 Oct 1. PMID: 24744981.
- Role of the intestinal microbiome in liver disease.Henao-Mejia J, Elinav E, Thaiss CA, Licona-Limon P, Flavell RA. J Autoimmun. 2013 Oct; 2013 Sep 24. PMID: 24075647.
- Upgrading protein synthesis for synthetic biology.O'Donoghue P, Ling J, Wang YS, Söll D. Nat Chem Biol. 2013 Oct. PMID: 24045798.
- The ins and outs of hepatitis C virus entry and assembly.Lindenbach BD, Rice CM. Nat Rev Microbiol. 2013 Oct; 2013 Sep 10. PMID: 24018384.
- Generating protective immunity against genital herpes.Shin H, Iwasaki A. Trends Immunol. 2013 Oct; 2013 Sep 3. PMID: 24012144.
- Pyrrolysyl-tRNA synthetase variants reveal ancestral aminoacylation function.Ko JH, Wang YS, Nakamura A, Guo LT, Söll D, Umehara T. FEBS Lett. 2013 Oct 1; 2013 Aug 28. PMID: 23994531.
- Compensatory mutants of the bovine papillomavirus E5 protein and the platelet-derived growth factor β receptor reveal a complex direct transmembrane interaction.Edwards AP, Xie Y, Bowers L, DiMaio D. J Virol. 2013 Oct; 2013 Aug 7. PMID: 23926343.
- The E5 proteins.DiMaio D, Petti LM. Virology. 2013 Oct; 2013 May 31. PMID: 23731971.
- Effect of a matrigel sandwich on endodermal differentiation of human embryonic stem cells.Lawton BR, Sosa JA, Roman S, Krause DS. Stem Cell Rev Rep. 2013 Oct. PMID: 23719997.
- Direct, quantitative, and noninvasive imaging of the transport of active agents through intact brain with positron emission tomography.Sirianni RW, Zheng MQ, Saltzman WM, Huang Y, Carson RE. Mol Imaging Biol. 2013 Oct. PMID: 23624949.
- Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases.Eiler D, Lin J, Simonetti A, Klaholz BP, Steitz TA. Proc Natl Acad Sci U S A. 2013 Sep 24; 2013 Sep 12. PMID: 24029018.
- A single amino acid substitution converts a transmembrane protein activator of the platelet-derived growth factor β receptor into an inhibitor.Petti LM, Talbert-Slagle K, Hochstrasser ML, DiMaio D. J Biol Chem. 2013 Sep 20; 2013 Aug 1. PMID: 23908351.
- Laminar and columnar development of barrel cortex relies on thalamocortical neurotransmission.Li H, Fertuzinhos S, Mohns E, Hnasko TS, Verhage M, Edwards R, Sestan N, Crair MC. Neuron. 2013 Sep 4. PMID: 24012009.
- Tissue-resident memory T cells.Shin H, Iwasaki A. Immunol Rev. 2013 Sep. PMID: 23947354.
- Hypoxia-inducible factor-1α in vascular smooth muscle regulates blood pressure homeostasis through a peroxisome proliferator-activated receptor-γ-angiotensin II receptor type 1 axis.Huang Y, Di Lorenzo A, Jiang W, Cantalupo A, Sessa WC, Giordano FJ. Hypertension. 2013 Sep; 2013 Aug 5. PMID: 23918749.
- Predicted group II intron lineages E and F comprise catalytically active ribozymes.Nagy V, Pirakitikulr N, Zhou KI, Chillón I, Luo J, Pyle AM. RNA. 2013 Sep; 2013 Jul 23. PMID: 23882113.
- High-risk human papillomavirus E6 inhibits monocyte differentiation to Langerhans cells.Iijima N, Goodwin EC, Dimaio D, Iwasaki A. Virology. 2013 Sep; 2013 Jul 18. PMID: 23871219.
- Piwi genes are dispensable for normal hematopoiesis in mice.Nolde MJ, Cheng EC, Guo S, Lin H. PLoS One. 2013; 2013 Aug 23. PMID: 24058407.
- Genetics. Mysterious ribosomopathies.McCann KL, Baserga SJ. Science. 2013 Aug 23. PMID: 23970686.
- Efficient influenza A virus replication in the respiratory tract requires signals from TLR7 and RIG-I.Pang IK, Pillai PS, Iwasaki A. Proc Natl Acad Sci U S A. 2013 Aug 20; 2013 Aug 5. PMID: 23918369.
- The initiation of mammalian protein synthesis and mRNA scanning mechanism.Lomakin IB, Steitz TA. Nature. 2013 Aug 15; 2013 Jul 21. PMID: 23873042.
- Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA.Moss WN, Steitz JA. BMC Genomics. 2013 Aug 9; 2013 Aug 9. PMID: 23937650.
- Ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG), components of the demethylation pathway, are direct targets of miRNA-29a.Zhang P, Huang B, Xu X, Sessa WC. Biochem Biophys Res Commun. 2013 Aug 2; 2013 Jun 29. PMID: 23820384.
- Innate sensors of pathogen and stress: linking inflammation to obesity.Jin C, Flavell RA. J Allergy Clin Immunol. 2013 Aug. PMID: 23905917.
- The genomic landscape of cohesin-associated chromatin interactions.DeMare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. Genome Res. 2013 Aug; 2013 May 23. PMID: 23704192.
- Telmisartan exerts pleiotropic effects in endothelial cells and promotes endothelial cell quiescence and survival.Siragusa M, Sessa WC. Arterioscler Thromb Vasc Biol. 2013 Aug; 2013 May 23. PMID: 23702662.
- Very small embryonic-like cells: biology and function of these potential endogenous pluripotent stem cells in adult tissues.Kassmer SH, Krause DS. Mol Reprod Dev. 2013 Aug; 2013 Apr 4. PMID: 23440892.
- Xyolide, a bioactive nonenolide from an Amazonian endophytic fungus, Xylaria feejeensis.Baraban EG, Morin JB, Phillips GM, Phillips AJ, Strobel SA, Handelsman J. Tetrahedron Lett. 2013 Jul 31. PMID: 23913990.
- Parvovirus evades interferon-dependent viral control in primary mouse embryonic fibroblasts.Mattei LM, Cotmore SF, Tattersall P, Iwasaki A. Virology. 2013 Jul 20; 2013 May 12. PMID: 23676303.
- Highly penetrative, drug-loaded nanocarriers improve treatment of glioblastoma.Zhou J, Patel TR, Sirianni RW, Strohbehn G, Zheng MQ, Duong N, Schafbauer T, Huttner AJ, Huang Y, Carson RE, Zhang Y, Sullivan DJ Jr, Piepmeier JM, Saltzman WM. Proc Natl Acad Sci U S A. 2013 Jul 16; 2013 Jul 1. PMID: 23818631.
- Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR. Viruses. 2013 Jul 8; 2013 Jul 8. PMID: 23881275.
- Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution.Fang G, Passalacqua KD, Hocking J, Llopis PM, Gerstein M, Bergman NH, Jacobs-Wagner C. BMC Genomics. 2013 Jul 5; 2013 Jul 5. PMID: 23829427.
- The evolution of lineage-specific regulatory activities in the human embryonic limb.Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. Cell. 2013 Jul 3. PMID: 23827682.
- A bacterial virulence protein promotes pathogenicity by inhibiting the bacterium's own F1Fo ATP synthase.Lee EJ, Pontes MH, Groisman EA. Cell. 2013 Jul 3. PMID: 23827679.
- Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline.Saxe JP, Chen M, Zhao H, Lin H. EMBO J. 2013 Jul 3; 2013 May 28. PMID: 23714778.
- Effect of laparoscopic Roux-en-Y gastric bypass surgery on type 2 diabetes mellitus with hypertension: a randomized controlled trial.Liang Z, Wu Q, Chen B, Yu P, Zhao H, Ouyang X. Diabetes Res Clin Pract. 2013 Jul; 2013 May 22. PMID: 23706413.
- Inflammasome biology in fibrogenesis.Ouyang X, Ghani A, Mehal WZ. Biochim Biophys Acta. 2013 Jul; 2013 Apr 3. PMID: 23562491.
- Small, highly active DNAs that hydrolyze DNA.Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. J Am Chem Soc. 2013 Jun 19; 2013 Jun 6. PMID: 23679108.
- Truncated form of TGF-βRII, but not its absence, induces memory CD8+ T cell expansion and lymphoproliferative disorder in mice.Ishigame H, Mosaheb MM, Sanjabi S, Flavell RA. J Immunol. 2013 Jun 15; 2013 May 17. PMID: 23686479.
- Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer.Hu B, Elinav E, Huber S, Strowig T, Hao L, Hafemann A, Jin C, Wunderlich C, Wunderlich T, Eisenbarth SC, Flavell RA. Proc Natl Acad Sci U S A. 2013 Jun 11; 2013 May 21. PMID: 23696660.
- Transcriptional regulation of gene expression in C. elegans.Reinke V, Krause M, Okkema P. WormBook. 2013 Jun 4; 2013 Jun 4. PMID: 23801596.
- How to define biomarkers of human T cell aging and immunocompetence?Herndler-Brandstetter D, Ishigame H, Flavell RA. Front Immunol. 2013; 2013 Jun 4. PMID: 23761794.
- Innate immune receptors: key regulators of metabolic disease progression.Jin C, Henao-Mejia J, Flavell RA. Cell Metab. 2013 Jun 4. PMID: 23747246.
- The lipopolysaccharide modification regulator PmrA limits Salmonella virulence by repressing the type three-secretion system Spi/Ssa.Choi J, Groisman EA. Proc Natl Acad Sci U S A. 2013 Jun 4; 2013 May 20. PMID: 23690578.
- Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products.Gu H, Breaker RR. Biotechniques. 2013 Jun. PMID: 23750543.
- TH2, allergy and group 2 innate lymphoid cells.Licona-Limón P, Kim LK, Palm NW, Flavell RA. Nat Immunol. 2013 Jun. PMID: 23685824.
- Conflicting roles for a cell surface modification in Salmonella.May JF, Groisman EA. Mol Microbiol. 2013 Jun; 2013 May 5. PMID: 23646936.
- Innate immune recognition of flagellin limits systemic persistence of Brucella.Terwagne M, Ferooz J, Rolán HG, Sun YH, Atluri V, Xavier MN, Franchi L, Núñez G, Legrand T, Flavell RA, De Bolle X, Letesson JJ, Tsolis RM. Cell Microbiol. 2013 Jun; 2013 Jan 7. PMID: 23227931.
- The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis.Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Limón P, Kaech SM, Nakayama M, Rinn JL, Flavell RA. Immunity. 2013 May 23; 2013 Apr 25. PMID: 23623381.
- Reduced caveolin-1 promotes hyperinflammation due to abnormal heme oxygenase-1 localization in lipopolysaccharide-challenged macrophages with dysfunctional cystic fibrosis transmembrane conductance regulator.Zhang PX, Murray TS, Villella VR, Ferrari E, Esposito S, D'Souza A, Raia V, Maiuri L, Krause DS, Egan ME, Bruscia EM. J Immunol. 2013 May 15; 2013 Apr 19. PMID: 23606537.
- IL-22 deficiency alters colonic microbiota to be transmissible and colitogenic.Zenewicz LA, Yin X, Wang G, Elinav E, Hao L, Zhao L, Flavell RA. J Immunol. 2013 May 15; 2013 Apr 12. PMID: 23585682.
- Microbiota keep the intestinal clock ticking.Henao-Mejia J, Strowig T, Flavell RA. Cell. 2013 May 9. PMID: 23663774.
- The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex.Zuo Y, Wang Y, Steitz TA. Mol Cell. 2013 May 9; 2013 Apr 25. PMID: 23623685.
- Aberrant endocrinology and ovarian response to clomiphene citrate during the course of an undiagnosed early intrauterine pregnancy: a case report.Kallen AN, Luk J, Pal L. J Reprod Med. 2013 May-Jun. PMID: 23763012.
- Now on display: a gallery of group II intron structures at different stages of catalysis.Marcia M, Somarowthu S, Pyle AM. Mob DNA. 2013 May 1; 2013 May 1. PMID: 23634971.
- Evolution of increased survival in RNA viruses specialized on cancer-derived cells.Brandon Ogbunugafor C, Alto BW, Overton TM, Bhushan A, Morales NM, Turner PE. Am Nat. 2013 May; 2013 Mar 14. PMID: 23594543.
- Improved regenerative myogenesis and muscular dystrophy in mice lacking Mkp5.Shi H, Verma M, Zhang L, Dong C, Flavell RA, Bennett AM. J Clin Invest. 2013 May; 2013 Apr 1. PMID: 23543058.
- Rapamycin inhibits smooth muscle cell proliferation and obstructive arteriopathy attributable to elastin deficiency.Li W, Li Q, Qin L, Ali R, Qyang Y, Tassabehji M, Pober BR, Sessa WC, Giordano FJ, Tellides G. Arterioscler Thromb Vasc Biol. 2013 May; 2013 Mar 14. PMID: 23493289.
- An electrospun scaffold integrating nucleic acid delivery for treatment of full-thickness wounds.Kobsa S, Kristofik NJ, Sawyer AJ, Bothwell AL, Kyriakides TR, Saltzman WM. Biomaterials. 2013 May; 2013 Feb 27. PMID: 23453058.
- Dynamic migration and cell-cell interactions of early reprogramming revealed by high-resolution time-lapse imaging.Megyola CM, Gao Y, Teixeira AM, Cheng J, Heydari K, Cheng EC, Nottoli T, Krause DS, Lu J, Guo S. Stem Cells. 2013 May. PMID: 23335078.
- IL-22 promotes fibroblast-mediated wound repair in the skin.McGee HM, Schmidt BA, Booth CJ, Yancopoulos GD, Valenzuela DM, Murphy AJ, Stevens S, Flavell RA, Horsley V. J Invest Dermatol. 2013 May; 2012 Dec 6. PMID: 23223145.
- Genome-wide siRNA screen identifies the retromer as a cellular entry factor for human papillomavirus.Lipovsky A, Popa A, Pimienta G, Wyler M, Bhan A, Kuruvilla L, Guie MA, Poffenberger AC, Nelson CD, Atwood WJ, DiMaio D. Proc Natl Acad Sci U S A. 2013 Apr 30; 2013 Apr 8. PMID: 23569269.
- Crystal structure of an insect antifreeze protein and its implications for ice binding.Hakim A, Nguyen JB, Basu K, Zhu DF, Thakral D, Davies PL, Isaacs FJ, Modis Y, Meng W. J Biol Chem. 2013 Apr 26; 2013 Mar 12. PMID: 23486477.
- Hypersensitive site 6 of the Th2 locus control region is essential for Th2 cytokine expression.Williams A, Lee GR, Spilianakis CG, Hwang SS, Eisenbarth SC, Flavell RA. Proc Natl Acad Sci U S A. 2013 Apr 23; 2013 Apr 8. PMID: 23569250.
- Excessive Th1 responses due to the absence of TGF-β signaling cause autoimmune diabetes and dysregulated Treg cell homeostasis.Ishigame H, Zenewicz LA, Sanjabi S, Licona-Limón P, Nakayama M, Leonard WJ, Flavell RA. Proc Natl Acad Sci U S A. 2013 Apr 23; 2013 Apr 8. PMID: 23569233.
- Repressing the repressor: a lincRNA as a MicroRNA sponge in embryonic stem cell self-renewal.Cheng EC, Lin H. Dev Cell. 2013 Apr 15. PMID: 23597480.
- Structure of the PolIIIα-τc-DNA complex suggests an atomic model of the replisome.Liu B, Lin J, Steitz TA. Structure. 2013 Apr 2; 2013 Mar 7. PMID: 23478062.
- Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism.Peng JC, Lin H. Curr Opin Cell Biol. 2013 Apr; 2013 Mar 4. PMID: 23465540.
- NO triggers RGS4 degradation to coordinate angiogenesis and cardiomyocyte growth.Jaba IM, Zhuang ZW, Li N, Jiang Y, Martin KA, Sinusas AJ, Papademetris X, Simons M, Sessa WC, Young LH, Tirziu D. J Clin Invest. 2013 Apr. PMID: 23454748.
- A major epigenetic programming mechanism guided by piRNAs.Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. Dev Cell. 2013 Mar 11; 2013 Feb 21. PMID: 23434410.
- Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing.Li S, Breaker RR. Nucleic Acids Res. 2013 Mar 1; 2013 Feb 1. PMID: 23376932.
- Triplex-forming peptide nucleic acids induce heritable elevations in gamma-globin expression in hematopoietic progenitor cells.Chin JY, Reza F, Glazer PM. Mol Ther. 2013 Mar; 2013 Jan 22. PMID: 23337982.
- IL-1R signaling in dendritic cells replaces pattern-recognition receptors in promoting CD8⁺ T cell responses to influenza A virus.Pang IK, Ichinohe T, Iwasaki A. Nat Immunol. 2013 Mar; 2013 Jan 13. PMID: 23314004.
- Toll-like receptor 9 in plasmacytoid dendritic cells fails to detect parvoviruses.Mattei LM, Cotmore SF, Li L, Tattersall P, Iwasaki A. J Virol. 2013 Mar; 2013 Jan 9. PMID: 23302877.
- Yeast response to LA virus indicates coadapted global gene expression during mycoviral infection.McBride RC, Boucher N, Park DS, Turner PE, Townsend JP. FEMS Yeast Res. 2013 Mar; 2013 Jan 2. PMID: 23122216.
- Different routes to the same destination.Hayashi K, Iwasaki A. Elife. 2013 Feb 19; 2013 Feb 19. PMID: 23426937.
- Induction of megakaryocyte differentiation drives nuclear accumulation and transcriptional function of MKL1 via actin polymerization and RhoA activation.Smith EC, Teixeira AM, Chen RC, Wang L, Gao Y, Hahn KL, Krause DS. Blood. 2013 Feb 14; 2012 Dec 14. PMID: 23243284.
- BRG1-mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling.Chaiyachati BH, Jani A, Wan Y, Huang H, Flavell R, Chi T. EMBO J. 2013 Feb 6; 2013 Jan 15. PMID: 23321680.
- Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase.Ritacco CJ, Kamtekar S, Wang J, Steitz TA. Nucleic Acids Res. 2013 Feb 1; 2012 Dec 28. PMID: 23275567.
- The structure and repertoire of small interfering RNAs in Leishmania (Viannia) braziliensis reveal diversification in the trypanosomatid RNAi pathway.Atayde VD, Shi H, Franklin JB, Carriero N, Notton T, Lye LF, Owens K, Beverley SM, Tschudi C, Ullu E. Mol Microbiol. 2013 Feb; 2012 Dec 26. PMID: 23217017.
- miRNAs as modulators of angiogenesis.Landskroner-Eiger S, Moneke I, Sessa WC. Cold Spring Harb Perspect Med. 2013 Feb 1; 2013 Feb 1. PMID: 23169571.
- Cell type-dependent requirement of autophagy in HSV-1 antiviral defense.Yordy B, Iwasaki A. Autophagy. 2013 Feb 1; 2012 Oct 24. PMID: 23095715.
- Caspase-11 stimulates rapid flagellin-independent pyroptosis in response to Legionella pneumophila.Case CL, Kohler LJ, Lima JB, Strowig T, de Zoete MR, Flavell RA, Zamboni DS, Roy CR. Proc Natl Acad Sci U S A. 2013 Jan 29; 2013 Jan 10. PMID: 23307811.
- Rewiring translation for elongation factor Tu-dependent selenocysteine incorporation.Aldag C, Bröcker MJ, Hohn MJ, Prat L, Hammond G, Plummer A, Söll D. Angew Chem Int Ed Engl. 2013 Jan 28; 2012 Nov 27. PMID: 23193031.
- Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity.Darricarrère N, Liu N, Watanabe T, Lin H. Proc Natl Acad Sci U S A. 2013 Jan 22; 2013 Jan 7. PMID: 23297219.
- Identification of c-di-GMP derivatives resistant to an EAL domain phosphodiesterase.Shanahan CA, Gaffney BL, Jones RA, Strobel SA. Biochemistry. 2013 Jan 15; 2013 Jan 3. PMID: 23256840.
- IL-13 receptor α2-arginase 2 pathway mediates IL-13-induced pulmonary hypertension.Cho WK, Lee CM, Kang MJ, Huang Y, Giordano FJ, Lee PJ, Trow TK, Homer RJ, Sessa WC, Elias JA, Lee CG. Am J Physiol Lung Cell Mol Physiol. 2013 Jan 15; 2012 Nov 2. PMID: 23125252.
- Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems.Townsend GE 2nd, Raghavan V, Zwir I, Groisman EA. Proc Natl Acad Sci U S A. 2013 Jan 8; 2012 Dec 19. PMID: 23256153.
- Endothelial glucocorticoid receptor is required for protection against sepsis.Goodwin JE, Feng Y, Velazquez H, Sessa WC. Proc Natl Acad Sci U S A. 2013 Jan 2; 2012 Dec 17. PMID: 23248291.
- Adenosine is required for sustained inflammasome activation via the A₂A receptor and the HIF-1α pathway.Ouyang X, Ghani A, Malik A, Wilder T, Colegio OR, Flavell RA, Cronstein BN, Mehal WZ. Nat Commun. 2013. PMID: 24352507.
- Thin layer chromatography.Santiago M, Strobel S. Methods Enzymol. 2013. PMID: 24182936.
- miR-181 and metabolic regulation in the immune system.Williams A, Henao-Mejia J, Harman CC, Flavell RA. Cold Spring Harb Symp Quant Biol. 2013; 2013 Oct 25. PMID: 24163395.
- Bacterial Mg2+ homeostasis, transport, and virulence.Groisman EA, Hollands K, Kriner MA, Lee EJ, Park SY, Pontes MH. Annu Rev Genet. 2013; 2013 Sep 20. PMID: 24079267.
- Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly.Liu B, Eliason WK, Steitz TA. Nat Commun. 2013. PMID: 24048025.
- Analysis of microbiota alterations in inflammasome-deficient mice.Elinav E, Thaiss CA, Flavell RA. Methods Mol Biol. 2013. PMID: 23852605.
- On the biological success of viruses.Wasik BR, Turner PE. Annu Rev Microbiol. 2013; 2013 Jun 28. PMID: 23808330.
- Canonical and non-canonical barriers facing antimiR cancer therapeutics.Cheng CJ, Saltzman WM, Slack FJ. Curr Med Chem. 2013. PMID: 23745563.
- The intestinal microbiota in chronic liver disease.Henao-Mejia J, Elinav E, Thaiss CA, Flavell RA. Adv Immunol. 2013. PMID: 23611286.
- Ribonucleoproteins in archaeal pre-rRNA processing and modification.Yip WS, Vincent NG, Baserga SJ. Archaea. 2013; 2013 Mar 10. PMID: 23554567.
- Interpretation of genomic variants using a unified biological network approach.Khurana E, Fu Y, Chen J, Gerstein M. PLoS Comput Biol. 2013; 2013 Mar 7. PMID: 23505346.
- Virion assembly and release.Lindenbach BD. Curr Top Microbiol Immunol. 2013. PMID: 23463202.
- Role of IRAK-M in alcohol induced liver injury.Wang Y, Hu Y, Chao C, Yuksel M, Colle I, Flavell RA, Ma Y, Yan H, Wen L. PLoS One. 2013; 2013 Feb 21. PMID: 23437317.
- Natural variation identifies multiple loci controlling petal shape and size in Arabidopsis thaliana.Abraham MC, Metheetrairut C, Irish VF. PLoS One. 2013; 2013 Feb 13. PMID: 23418598.
- Human hemato-lymphoid system mice: current use and future potential for medicine.Rongvaux A, Takizawa H, Strowig T, Willinger T, Eynon EE, Flavell RA, Manz MG. Annu Rev Immunol. 2013; 2013 Jan 16. PMID: 23330956.
- Child development and structural variation in the human genome.Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child Dev. 2013 Jan-Feb; 2013 Jan 13. PMID: 23311762.
- Capture hybridization analysis of RNA targets (CHART).Simon MD. Curr Protoc Mol Biol. 2013. PMID: 23288463.
- Duplex RNA activated ATPases (DRAs): platforms for RNA sensing, signaling and processing.Luo D, Kohlway A, Pyle AM. RNA Biol. 2013 Jan; 2012 Dec 10. PMID: 23228901.
- Autophagy and selective deployment of Atg proteins in antiviral defense.Yordy B, Tal MC, Hayashi K, Arojo O, Iwasaki A. Int Immunol. 2013 Jan; 2012 Oct 5. PMID: 23042773.
- Reducing mitochondrial ROS improves disease-related pathology in a mouse model of ataxia-telangiectasia.D'Souza AD, Parish IA, Krause DS, Kaech SM, Shadel GS. Mol Ther. 2013 Jan; 2012 Sep 25. PMID: 23011031.
2012
- Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay.Alexandrov A, Colognori D, Shu MD, Steitz JA. Proc Natl Acad Sci U S A. 2012 Dec 26; 2012 Dec 10. PMID: 23236153.
- Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM. Nature. 2012 Dec 20; 2012 Nov 18. PMID: 23160490.
- Carbon source-dependent expansion of the genetic code in bacteria.Prat L, Heinemann IU, Aerni HR, Rinehart J, O'Donoghue P, Söll D. Proc Natl Acad Sci U S A. 2012 Dec 18; 2012 Nov 26. PMID: 23185002.
- NLRP1 joins the dark side?de Zoete MR, Flavell RA. Immunity. 2012 Dec 14. PMID: 23244714.
- Noncanonical autophagy is required for type I interferon secretion in response to DNA-immune complexes.Henault J, Martinez J, Riggs JM, Tian J, Mehta P, Clarke L, Sasai M, Latz E, Brinkmann MM, Iwasaki A, Coyle AJ, Kolbeck R, Green DR, Sanjuan MA. Immunity. 2012 Dec 14; 2012 Dec 6. PMID: 23219390.
- Protein aggregation caused by aminoglycoside action is prevented by a hydrogen peroxide scavenger.Ling J, Cho C, Guo LT, Aerni HR, Rinehart J, Söll D. Mol Cell. 2012 Dec 14; 2012 Oct 30. PMID: 23122414.
- The bacterial second messenger c-di-GMP: probing interactions with protein and RNA binding partners using cyclic dinucleotide analogs.Shanahan CA, Strobel SA. Org Biomol Chem. 2012 Dec 14; 2012 Oct 29. PMID: 23108253.
- The thermodynamic basis for viral RNA detection by the RIG-I innate immune sensor.Vela A, Fedorova O, Ding SC, Pyle AM. J Biol Chem. 2012 Dec 14; 2012 Oct 10. PMID: 23055530.
- Developmental progression to infectivity in Trypanosoma brucei triggered by an RNA-binding protein.Kolev NG, Ramey-Butler K, Cross GA, Ullu E, Tschudi C. Science. 2012 Dec 7. PMID: 23224556.
- miR-1 and miR-206 regulate angiogenesis by modulating VegfA expression in zebrafish.Stahlhut C, Suárez Y, Lu J, Mishima Y, Giraldez AJ. Development. 2012 Dec 1. PMID: 23132244.
- On sports and genes.Zilberman-Schapira G, Chen J, Gerstein M. Recent Pat DNA Gene Seq. 2012 Dec. PMID: 22762737.
- LoxP-FRT Trap (LOFT): a simple and flexible system for conventional and reversible gene targeting.Chaiyachati BH, Kaundal RK, Zhao J, Wu J, Flavell R, Chi T. BMC Biol. 2012 Nov 30; 2012 Nov 30. PMID: 23198860.
- Surface modified poly(β amino ester)-containing nanoparticles for plasmid DNA delivery.Fields RJ, Cheng CJ, Quijano E, Weller C, Kristofik N, Duong N, Hoimes C, Egan ME, Saltzman WM. J Control Release. 2012 Nov 28; 2012 Oct 5. PMID: 23041278.
- Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs.Brown JA, Valenstein ML, Yario TA, Tycowski KT, Steitz JA. Proc Natl Acad Sci U S A. 2012 Nov 20; 2012 Nov 5. PMID: 23129630.
- Does Lin28 Antagonize miRNA-Mediated Repression by Displacing miRISC from Target mRNAs?Kallen AN, Ma J, Huang Y. Front Genet. 2012; 2012 Nov 16. PMID: 23162570.
- A vaccine strategy that protects against genital herpes by establishing local memory T cells.Shin H, Iwasaki A. Nature. 2012 Nov 15; 2012 Oct 17. PMID: 23075848.
- Capturing the cloud: UAP56 in nuage assembly and function.Lin H. Cell. 2012 Nov 9. PMID: 23141532.
- IL-22BP is regulated by the inflammasome and modulates tumorigenesis in the intestine.Huber S, Gagliani N, Zenewicz LA, Huber FJ, Bosurgi L, Hu B, Hedl M, Zhang W, O'Connor W Jr, Murphy AJ, Valenzuela DM, Yancopoulos GD, Booth CJ, Cho JH, Ouyang W, Abraham C, Flavell RA. Nature. 2012 Nov 8; 2012 Oct 17. PMID: 23075849.
- Visualizing the determinants of viral RNA recognition by innate immune sensor RIG-I.Luo D, Kohlway A, Vela A, Pyle AM. Structure. 2012 Nov 7; 2012 Sep 27. PMID: 23022350.
- Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion.O'Donoghue P, Prat L, Heinemann IU, Ling J, Odoi K, Liu WR, Söll D. FEBS Lett. 2012 Nov 2; 2012 Oct 1. PMID: 23036644.
- AUF1/hnRNP D is a novel protein partner of the EBER1 noncoding RNA of Epstein-Barr virus.Lee N, Pimienta G, Steitz JA. RNA. 2012 Nov; 2012 Sep 25. PMID: 23012480.
- Hypoxia-induced protein CAIX is associated with somatic loss of BRCA1 protein and pathway activity in triple negative breast cancer.Neumeister VM, Sullivan CA, Lindner R, Lezon-Geyda K, Li J, Zavada J, Martel M, Glazer PM, Tuck DP, Rimm DL, Harris L. Breast Cancer Res Treat. 2012 Nov; 2012 Sep 14. PMID: 22976806.
- Engineered zinc-finger proteins can compensate genetic haploinsufficiency by transcriptional activation of the wild-type allele: application to Willams-Beuren syndrome and supravalvular aortic stenosis.Zhang P, Huang A, Morales-Ruiz M, Starcher BC, Huang Y, Sessa WC, Niklason LE, Giordano FJ. Hum Gene Ther. 2012 Nov. PMID: 22891920.
- Receptor interacting protein-2 contributes to host defense against Anaplasma phagocytophilum infection.Sukumaran B, Ogura Y, Pedra JH, Kobayashi KS, Flavell RA, Fikrig E. FEMS Immunol Med Microbiol. 2012 Nov; 2012 Jul 23. PMID: 22747758.
- Successful collection and engraftment of autologous peripheral blood progenitor cells in poorly mobilized patients receiving high-dose granulocyte colony-stimulating factor.Cooper DL, Proytcheva M, Medoff E, Seropian SE, Snyder EL, Krause DS, Wu Y. J Clin Apher. 2012 Nov; 2012 May 7. PMID: 22566214.
- IBI series winner. Student-directed discovery of the plant microbiome and its products.Bascom-Slack CA, Arnold AE, Strobel SA. Science. 2012 Oct 26. PMID: 23112324.
- Long noncoding RNAs as sinks in Prader-Willi syndrome.McCann KL, Baserga SJ. Mol Cell. 2012 Oct 26. PMID: 23102265.
- Visualizing group II intron catalysis through the stages of splicing.Marcia M, Pyle AM. Cell. 2012 Oct 26. PMID: 23101623.
- Targeting cancer with a lupus autoantibody.Hansen JE, Chan G, Liu Y, Hegan DC, Dalal S, Dray E, Kwon Y, Xu Y, Xu X, Peterson-Roth E, Geiger E, Liu Y, Gera J, Sweasy JB, Sung P, Rockwell S, Nishimura RN, Weisbart RH, Glazer PM. Sci Transl Med. 2012 Oct 24. PMID: 23100628.
- Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion.Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L, Olds W, Fischer JT, Söll D, Isaacs FJ, Rinehart J. FEBS Lett. 2012 Oct 19; 2012 Sep 13. PMID: 22982858.
- The hexameric helicase DnaB adopts a nonplanar conformation during translocation.Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. Cell. 2012 Oct 12; 2012 Sep 27. PMID: 23022319.
- Complex oncogene dependence in microRNA-125a-induced myeloproliferative neoplasms.Guo S, Bai H, Megyola CM, Halene S, Krause DS, Scadden DT, Lu J. Proc Natl Acad Sci U S A. 2012 Oct 9; 2012 Sep 24. PMID: 23012470.
- piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism.Beyret E, Liu N, Lin H. Cell Res. 2012 Oct; 2012 Aug 21. PMID: 22907665.
- Tandem attenuators control expression of the Salmonella mgtCBR virulence operon.Lee EJ, Groisman EA. Mol Microbiol. 2012 Oct; 2012 Aug 26. PMID: 22857388.
- Transmembrane protein aptamers that inhibit CCR5 expression and HIV coreceptor function.Scheideman EH, Marlatt SA, Xie Y, Hu Y, Sutton RE, DiMaio D. J Virol. 2012 Oct; 2012 Jul 18. PMID: 22811524.
- Combination delivery of TGF-β inhibitor and IL-2 by nanoscale liposomal polymeric gels enhances tumour immunotherapy.Park J, Wrzesinski SH, Stern E, Look M, Criscione J, Ragheb R, Jay SM, Demento SL, Agawu A, Licona Limon P, Ferrandino AF, Gonzalez D, Habermann A, Flavell RA, Fahmy TM. Nat Mater. 2012 Oct; 2012 Jul 15. PMID: 22797827.
- The GENCODE pseudogene resource.Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. Genome Biol. 2012 Sep 26; 2012 Sep 26. PMID: 22951037.
- Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Genome Biol. 2012 Sep 26; 2012 Sep 26. PMID: 22950945.
- Innate immune recognition of HIV-1.Iwasaki A. Immunity. 2012 Sep 21. PMID: 22999945.
- The brace for a growing scaffold: Mss116 protein promotes RNA folding by stabilizing an early assembly intermediate.Fedorova O, Pyle AM. J Mol Biol. 2012 Sep 21; 2012 Jun 13. PMID: 22705286.
- Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH.Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, Eom SH, Konigsberg WH, Söll D, Wang J. Proc Natl Acad Sci U S A. 2012 Sep 18; 2012 Sep 4. PMID: 22949672.
- Neuroscience. The emerging biology of autism spectrum disorders.State MW, Šestan N. Science. 2012 Sep 14. PMID: 22984058.
- A neuron-specific role for autophagy in antiviral defense against herpes simplex virus.Yordy B, Iijima N, Huttner A, Leib D, Iwasaki A. Cell Host Microbe. 2012 Sep 13. PMID: 22980330.
- MKL1 and MKL2 play redundant and crucial roles in megakaryocyte maturation and platelet formation.Smith EC, Thon JN, Devine MT, Lin S, Schulz VP, Guo Y, Massaro SA, Halene S, Gallagher P, Italiano JE Jr, Krause DS. Blood. 2012 Sep 13; 2012 Jul 17. PMID: 22806889.
- Architecture of the human regulatory network derived from ENCODE data.Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Nature. 2012 Sep 6. PMID: 22955619.
- Understanding transcriptional regulation by integrative analysis of transcription factor binding data.Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. Genome Res. 2012 Sep. PMID: 22955978.
- Life, death, and miracles: Th17 cells in the intestine.Huber S, Gagliani N, Flavell RA. Eur J Immunol. 2012 Sep. PMID: 22949322.
- VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. Bioinformatics. 2012 Sep 1; 2012 Jun 28. PMID: 22743228.
- Rational design and directed evolution of a bacterial-type glutaminyl-tRNA synthetase precursor.Guo LT, Helgadóttir S, Söll D, Ling J. Nucleic Acids Res. 2012 Sep; 2012 May 31. PMID: 22661575.
- Skin T(RM) mediates distributed border patrol.Shin H, Iwasaki A. Cell Res. 2012 Sep; 2012 May 8. PMID: 22565287.
- Novel insights through the integration of structural and functional genomics data with protein networks.Clarke D, Bhardwaj N, Gerstein MB. J Struct Biol. 2012 Sep; 2012 Feb 11. PMID: 22343087.
- Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei.Tschudi C, Shi H, Franklin JB, Ullu E. BMC Genomics. 2012 Aug 27; 2012 Aug 27. PMID: 22925482.
- Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6.Turner PE, McBride RC, Duffy S, Montville R, Wang LS, Yang YW, Lee SJ, Kim J. BMC Evol Biol. 2012 Aug 22; 2012 Aug 22. PMID: 22913547.
- Polymer nanoparticles encapsulating siRNA for treatment of HSV-2 genital infection.Steinbach JM, Weller CE, Booth CJ, Saltzman WM. J Control Release. 2012 Aug 20; 2012 Jun 15. PMID: 22705461.
- The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase.Ling J, Peterson KM, Simonovic I, Söll D, Simonovic M. J Biol Chem. 2012 Aug 17; 2012 Jul 6. PMID: 22773845.
- Identification of ligand analogues that control c-di-GMP riboswitches.Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker RR. ACS Chem Biol. 2012 Aug 17; 2012 Jun 19. PMID: 22646696.
- Discrete RNA libraries from pseudo-torsional space.Humphris-Narayanan E, Pyle AM. J Mol Biol. 2012 Aug 3; 2012 Mar 13. PMID: 22425640.
- RCrane: semi-automated RNA model building.Keating KS, Pyle AM. Acta Crystallogr D Biol Crystallogr. 2012 Aug; 2012 Jul 17. PMID: 22868764.
- RNA science and its applications-a look toward the future: Albany, NY USA, November 3-4, 2011.Breaker RR, Conklin DS, Gold L, Söll D, Montimurro JS, Agris PF. RNA Biol. 2012 Aug; 2012 Aug 1. PMID: 22858674.
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- Tracking expression and subcellular localization of RNA and protein species using high-throughput single cell imaging flow cytometry.Borah S, Nichols LA, Hassman LM, Kedes DH, Steitz JA. RNA. 2012 Aug; 2012 Jun 28. PMID: 22745225.
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- Dendritic cell-mediated activation-induced cytidine deaminase (AID)-dependent induction of genomic instability in human myeloma.Koduru S, Wong E, Strowig T, Sundaram R, Zhang L, Strout MP, Flavell RA, Schatz DG, Dhodapkar KM, Dhodapkar MV. Blood. 2012 Mar 8; 2012 Jan 10. PMID: 22234692.
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- The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge B2a of the ribosome.Bulkley D, Johnson F, Steitz TA. J Mol Biol. 2012 Mar 2; 2012 Jan 2. PMID: 22240456.
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- Increased tubular proliferation as an adaptive response to glomerular albuminuria.Guo JK, Marlier A, Shi H, Shan A, Ardito TA, Du ZP, Kashgarian M, Krause DS, Biemesderfer D, Cantley LG. J Am Soc Nephrol. 2012 Mar; 2011 Dec 22. PMID: 22193389.
- Nonhematopoietic cells are the primary source of bone marrow-derived lung epithelial cells.Kassmer SH, Bruscia EM, Zhang PX, Krause DS. Stem Cells. 2012 Mar. PMID: 22162244.
- Preclinical evaluation of Laromustine for use in combination with radiation therapy in the treatment of solid tumors.Rockwell S, Liu Y, Seow HA, Ishiguro K, Baumann RP, Penketh PG, Shyam K, Akintujoye OM, Glazer PM, Sartorelli AC. Int J Radiat Biol. 2012 Mar; 2011 Dec 20. PMID: 22111842.
- Inhibition of microRNA-29 enhances elastin levels in cells haploinsufficient for elastin and in bioengineered vessels--brief report.Zhang P, Huang A, Ferruzzi J, Mecham RP, Starcher BC, Tellides G, Humphrey JD, Giordano FJ, Niklason LE, Sessa WC. Arterioscler Thromb Vasc Biol. 2012 Mar; 2011 Nov 17. PMID: 22095981.
- Enhanced growth and hepatic differentiation of fetal liver epithelial cells through combinational and temporal adjustment of soluble factors.Qian L, Krause DS, Saltzman WM. Biotechnol J. 2012 Mar; 2011 Oct 26. PMID: 21922669.
- Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment.Ling J, Peterson KM, Simonović I, Cho C, Söll D, Simonović M. Proc Natl Acad Sci U S A. 2012 Feb 28; 2012 Feb 17. PMID: 22343532.
- Pancreatic islet expression of chemokine CCL2 suppresses autoimmune diabetes via tolerogenic CD11c+ CD11b+ dendritic cells.Kriegel MA, Rathinam C, Flavell RA. Proc Natl Acad Sci U S A. 2012 Feb 28; 2012 Feb 10. PMID: 22328150.
- Catalytic mechanism of Sep-tRNA:Cys-tRNA synthase: sulfur transfer is mediated by disulfide and persulfide.Liu Y, Dos Santos PC, Zhu X, Orlando R, Dean DR, Söll D, Yuan J. J Biol Chem. 2012 Feb 17; 2011 Dec 13. PMID: 22167197.
- Intrinsic negative feedback governs activation surge in two-component regulatory systems.Yeo WS, Zwir I, Huang HV, Shin D, Kato A, Groisman EA. Mol Cell. 2012 Feb 10. PMID: 22325356.
- Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity.Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ, Camporez JP, Shulman GI, Gordon JI, Hoffman HM, Flavell RA. Nature. 2012 Feb 1; 2012 Feb 1. PMID: 22297845.
- The Intestine: where amazing things happen.Gagliani N, Huber S, Flavell RA. Cell Res. 2012 Feb; 2011 Dec 20. PMID: 22184010.
- Reperfusion injury intensifies the adaptive human T cell alloresponse in a human-mouse chimeric artery model.Yi T, Fogal B, Hao Z, Tobiasova Z, Wang C, Rao DA, Al-Lamki RS, Kirkiles-Smith NC, Kulkarni S, Bradley JR, Bothwell AL, Sessa WC, Tellides G, Pober JS. Arterioscler Thromb Vasc Biol. 2012 Feb; 2011 Nov 3. PMID: 22053072.
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- Notch signaling inhibits axon regeneration.El Bejjani R, Hammarlund M. Neuron. 2012 Jan 26. PMID: 22284182.
- Teplizumab induces human gut-tropic regulatory cells in humanized mice and patients.Waldron-Lynch F, Henegariu O, Deng S, Preston-Hurlburt P, Tooley J, Flavell R, Herold KC. Sci Transl Med. 2012 Jan 25. PMID: 22277969.
- Inflammasomes in health and disease.Strowig T, Henao-Mejia J, Elinav E, Flavell R. Nature. 2012 Jan 18; 2012 Jan 18. PMID: 22258606.
- Widespread genetic switches and toxicity resistance proteins for fluoride.Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR. Science. 2012 Jan 13; 2011 Dec 22. PMID: 22194412.
- Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.Smith KD, Lipchock SV, Strobel SA. Biochemistry. 2012 Jan 10; 2011 Dec 27. PMID: 22148472.
- Primary human cervical carcinoma cells require human papillomavirus E6 and E7 expression for ongoing proliferation.Magaldi TG, Almstead LL, Bellone S, Prevatt EG, Santin AD, DiMaio D. Virology. 2012 Jan 5; 2011 Nov 5. PMID: 22056390.
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- The microRNA regulation of stem cells.Huang XA, Lin H. Wiley Interdiscip Rev Dev Biol. 2012 Jan-Feb; 2011 Nov 17. PMID: 23801669.
- Selective pressure causes an RNA virus to trade reproductive fitness for increased structural and thermal stability of a viral enzyme.Dessau M, Goldhill D, McBride R, Turner PE, Modis Y. PLoS Genet. 2012; 2012 Nov 29. PMID: 23209446.
- MyD88 signalling in colonic mononuclear phagocytes drives colitis in IL-10-deficient mice.Hoshi N, Schenten D, Nish SA, Walther Z, Gagliani N, Flavell RA, Reizis B, Shen Z, Fox JG, Iwasaki A, Medzhitov R. Nat Commun. 2012. PMID: 23047678.
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- IL-22 signaling contributes to West Nile encephalitis pathogenesis.Wang P, Bai F, Zenewicz LA, Dai J, Gate D, Cheng G, Yang L, Qian F, Yuan X, Montgomery RR, Flavell RA, Town T, Fikrig E. PLoS One. 2012; 2012 Aug 28. PMID: 22952908.
- NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing.Freed EF, Prieto JL, McCann KL, McStay B, Baserga SJ. PLoS Genet. 2012; 2012 Aug 16. PMID: 22916032.
- A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins.Simon MD, Shokat KM. Methods Enzymol. 2012. PMID: 22910202.
- Effector CD4+ T cell expression signatures and immune-mediated disease associated genes.Zhang W, Ferguson J, Ng SM, Hui K, Goh G, Lin A, Esplugues E, Flavell RA, Abraham C, Zhao H, Cho JH. PLoS One. 2012; 2012 Jun 8. PMID: 22715389.
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- Comparative genomics reveals two novel RNAi factors in Trypanosoma brucei and provides insight into the core machinery.Barnes RL, Shi H, Kolev NG, Tschudi C, Ullu E. PLoS Pathog. 2012; 2012 May 24. PMID: 22654659.
- Proteomic identification of S-nitrosylated Golgi proteins: new insights into endothelial cell regulation by eNOS-derived NO.Sangwung P, Greco TM, Wang Y, Ischiropoulos H, Sessa WC, Iwakiri Y. PLoS One. 2012; 2012 Feb 21. PMID: 22363674.
- Endothelium derived nitric oxide synthase negatively regulates the PDGF-survivin pathway during flow-dependent vascular remodeling.Yu J, Zhang Y, Zhang X, Rudic RD, Bauer PM, Altieri DC, Sessa WC. PLoS One. 2012; 2012 Feb 15. PMID: 22355372.
- Mechanism and distribution of glmS ribozymes.McCown PJ, Winkler WC, Breaker RR. Methods Mol Biol. 2012. PMID: 22315066.
- Novel delivery strategies for glioblastoma.Zhou J, Atsina KB, Himes BT, Strohbehn GW, Saltzman WM. Cancer J. 2012 Jan-Feb. PMID: 22290262.
- IQSeq: integrated isoform quantification analysis based on next-generation sequencing.Du J, Leng J, Habegger L, Sboner A, McDermott D, Gerstein M. PLoS One. 2012; 2012 Jan 6. PMID: 22238592.
- Control of antiviral immunity by pattern recognition and the microbiome.Pang IK, Iwasaki A. Immunol Rev. 2012 Jan. PMID: 22168422.
- High-throughput analysis of growth differences among phage strains.Turner PE, Draghi JA, Wilpiszeski R. J Microbiol Methods. 2012 Jan; 2011 Nov 12. PMID: 22101310.
- Octa-functional PLGA nanoparticles for targeted and efficient siRNA delivery to tumors.Zhou J, Patel TR, Fu M, Bertram JP, Saltzman WM. Biomaterials. 2012 Jan; 2011 Oct 19. PMID: 22014944.
- Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells.Cheng C, Gerstein M. Nucleic Acids Res. 2012 Jan; 2011 Sep 16. PMID: 21926158.
- tRNAHis-guanylyltransferase establishes tRNAHis identity.Heinemann IU, Nakamura A, O'Donoghue P, Eiler D, Söll D. Nucleic Acids Res. 2012 Jan; 2011 Sep 2. PMID: 21890903.
- Targeted gene modification of hematopoietic progenitor cells in mice following systemic administration of a PNA-peptide conjugate.Rogers FA, Lin SS, Hegan DC, Krause DS, Glazer PM. Mol Ther. 2012 Jan; 2011 Aug 9. PMID: 21829173.
2011
- Systematic control of protein interactions for systems biology.Bhardwaj N, Clarke D, Gerstein M. Proc Natl Acad Sci U S A. 2011 Dec 20; 2011 Dec 12. PMID: 22160691.
- Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase.O'Donoghue P, Sheppard K, Nureki O, Söll D. Proc Natl Acad Sci U S A. 2011 Dec 20; 2011 Dec 7. PMID: 22158897.
- Inflammasome components Asc and caspase-1 mediate biomaterial-induced inflammation and foreign body response.Malik AF, Hoque R, Ouyang X, Ghani A, Hong E, Khan K, Moore LB, Ng G, Munro F, Flavell RA, Shi Y, Kyriakides TR, Mehal WZ. Proc Natl Acad Sci U S A. 2011 Dec 13; 2011 Nov 22. PMID: 22109549.
- In vivo distribution of surface-modified PLGA nanoparticles following intravaginal delivery.Cu Y, Booth CJ, Saltzman WM. J Control Release. 2011 Dec 10; 2011 Jul 8. PMID: 21763739.
- Minimal transition state charge stabilization of the oxyanion during peptide bond formation by the ribosome.Carrasco N, Hiller DA, Strobel SA. Biochemistry. 2011 Dec 6; 2011 Nov 9. PMID: 22035282.
- Biodegradable poly(amine-co-ester) terpolymers for targeted gene delivery.Zhou J, Liu J, Cheng CJ, Patel TR, Weller CE, Piepmeier JM, Jiang Z, Saltzman WM. Nat Mater. 2011 Dec 4; 2011 Dec 4. PMID: 22138789.
- A high-resolution whole-genome map of key chromatin modifications in the adult Drosophila melanogaster.Yin H, Sweeney S, Raha D, Snyder M, Lin H. PLoS Genet. 2011 Dec; 2011 Dec 15. PMID: 22194694.
- Genomics and privacy: implications of the new reality of closed data for the field.Greenbaum D, Sboner A, Mu XJ, Gerstein M. PLoS Comput Biol. 2011 Dec; 2011 Dec 1. PMID: 22144881.
- Use of target protector morpholinos to analyze the physiological roles of specific miRNA-mRNA pairs in vivo.Staton AA, Giraldez AJ. Nat Protoc. 2011 Dec 1; 2011 Dec 1. PMID: 22134127.
- TIP: a probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.Cheng C, Min R, Gerstein M. Bioinformatics. 2011 Dec 1; 2011 Oct 29. PMID: 22039215.
- Reduced level of ribonucleotide reductase R2 subunits increases dependence on homologous recombination repair of cisplatin-induced DNA damage.Lin ZP, Lee Y, Lin F, Belcourt MF, Li P, Cory JG, Glazer PM, Sartorelli AC. Mol Pharmacol. 2011 Dec; 2011 Aug 29. PMID: 21875941.
- Structure of Golgi transport proteins.Kümmel D, Reinisch KM. Cold Spring Harb Perspect Biol. 2011 Dec 1; 2011 Dec 1. PMID: 21813399.
- Gene duplication and loss in a MADS box gene transcription factor circuit.Lee HL, Irish VF. Mol Biol Evol. 2011 Dec; 2011 Jun 28. PMID: 21712469.
- Enhancement of surface ligand display on PLGA nanoparticles with amphiphilic ligand conjugates.Park J, Mattessich T, Jay SM, Agawu A, Saltzman WM, Fahmy TM. J Control Release. 2011 Nov 30; 2011 Jun 24. PMID: 21723893.
- Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate.Wu X, Bradley MJ, Cai Y, Kümmel D, De La Cruz EM, Barr FA, Reinisch KM. Proc Natl Acad Sci U S A. 2011 Nov 15; 2011 Nov 7. PMID: 22065758.
- Inhibition of hypoxia-induced miR-155 radiosensitizes hypoxic lung cancer cells.Babar IA, Czochor J, Steinmetz A, Weidhaas JB, Glazer PM, Slack FJ. Cancer Biol Ther. 2011 Nov 15; 2011 Nov 15. PMID: 22027557.
- Endothelial nitric oxide synthase controls the expression of the angiogenesis inhibitor thrombospondin 2.MacLauchlan S, Yu J, Parrish M, Asoulin TA, Schleicher M, Krady MM, Zeng J, Huang PL, Sessa WC, Kyriakides TR. Proc Natl Acad Sci U S A. 2011 Nov 15; 2011 Sep 26. PMID: 21949402.
- Functional and physical interaction between the mismatch repair and FA-BRCA pathways.Williams SA, Wilson JB, Clark AP, Mitson-Salazar A, Tomashevski A, Ananth S, Glazer PM, Semmes OJ, Bale AE, Jones NJ, Kupfer GM. Hum Mol Genet. 2011 Nov 15; 2011 Aug 24. PMID: 21865299.
- Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.Cheng C, Shou C, Yip KY, Gerstein MB. Genome Biol. 2011 Nov 7; 2011 Nov 7. PMID: 22060676.
- Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. PLoS Comput Biol. 2011 Nov; 2011 Nov 17. PMID: 22125477.
- The role of cloud computing in managing the deluge of potentially private genetic data.Greenbaum D, Gerstein M. Am J Bioeth. 2011 Nov. PMID: 22047125.
- MicroRNA regulation of cardiovascular functions.Sessa WC. Arterioscler Thromb Vasc Biol. 2011 Nov. PMID: 22011748.
- Mechanism for gene control by a natural allosteric group I ribozyme.Chen AG, Sudarsan N, Breaker RR. RNA. 2011 Nov; 2011 Sep 29. PMID: 21960486.
- Splice isoform estrogen receptors as integral transmembrane proteins.Kim KH, Toomre D, Bender JR. Mol Biol Cell. 2011 Nov; 2011 Sep 21. PMID: 21937726.
- A new way to see RNA.Keating KS, Humphris EL, Pyle AM. Q Rev Biophys. 2011 Nov; 2011 May 18. PMID: 21729350.
- The roles of RNA in the synthesis of protein.Moore PB, Steitz TA. Cold Spring Harb Perspect Biol. 2011 Nov 1; 2011 Nov 1. PMID: 21068149.
- Polymer delivery systems for site-specific genome editing.McNeer NA, Schleifman EB, Glazer PM, Saltzman WM. J Control Release. 2011 Oct 30; 2011 May 18. PMID: 21620910.
- The chemical versatility of RNA.Hiller DA, Strobel SA. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27. PMID: 21930584.
- Spatio-temporal transcriptome of the human brain.Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N. Nature. 2011 Oct 26; 2011 Oct 26. PMID: 22031440.
- Structural insights into RNA recognition by RIG-I.Luo D, Ding SC, Vela A, Kohlway A, Lindenbach BD, Pyle AM. Cell. 2011 Oct 14. PMID: 22000018.
- Differential analogue binding by two classes of c-di-GMP riboswitches.Shanahan CA, Gaffney BL, Jones RA, Strobel SA. J Am Chem Soc. 2011 Oct 5; 2011 Sep 8. PMID: 21838307.
- Prevention of K-Ras- and Pten-mediated intravaginal tumors by treatment with camptothecin-loaded PLGA nanoparticles.Blum JS, Weller CE, Booth CJ, Babar IA, Liang X, Slack FJ, Saltzman WM. Drug Deliv Transl Res. 2011 Oct 1. PMID: 25419505.
- Trafficking of hepatitis C virus core protein during virus particle assembly.Counihan NA, Rawlinson SM, Lindenbach BD. PLoS Pathog. 2011 Oct; 2011 Oct 20. PMID: 22028650.
- A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression.Borah S, Darricarrère N, Darnell A, Myoung J, Steitz JA. PLoS Pathog. 2011 Oct; 2011 Oct 13. PMID: 22022268.
- RNA helicases and remodeling proteins.Pyle AM. Curr Opin Chem Biol. 2011 Oct; 2011 Aug 20. PMID: 21862383.
- Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Protein Sci. 2011 Oct; 2011 Sep 15. PMID: 21826754.
- Targeted disruption of the CCR5 gene in human hematopoietic stem cells stimulated by peptide nucleic acids.Schleifman EB, Bindra R, Leif J, del Campo J, Rogers FA, Uchil P, Kutsch O, Shultz LD, Kumar P, Greiner DL, Glazer PM. Chem Biol. 2011 Sep 23. PMID: 21944757.
- A primate herpesvirus uses the integrator complex to generate viral microRNAs.Cazalla D, Xie M, Steitz JA. Mol Cell. 2011 Sep 16. PMID: 21925386.
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- A new shield for a cytokine storm.Iwasaki A, Medzhitov R. Cell. 2011 Sep 16. PMID: 21925310.
- Efficient differentiation and function of human macrophages in humanized CSF-1 mice.Rathinam C, Poueymirou WT, Rojas J, Murphy AJ, Valenzuela DM, Yancopoulos GD, Rongvaux A, Eynon EE, Manz MG, Flavell RA. Blood. 2011 Sep 15; 2011 Jul 25. PMID: 21791433.
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- Autophagy in the control and pathogenesis of viral infection.Yordy B, Iwasaki A. Curr Opin Virol. 2011 Sep. PMID: 21927636.
- Mitoxosome: a mitochondrial platform for cross-talk between cellular stress and antiviral signaling.Tal MC, Iwasaki A. Immunol Rev. 2011 Sep. PMID: 21884179.
- New translational possibilities for microenvironmental modulation of radiosensitivity.Glazer PM, Le QT, Bristow R, Helleday T, Pelroy R, Bernhard EJ. Radiat Res. 2011 Sep; 2011 Jul 8. PMID: 21867431.
- Radiation Resistance in Cancer Therapy: meeting summary and research opportunities. Report of an NCI Workshop held September 1-3, 2010.Glazer PM, Grandis J, Powell SN, Brown JM, Helleday T, Bristow R, Powis G, Hill RP, Le QT, Pelroy R, Mohla S, Bernhard EJ. Radiat Res. 2011 Sep; 2011 Jul 8. PMID: 21867428.
- Biodegradation of polyester polyurethane by endophytic fungi.Russell JR, Huang J, Anand P, Kucera K, Sandoval AG, Dantzler KW, Hickman D, Jee J, Kimovec FM, Koppstein D, Marks DH, Mittermiller PA, Núñez SJ, Santiago M, Townes MA, Vishnevetsky M, Williams NE, Vargas MP, Boulanger LA, Bascom-Slack C, Strobel SA. Appl Environ Microbiol. 2011 Sep; 2011 Jul 15. PMID: 21764951.
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- Genome-wide detection of novel regulatory RNAs in E. coli.Raghavan R, Groisman EA, Ochman H. Genome Res. 2011 Sep; 2011 Jun 10. PMID: 21665928.
- Enhanced siRNA delivery into cells by exploiting the synergy between targeting ligands and cell-penetrating peptides.Cheng CJ, Saltzman WM. Biomaterials. 2011 Sep; 2011 Jun 12. PMID: 21664689.
- Biodegradation, biocompatibility, and drug delivery in poly(ω-pentadecalactone-co-p-dioxanone) copolyesters.Liu J, Jiang Z, Zhang S, Liu C, Gross RA, Kyriakides TR, Saltzman WM. Biomaterials. 2011 Sep. PMID: 21641030.
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- Bi-allelic deletions within 13q14 and transient trisomy 21 with absence of GATA1s in pediatric acute megakaryoblastic leukemia.Massaro SA, Bajaj R, Pashankar FD, Ornstein D, Gallagher PG, Krause DS, Li P. Pediatr Blood Cancer. 2011 Sep; 2011 Apr 29. PMID: 21538823.
- Expanding the genetic code of Escherichia coli with phosphoserine.Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM, Benner J, Noren CJ, Rinehart J, Söll D. Science. 2011 Aug 26. PMID: 21868676.
- The real cost of sequencing: higher than you think!Sboner A, Mu XJ, Greenbaum D, Auerbach RK, Gerstein MB. Genome Biol. 2011 Aug 25; 2011 Aug 25. PMID: 21867570.
- glmS Riboswitch binding to the glucosamine-6-phosphate α-anomer shifts the pKa toward neutrality.Davis JH, Dunican BF, Strobel SA. Biochemistry. 2011 Aug 23; 2011 Jul 27. PMID: 21770472.
- B-Myb, cancer, senescence, and microRNAs.Martinez I, Dimaio D. Cancer Res. 2011 Aug 15; 2011 Aug 9. PMID: 21828240.
- Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.Yip KY, Utz L, Sitwell S, Hu X, Sidhu SS, Turk BE, Gerstein M, Kim PM. BMC Biol. 2011 Aug 11; 2011 Aug 11. PMID: 21835011.
- Transgenic expression of human signal regulatory protein alpha in Rag2-/-gamma(c)-/- mice improves engraftment of human hematopoietic cells in humanized mice.Strowig T, Rongvaux A, Rathinam C, Takizawa H, Borsotti C, Philbrick W, Eynon EE, Manz MG, Flavell RA. Proc Natl Acad Sci U S A. 2011 Aug 9; 2011 Jul 25. PMID: 21788509.
- AlleleSeq: analysis of allele-specific expression and binding in a network framework.Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. Mol Syst Biol. 2011 Aug 2; 2011 Aug 2. PMID: 21811232.
- Cardiovascular disease and ovarian function.Kallen AN, Pal L. Curr Opin Obstet Gynecol. 2011 Aug. PMID: 21681091.
- Hypoxia-induced epigenetic regulation and silencing of the BRCA1 promoter.Lu Y, Chu A, Turker MS, Glazer PM. Mol Cell Biol. 2011 Aug; 2011 Jun 13. PMID: 21670155.
- Tissue-engineered vascular grafts form neovessels that arise from regeneration of the adjacent blood vessel.Hibino N, Villalona G, Pietris N, Duncan DR, Schoffner A, Roh JD, Yi T, Dobrucki LW, Mejias D, Sawh-Martinez R, Harrington JK, Sinusas A, Krause DS, Kyriakides T, Saltzman WM, Pober JS, Shin'oka T, Breuer CK. FASEB J. 2011 Aug; 2011 May 12. PMID: 21566209.
- Complexin cross-links prefusion SNAREs into a zigzag array.Kümmel D, Krishnakumar SS, Radoff DT, Li F, Giraudo CG, Pincet F, Rothman JE, Reinisch KM. Nat Struct Mol Biol. 2011 Jul 24; 2011 Jul 24. PMID: 21785414.
- A conformational switch in complexin is required for synaptotagmin to trigger synaptic fusion.Krishnakumar SS, Radoff DT, Kümmel D, Giraudo CG, Li F, Khandan L, Baguley SW, Coleman J, Reinisch KM, Pincet F, Rothman JE. Nat Struct Mol Biol. 2011 Jul 24; 2011 Jul 24. PMID: 21785412.
- Love triangle between Unc93B1, TLR7, and TLR9 prevents fatal attraction.Sasai M, Iwasaki A. Immunity. 2011 Jul 22. PMID: 21777792.
- Control of TH17 cells occurs in the small intestine.Esplugues E, Huber S, Gagliani N, Hauser AE, Town T, Wan YY, O'Connor W Jr, Rongvaux A, Van Rooijen N, Haberman AM, Iwakura Y, Kuchroo VK, Kolls JK, Bluestone JA, Herold KC, Flavell RA. Nature. 2011 Jul 17; 2011 Jul 17. PMID: 21765430.
- A two-step chemical mechanism for ribosome-catalysed peptide bond formation.Hiller DA, Singh V, Zhong M, Strobel SA. Nature. 2011 Jul 17; 2011 Jul 17. PMID: 21765427.
- Precise manipulation of chromosomes in vivo enables genome-wide codon replacement.Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Science. 2011 Jul 15. PMID: 21764749.
- Radiation Resistance in Cancer Therapy: Meeting Summary and Research Opportunities: Report of an NCI Workshop held September 1-3, 2010.Glazer PM, Grandis J, Powell SN, Brown JM, Helleday T, Bristow R, Powis G, Hill RP, Le QT, Pelroy R, Mohla S, Bernhard EJ. Radiat Res. 2011 Jul 8; 2011 Jul 8. PMID: 21740251.
- Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development.Ouyang X, Li J, Li G, Li B, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, Li S, Wang H, Deng XW. Plant Cell. 2011 Jul; 2011 Jul 29. PMID: 21803941.
- Improving human hemato-lymphoid-system mice by cytokine knock-in gene replacement.Willinger T, Rongvaux A, Strowig T, Manz MG, Flavell RA. Trends Immunol. 2011 Jul; 2011 Jun 21. PMID: 21697012.
- Genetic analysis of selenocysteine biosynthesis in the archaeon Methanococcus maripaludis.Hohn MJ, Palioura S, Su D, Yuan J, Söll D. Mol Microbiol. 2011 Jul; 2011 May 18. PMID: 21564332.
- The emerging world of small silencing RNAs in protozoan parasites.Atayde VD, Tschudi C, Ullu E. Trends Parasitol. 2011 Jul; 2011 Apr 15. PMID: 21497553.
- TLR9 and the NLRP3 inflammasome link acinar cell death with inflammation in acute pancreatitis.Hoque R, Sohail M, Malik A, Sarwar S, Luo Y, Shah A, Barrat F, Flavell R, Gorelick F, Husain S, Mehal W. Gastroenterology. 2011 Jul; 2011 Mar 24. PMID: 21439959.
- The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing.Dutca LM, Gallagher JE, Baserga SJ. Nucleic Acids Res. 2011 Jul; 2011 Feb 23. PMID: 21349877.
- Pattern of hypomethylating agents use among elderly patients with myelodysplastic syndromes.Wang R, Gross CP, Maggiore RJ, Halene S, Soulos PR, Raza A, Galili N, Ma X. Leuk Res. 2011 Jul; 2010 Nov 9. PMID: 21067809.
- Abnormal trafficking and degradation of TLR4 underlie the elevated inflammatory response in cystic fibrosis.Bruscia EM, Zhang PX, Satoh A, Caputo C, Medzhitov R, Shenoy A, Egan ME, Krause DS. J Immunol. 2011 Jun 15; 2011 May 18. PMID: 21593379.
- Inflammasome-mediated suppression of inflammation-induced colorectal cancer progression is mediated by direct regulation of epithelial cell proliferation.Hu B, Elinav E, Flavell RA. Cell Cycle. 2011 Jun 15; 2011 Jun 15. PMID: 21555913.
- BiP and multiple DNAJ molecular chaperones in the endoplasmic reticulum are required for efficient simian virus 40 infection.Goodwin EC, Lipovsky A, Inoue T, Magaldi TG, Edwards AP, Van Goor KE, Paton AW, Paton JC, Atwood WJ, Tsai B, DiMaio D. mBio. 2011; 2011 Jun 14. PMID: 21673190.
- Mechanism of Mss116 ATPase reveals functional diversity of DEAD-Box proteins.Cao W, Coman MM, Ding S, Henn A, Middleton ER, Bradley MJ, Rhoades E, Hackney DD, Pyle AM, De La Cruz EM. J Mol Biol. 2011 Jun 10; 2011 Apr 9. PMID: 21501623.
- Recessive LAMC3 mutations cause malformations of occipital cortical development.Barak T, Kwan KY, Louvi A, Demirbilek V, Saygı S, Tüysüz B, Choi M, Boyacı H, Doerschner K, Zhu Y, Kaymakçalan H, Yılmaz S, Bakırcıoğlu M, Cağlayan AO, Oztürk AK, Yasuno K, Brunken WJ, Atalar E, Yalçınkaya C, Dinçer A, Bronen RA, Mane S, Ozçelik T, Lifton RP, Sestan N, Bilgüvar K, Günel M. Nat Genet. 2011 Jun; 2011 May 15. PMID: 21572413.
- NFBD1/MDC1 regulates Cav1 and Cav2 independently of DNA damage and p53.Wilson KA, Colavito SA, Schulz V, Wakefield PH, Sessa W, Tuck D, Stern DF. Mol Cancer Res. 2011 Jun; 2011 May 6. PMID: 21551225.
- CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.Abyzov A, Urban AE, Snyder M, Gerstein M. Genome Res. 2011 Jun; 2011 Feb 7. PMID: 21324876.
- An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine.Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J. Nucleic Acids Res. 2011 Jun; 2011 Feb 14. PMID: 21321019.
- Regulation of the antimicrobial response by NLR proteins.Elinav E, Strowig T, Henao-Mejia J, Flavell RA. Immunity. 2011 May 27. PMID: 21616436.
- NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis.Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, Flavell RA. Cell. 2011 May 27; 2011 May 12. PMID: 21565393.
- CD4+ T cells support cytotoxic T lymphocyte priming by controlling lymph node input.Kumamoto Y, Mattei LM, Sellers S, Payne GW, Iwasaki A. Proc Natl Acad Sci U S A. 2011 May 24; 2011 May 9. PMID: 21555577.
- In vivo laser axotomy in C. elegans.Byrne AB, Edwards TJ, Hammarlund M. J Vis Exp. 2011 May 19; 2011 May 19. PMID: 21633331.
- Human eIF4AIII interacts with an eIF4G-like partner, NOM1, revealing an evolutionarily conserved function outside the exon junction complex.Alexandrov A, Colognori D, Steitz JA. Genes Dev. 2011 May 15. PMID: 21576267.
- RIG-like helicase innate immunity inhibits vascular endothelial growth factor tissue responses via a type I IFN-dependent mechanism.Ma B, Dela Cruz CS, Hartl D, Kang MJ, Takyar S, Homer RJ, Lee CG, Elias JA. Am J Respir Crit Care Med. 2011 May 15; 2011 Jan 28. PMID: 21278304.
- Nogo-B receptor is necessary for cellular dolichol biosynthesis and protein N-glycosylation.Harrison KD, Park EJ, Gao N, Kuo A, Rush JS, Waechter CJ, Lehrman MA, Sessa WC. EMBO J. 2011 May 13; 2011 May 13. PMID: 21572394.
- Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches.Smith KD, Shanahan CA, Moore EL, Simon AC, Strobel SA. Proc Natl Acad Sci U S A. 2011 May 10; 2011 Apr 25. PMID: 21518891.
- Memory/effector (CD45RB(lo)) CD4 T cells are controlled directly by IL-10 and cause IL-22-dependent intestinal pathology.Kamanaka M, Huber S, Zenewicz LA, Gagliani N, Rathinam C, O'Connor W Jr, Wan YY, Nakae S, Iwakura Y, Hao L, Flavell RA. J Exp Med. 2011 May 9; 2011 Apr 25. PMID: 21518800.
- Identification of hammerhead ribozymes in all domains of life reveals novel structural variations.Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR. PLoS Comput Biol. 2011 May; 2011 May 5. PMID: 21573207.
- Social considerations in research: consider them but don't use them.Greenbaum D, Gerstein M. Am J Bioeth. 2011 May. PMID: 21534147.
- Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF, Deng XW, Wang H. Nat Cell Biol. 2011 May; 2011 Apr 17. PMID: 21499259.
- The E3 ligase Itch is a negative regulator of the homeostasis and function of hematopoietic stem cells.Rathinam C, Matesic LE, Flavell RA. Nat Immunol. 2011 May; 2011 Apr 10. PMID: 21478879.
- In vivo diabetogenic action of CD4+ T lymphocytes requires Fas expression and is independent of IL-1 and IL-18.Wen L, Green EA, Stratmann T, Panosa A, Gomis R, Eynon EE, Flavell RA, Mezquita JA, Mora C. Eur J Immunol. 2011 May; 2011 Apr 13. PMID: 21469125.
- PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition.Liu L, Qi H, Wang J, Lin H. Development. 2011 May; 2011 Mar 29. PMID: 21447556.
- C. elegans meg-1 and meg-2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival.Kapelle WS, Reinke V. Genesis. 2011 May. PMID: 21305687.
- Can microRNAs control vascular smooth muscle phenotypic modulation and the response to injury?Albinsson S, Sessa WC. Physiol Genomics. 2011 May 1; 2010 Sep 14. PMID: 20841497.
- Smooth muscle miRNAs are critical for post-natal regulation of blood pressure and vascular function.Albinsson S, Skoura A, Yu J, DiLorenzo A, Fernández-Hernando C, Offermanns S, Miano JM, Sessa WC. PLoS One. 2011 Apr 22; 2011 Apr 22. PMID: 21526127.
- Th17 cells express interleukin-10 receptor and are controlled by Foxp3⁻ and Foxp3+ regulatory CD4+ T cells in an interleukin-10-dependent manner.Huber S, Gagliani N, Esplugues E, O'Connor W Jr, Huber FJ, Chaudhry A, Kamanaka M, Kobayashi Y, Booth CJ, Rudensky AY, Roncarolo MG, Battaglia M, Flavell RA. Immunity. 2011 Apr 22. PMID: 21511184.
- ACT: aggregation and correlation toolbox for analyses of genome tracks.Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M. Bioinformatics. 2011 Apr 15; 2011 Feb 23. PMID: 21349863.
- Reticulon 4B (Nogo-B) is a novel regulator of hepatic fibrosis.Zhang D, Utsumi T, Huang HC, Gao L, Sangwung P, Chung C, Shibao K, Okamoto K, Yamaguchi K, Groszmann RJ, Jozsef L, Hao Z, Sessa WC, Iwakiri Y. Hepatology. 2011 Apr. PMID: 21480333.
- Interactions of the c-di-GMP riboswitch with its second messenger ligand.Smith KD, Strobel SA. Biochem Soc Trans. 2011 Apr. PMID: 21428955.
- Genome-virome interactions: examining the role of common viral infections in complex disease.Foxman EF, Iwasaki A. Nat Rev Microbiol. 2011 Apr. PMID: 21407242.
- An expanded collection and refined consensus model of glmS ribozymes.McCown PJ, Roth A, Breaker RR. RNA. 2011 Apr; 2011 Mar 2. PMID: 21367971.
- Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.Vaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman S. J Child Psychol Psychiatry. 2011 Apr; 2011 Jan 4. PMID: 21204834.
- Renalase deficiency aggravates ischemic myocardial damage.Wu Y, Xu J, Velazquez H, Wang P, Li G, Liu D, Sampaio-Maia B, Quelhas-Santos J, Russell K, Russell R, Flavell RA, Pestana M, Giordano F, Desir GV. Kidney Int. 2011 Apr; 2010 Dec 22. PMID: 21178975.
- Microbiota regulates immune defense against respiratory tract influenza A virus infection.Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, Iwasaki A. Proc Natl Acad Sci U S A. 2011 Mar 29; 2011 Mar 14. PMID: 21402903.
- Structural basis of cooperative ligand binding by the glycine riboswitch.Butler EB, Xiong Y, Wang J, Strobel SA. Chem Biol. 2011 Mar 25. PMID: 21439473.
- MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline.Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakano T, Nakatsuji N, Lin H, Sasaki H. Dev Cell. 2011 Mar 15. PMID: 21397847.
- Eph-B4 prevents venous adaptive remodeling in the adult arterial environment.Muto A, Yi T, Harrison KD, Dávalos A, Fancher TT, Ziegler KR, Feigel A, Kondo Y, Nishibe T, Sessa WC, Dardik A. J Exp Med. 2011 Mar 14; 2011 Feb 21. PMID: 21339325.
- Assembling a protein-protein interaction map of the SSU processome from existing datasets.Lim YH, Charette JM, Baserga SJ. PLoS One. 2011 Mar 10; 2011 Mar 10. PMID: 21423703.
- Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells.Peng S, Chen LL, Lei XX, Yang L, Lin H, Carmichael GG, Huang Y. Stem Cells. 2011 Mar. PMID: 21425412.
- Recent advances in IL-22 biology.Zenewicz LA, Flavell RA. Int Immunol. 2011 Mar. PMID: 21393631.
- Extrinsic and intrinsic control of germ cell proliferation in Caenorhabditis elegans.Waters KA, Reinke V. Mol Reprod Dev. 2011 Mar; 2011 Feb 17. PMID: 21337453.
- The kinase VRK1 is required for normal meiotic progression in mammalian oogenesis.Schober CS, Aydiner F, Booth CJ, Seli E, Reinke V. Mech Dev. 2011 Mar-Apr; 2011 Jan 26. PMID: 21277975.
- miRNA regulation of Sdf1 chemokine signaling provides genetic robustness to germ cell migration.Staton AA, Knaut H, Giraldez AJ. Nat Genet. 2011 Mar; 2011 Jan 23. PMID: 21258340.
- AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.Abyzov A, Gerstein M. Bioinformatics. 2011 Mar 1; 2011 Jan 13. PMID: 21233167.
- Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering.Marlatt SA, Kong Y, Cammett TJ, Korbel G, Noonan JP, Dimaio D. Protein Eng Des Sel. 2011 Mar; 2010 Dec 10. PMID: 21149273.
- Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/tRNAHis pair.Yuan J, Gogakos T, Babina AM, Söll D, Randau L. Nucleic Acids Res. 2011 Mar; 2010 Nov 17. PMID: 21087993.
- Noncoding RNPs of viral origin.Steitz J, Borah S, Cazalla D, Fok V, Lytle R, Mitton-Fry R, Riley K, Samji T. Cold Spring Harb Perspect Biol. 2011 Mar 1; 2011 Mar 1. PMID: 20719877.
- Tiling array data analysis: a multiscale approach using wavelets.Karpikov A, Rozowsky J, Gerstein M. BMC Bioinformatics. 2011 Feb 21; 2011 Feb 21. PMID: 21338513.
- Endothelial reticulon-4B (Nogo-B) regulates ICAM-1-mediated leukocyte transmigration and acute inflammation.Di Lorenzo A, Manes TD, Davalos A, Wright PL, Sessa WC. Blood. 2011 Feb 17; 2010 Dec 23. PMID: 21183689.
- TBR1 directly represses Fezf2 to control the laminar origin and development of the corticospinal tract.Han W, Kwan KY, Shim S, Lam MM, Shin Y, Xu X, Zhu Y, Li M, Sestan N. Proc Natl Acad Sci U S A. 2011 Feb 15; 2011 Feb 1. PMID: 21285371.
- Human thrombopoietin knockin mice efficiently support human hematopoiesis in vivo.Rongvaux A, Willinger T, Takizawa H, Rathinam C, Auerbach W, Murphy AJ, Valenzuela DM, Yancopoulos GD, Eynon EE, Stevens S, Manz MG, Flavell RA. Proc Natl Acad Sci U S A. 2011 Feb 8; 2011 Jan 24. PMID: 21262827.
- Human IL-3/GM-CSF knock-in mice support human alveolar macrophage development and human immune responses in the lung.Willinger T, Rongvaux A, Takizawa H, Yancopoulos GD, Valenzuela DM, Murphy AJ, Auerbach W, Eynon EE, Stevens S, Manz MG, Flavell RA. Proc Natl Acad Sci U S A. 2011 Feb 8; 2011 Jan 24. PMID: 21262803.
- The Yb body, a major site for Piwi-associated RNA biogenesis and a gateway for Piwi expression and transport to the nucleus in somatic cells.Qi H, Watanabe T, Ku HY, Liu N, Zhong M, Lin H. J Biol Chem. 2011 Feb 4; 2010 Nov 24. PMID: 21106531.
- Convection-enhanced delivery of camptothecin-loaded polymer nanoparticles for treatment of intracranial tumors.Sawyer AJ, Saucier-Sawyer JK, Booth CJ, Liu J, Patel T, Piepmeier JM, Saltzman WM. Drug Deliv Transl Res. 2011 Feb 1. PMID: 21691426.
- MicroRNAs and senescence.Martinez I, Almstead LL, DiMaio D. Aging (Albany NY). 2011 Feb. PMID: 21304181.
- Drosophila Piwi functions in Hsp90-mediated suppression of phenotypic variation.Gangaraju VK, Yin H, Weiner MM, Wang J, Huang XA, Lin H. Nat Genet. 2011 Feb; 2010 Dec 26. PMID: 21186352.
- Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177971.
- Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177963.
- Insights into base selectivity from the 1.8 Å resolution structure of an RB69 DNA polymerase ternary complex.Wang M, Xia S, Blaha G, Steitz TA, Konigsberg WH, Wang J. Biochemistry. 2011 Feb 1; 2010 Dec 30. PMID: 21158418.
- Hepatitis C virus NS2 coordinates virus particle assembly through physical interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes.Stapleford KA, Lindenbach BD. J Virol. 2011 Feb; 2010 Dec 8. PMID: 21147927.
- The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly.Phan T, Kohlway A, Dimberu P, Pyle AM, Lindenbach BD. J Virol. 2011 Feb; 2010 Nov 3. PMID: 21047963.
- C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JM, Söll D, Nureki O. Nucleic Acids Res. 2011 Feb; 2010 Sep 24. PMID: 20870747.
- Polymer nanoparticles containing tumor lysates as antigen delivery vehicles for dendritic cell-based antitumor immunotherapy.Prasad S, Cody V, Saucier-Sawyer JK, Saltzman WM, Sasaki CT, Edelson RL, Birchall MA, Hanlon DJ. Nanomedicine. 2011 Feb; 2010 Aug 6. PMID: 20692374.
- Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation.Englert M, Sheppard K, Aslanian A, Yates JR 3rd, Söll D. Proc Natl Acad Sci U S A. 2011 Jan 25; 2011 Jan 5. PMID: 21209330.
- Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia.Bajaj R, Xu F, Xiang B, Wilcox K, Diadamo AJ, Kumar R, Pietraszkiewicz A, Halene S, Li P. Mol Cytogenet. 2011 Jan 20; 2011 Jan 20. PMID: 21251322.
- Understanding how hepatitis C virus builds its unctuous home.Lindenbach BD. Cell Host Microbe. 2011 Jan 20. PMID: 21238940.
- MicroRNAs sculpt gene expression in embryonic development: new insights from plants.Bazzini AA, Giraldez AJ. Dev Cell. 2011 Jan 18. PMID: 21238918.
- RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. Bioinformatics. 2011 Jan 15; 2010 Dec 5. PMID: 21134889.
- miR-29 and miR-30 regulate B-Myb expression during cellular senescence.Martinez I, Cazalla D, Almstead LL, Steitz JA, DiMaio D. Proc Natl Acad Sci U S A. 2011 Jan 11; 2010 Dec 27. PMID: 21187425.
- Measuring the evolutionary rewiring of biological networks.Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. PLoS Comput Biol. 2011 Jan 6; 2011 Jan 6. PMID: 21253555.
- R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.Weinberg Z, Breaker RR. BMC Bioinformatics. 2011 Jan 4; 2011 Jan 4. PMID: 21205310.
- Recruited inflammatory monocytes stimulate antiviral Th1 immunity in infected tissue.Iijima N, Mattei LM, Iwasaki A. Proc Natl Acad Sci U S A. 2011 Jan 4; 2010 Dec 20. PMID: 21173243.
- IL-10 signaling in CD4+ T cells is critical for the pathogenesis of collagen-induced arthritis.Tao J, Kamanaka M, Hao J, Hao Z, Jiang X, Craft JE, Flavell RA, Wu Z, Hong Z, Zhao L, Yin Z. Arthritis Res Ther. 2011; 2011 Dec 22. PMID: 22192790.
- Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms.Juliano C, Wang J, Lin H. Annu Rev Genet. 2011; 2011 Sep 19. PMID: 21942366.
- The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.Yan KK, Gerstein M. PLoS One. 2011; 2011 May 16. PMID: 21603617.
- A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M. Genome Biol. 2011; 2011 Feb 16. PMID: 21324173.
- The small subunit processome in ribosome biogenesis—progress and prospects.Phipps KR, Charette J, Baserga SJ. Wiley Interdiscip Rev RNA. 2011 Jan-Feb. PMID: 21318072.
- Challenges of ligand identification for riboswitch candidates.Meyer MM, Hammond MC, Salinas Y, Roth A, Sudarsan N, Breaker RR. RNA Biol. 2011 Jan-Feb; 2011 Jan 1. PMID: 21317561.
- Bacterial aptamers that selectively bind glutamine.Ames TD, Breaker RR. RNA Biol. 2011 Jan-Feb; 2011 Jan 1. PMID: 21282981.
- Gene inactivation and its implications for annotation in the era of personal genomics.Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Genes Dev. 2011 Jan 1. PMID: 21205862.
- Association of OLE RNA with bacterial membranes via an RNA-protein interaction.Block KF, Puerta-Fernandez E, Wallace JG, Breaker RR. Mol Microbiol. 2011 Jan; 2010 Nov 16. PMID: 21166891.
- Inflammasomes as mediators of immunity against influenza virus.Pang IK, Iwasaki A. Trends Immunol. 2011 Jan; 2010 Dec 14. PMID: 21147034.
- Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch.Erion TV, Strobel SA. RNA. 2011 Jan; 2010 Nov 23. PMID: 21098652.
- Nanoparticles deliver triplex-forming PNAs for site-specific genomic recombination in CD34+ human hematopoietic progenitors.McNeer NA, Chin JY, Schleifman EB, Fields RJ, Glazer PM, Saltzman WM. Mol Ther. 2011 Jan; 2010 Sep 21. PMID: 20859257.
2010
- T cell LFA-1 engagement induces HuR-dependent cytokine mRNA stabilization through a Vav-1, Rac1/2, p38MAPK and MKK3 signaling cascade.Ramgolam VS, DeGregorio SD, Rao GK, Collinge M, Subaran SS, Markovic-Plese S, Pardi R, Bender JR. PLoS One. 2010 Dec 29; 2010 Dec 29. PMID: 21206905.
- Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Science. 2010 Dec 24; 2010 Dec 22. PMID: 21177976.
- Inflammation-induced tumorigenesis in the colon is regulated by caspase-1 and NLRC4.Hu B, Elinav E, Huber S, Booth CJ, Strowig T, Jin C, Eisenbarth SC, Flavell RA. Proc Natl Acad Sci U S A. 2010 Dec 14; 2010 Nov 30. PMID: 21118981.
- High-efficiency siRNA-based gene knockdown in human embryonic stem cells.Ma Y, Jin J, Dong C, Cheng EC, Lin H, Huang Y, Qiu C. RNA. 2010 Dec; 2010 Oct 26. PMID: 20978109.
- Identification and regulation of reticulon 4B (Nogo-B) in renal tubular epithelial cells.Marin EP, Moeckel G, Al-Lamki R, Bradley J, Yan Q, Wang T, Wright PL, Yu J, Sessa WC. Am J Pathol. 2010 Dec; 2010 Oct 22. PMID: 20971739.
- Volatile organic compound production by organisms in the genus Ascocoryne and a re-evaluation of myco-diesel production by NRRL 50072.Griffin MA, Spakowicz DJ, Gianoulis TA, Strobel SA. Microbiology (Reading). 2010 Dec; 2010 Aug 12. PMID: 20705658.
- Dissecting the role of conserved box C/D sRNA sequences in di-sRNP assembly and function.Bleichert F, Baserga SJ. Nucleic Acids Res. 2010 Dec; 2010 Aug 6. PMID: 20693534.
- Poly(A) tail recognition by a viral RNA element through assembly of a triple helix.Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA. Science. 2010 Nov 26. PMID: 21109672.
- Epithelial reticulon 4B (Nogo-B) is an endogenous regulator of Th2-driven lung inflammation.Wright PL, Yu J, Di YP, Homer RJ, Chupp G, Elias JA, Cohn L, Sessa WC. J Exp Med. 2010 Nov 22; 2010 Oct 25. PMID: 20975041.
- How the CCA-adding enzyme selects adenine over cytosine at position 76 of tRNA.Pan B, Xiong Y, Steitz TA. Science. 2010 Nov 12. PMID: 21071662.
- Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators.Bhardwaj N, Kim PM, Gerstein MB. Sci Signal. 2010 Nov 2; 2010 Nov 2. PMID: 21045205.
- The DEAD-box RNA helicase-like Utp25 is an SSU processome component.Charette JM, Baserga SJ. RNA. 2010 Nov; 2010 Sep 30. PMID: 20884785.
- Role of evolved host breadth in the initial emergence of an RNA virus.Turner PE, Morales NM, Alto BW, Remold SK. Evolution. 2010 Nov. PMID: 20633045.
- Segmental duplications in the human genome reveal details of pseudogene formation.Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB. Nucleic Acids Res. 2010 Nov; 2010 Jul 8. PMID: 20615899.
- A mouse model for the human pathogen Salmonella typhi.Song J, Willinger T, Rongvaux A, Eynon EE, Stevens S, Manz MG, Flavell RA, Galán JE. Cell Host Microbe. 2010 Oct 21. PMID: 20951970.
- Myeloid leukemia development in c-Cbl RING finger mutant mice is dependent on FLT3 signaling.Rathinam C, Thien CB, Flavell RA, Langdon WY. Cancer Cell. 2010 Oct 19. PMID: 20951944.
- Revisiting the structures of several antibiotics bound to the bacterial ribosome.Bulkley D, Innis CA, Blaha G, Steitz TA. Proc Natl Acad Sci U S A. 2010 Oct 5; 2010 Sep 27. PMID: 20876130.
- The tumor microenvironment and DNA repair.Klein TJ, Glazer PM. Semin Radiat Oncol. 2010 Oct. PMID: 20832021.
- Antiviral immune responses in the genital tract: clues for vaccines.Iwasaki A. Nat Rev Immunol. 2010 Oct; 2010 Sep 10. PMID: 20829886.
- The transcription cofactor Hopx is required for regulatory T cell function in dendritic cell-mediated peripheral T cell unresponsiveness.Hawiger D, Wan YY, Eynon EE, Flavell RA. Nat Immunol. 2010 Oct; 2010 Aug 29. PMID: 20802482.
- Survival of hepatitis C virus in syringes: implication for transmission among injection drug users.Paintsil E, He H, Peters C, Lindenbach BD, Heimer R. J Infect Dis. 2010 Oct 1. PMID: 20726768.
- A Drosophila chromatin factor interacts with the Piwi-interacting RNA mechanism in niche cells to regulate germline stem cell self-renewal.Smulders-Srinivasan TK, Szakmary A, Lin H. Genetics. 2010 Oct; 2010 Jul 20. PMID: 20647505.
- Quantitative proteomics of caveolin-1-regulated proteins: characterization of polymerase i and transcript release factor/CAVIN-1 IN endothelial cells.Dávalos A, Fernández-Hernando C, Sowa G, Derakhshan B, Lin MI, Lee JY, Zhao H, Luo R, Colangelo C, Sessa WC. Mol Cell Proteomics. 2010 Oct; 2010 Jun 28. PMID: 20585024.
- Ribonucleoprotein multimers and their functions.Bleichert F, Baserga SJ. Crit Rev Biochem Mol Biol. 2010 Oct. PMID: 20572804.
- Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron.Zingler N, Solem A, Pyle AM. Nucleic Acids Res. 2010 Oct; 2010 Jun 16. PMID: 20554854.
- Geographic differences in sexual reassortment in RNA phage.O'Keefe KJ, Silander OK, McCreery H, Weinreich DM, Wright KM, Chao L, Edwards SV, Remold SK, Turner PE. Evolution. 2010 Oct; 2010 Aug 19. PMID: 20500219.
- Branchiostoma floridae has separate healing and sealing enzymes for 5'-phosphate RNA ligation.Englert M, Sheppard K, Gundllapalli S, Beier H, Söll D. Proc Natl Acad Sci U S A. 2010 Sep 28; 2010 Sep 13. PMID: 20837552.
- Bifurcation of Toll-like receptor 9 signaling by adaptor protein 3.Sasai M, Linehan MM, Iwasaki A. Science. 2010 Sep 17. PMID: 20847273.
- Serum response factor is an essential transcription factor in megakaryocytic maturation.Halene S, Gao Y, Hahn K, Massaro S, Italiano JE Jr, Schulz V, Lin S, Kupfer GM, Krause DS. Blood. 2010 Sep 16; 2010 Jun 4. PMID: 20525922.
- The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution.Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C. PLoS Pathog. 2010 Sep 9; 2010 Sep 9. PMID: 20838601.
- Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations.Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, Choi M, Tatli B, Yalnizoğlu D, Tüysüz B, Cağlayan AO, Gökben S, Kaymakçalan H, Barak T, Bakircioğlu M, Yasuno K, Ho W, Sanders S, Zhu Y, Yilmaz S, Dinçer A, Johnson MH, Bronen RA, Koçer N, Per H, Mane S, Pamir MN, Yalçinkaya C, Kumandaş S, Topçu M, Ozmen M, Sestan N, Lifton RP, State MW, Günel M. Nature. 2010 Sep 9; 2010 Aug 22. PMID: 20729831.
- Molecular mechanism of NLRP3 inflammasome activation.Jin C, Flavell RA. J Clin Immunol. 2010 Sep; 2010 Jun 30. PMID: 20589420.
- The archaeal transamidosome for RNA-dependent glutamine biosynthesis.Rampias T, Sheppard K, Söll D. Nucleic Acids Res. 2010 Sep; 2010 May 10. PMID: 20457752.
- MicroRNAs as genetic sculptors: fishing for clues.Takacs CM, Giraldez AJ. Semin Cell Dev Biol. 2010 Sep; 2010 Feb 10. PMID: 20152922.
- Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch .Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA. Biochemistry. 2010 Aug 31. PMID: 20690679.
- Checks and balances: IL-23 in the intestine.Huber S, Flavell RA. Immunity. 2010 Aug 27. PMID: 20732638.
- Structured digital tables on the Semantic Web: toward a structured digital literature.Cheung KH, Samwald M, Auerbach RK, Gerstein MB. Mol Syst Biol. 2010 Aug 24. PMID: 20739925.
- Structure and function of the polymerase core of TRAMP, a RNA surveillance complex.Hamill S, Wolin SL, Reinisch KM. Proc Natl Acad Sci U S A. 2010 Aug 24; 2010 Aug 9. PMID: 20696927.
- 3'-5' tRNAHis guanylyltransferase in bacteria.Heinemann IU, Randau L, Tomko RJ Jr, Söll D. FEBS Lett. 2010 Aug 20; 2010 Jul 23. PMID: 20650272.
- Genome-wide analysis of germ cell proliferation in C.elegans identifies VRK-1 as a key regulator of CEP-1/p53.Waters K, Yang AZ, Reinke V. Dev Biol. 2010 Aug 15; 2010 Jun 23. PMID: 20599896.
- An allosteric self-splicing ribozyme triggered by a bacterial second messenger.Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR. Science. 2010 Aug 13. PMID: 20705859.
- Sin1-mTORC2 suppresses rag and il7r gene expression through Akt2 in B cells.Lazorchak AS, Liu D, Facchinetti V, Di Lorenzo A, Sessa WC, Schatz DG, Su B. Mol Cell. 2010 Aug 13. PMID: 20705244.
- Double-stranded RNA-dependent ATPase DRH-3: insight into its role in RNAsilencing in Caenorhabditis elegans.Matranga C, Pyle AM. J Biol Chem. 2010 Aug 13; 2010 Jun 7. PMID: 20529861.
- Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes.Vasan N, Hutagalung A, Novick P, Reinisch KM. Proc Natl Acad Sci U S A. 2010 Aug 10; 2010 Jul 26. PMID: 20660722.
- VEGF blockade inhibits lymphocyte recruitment and ameliorates immune-mediated vascular remodeling.Zhang J, Silva T, Yarovinsky T, Manes TD, Tavakoli S, Nie L, Tellides G, Pober JS, Bender JR, Sadeghi MM. Circ Res. 2010 Aug 6; 2010 Jun 10. PMID: 20538685.
- Different roles of G protein subunits beta1 and beta2 in neutrophil function revealed by gene expression silencing in primary mouse neutrophils.Zhang Y, Tang W, Jones MC, Xu W, Halene S, Wu D. J Biol Chem. 2010 Aug 6; 2010 Jun 4. PMID: 20525682.
- A new way to lower blood pressure: pass the chili peppers please!Sessa WC. Cell Metab. 2010 Aug 4. PMID: 20674855.
- Hidden variability of floral homeotic B genes in Solanaceae provides a molecular basis for the evolution of novel functions.Geuten K, Irish V. Plant Cell. 2010 Aug; 2010 Aug 31. PMID: 20807882.
- Annotating non-coding regions of the genome.Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. Nat Rev Genet. 2010 Aug; 2010 Jul 13. PMID: 20628352.
- The polarization of immune cells in the tumour environment by TGFbeta.Flavell RA, Sanjabi S, Wrzesinski SH, Licona-Limón P. Nat Rev Immunol. 2010 Aug; 2010 Jul 9. PMID: 20616810.
- Endothelial-specific overexpression of caveolin-1 accelerates atherosclerosis in apolipoprotein E-deficient mice.Fernández-Hernando C, Yu J, Dávalos A, Prendergast J, Sessa WC. Am J Pathol. 2010 Aug; 2010 Jun 25. PMID: 20581061.
- Evidence for widespread gene control function by the ydaO riboswitch candidate.Block KF, Hammond MC, Breaker RR. J Bacteriol. 2010 Aug; 2010 May 28. PMID: 20511502.
- microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming.Giraldez AJ. Curr Opin Genet Dev. 2010 Aug; 2010 May 6. PMID: 20452200.
- The C-terminus of Utp4, mutated in childhood cirrhosis, is essential for ribosome biogenesis.Freed EF, Baserga SJ. Nucleic Acids Res. 2010 Aug; 2010 Apr 12. PMID: 20385600.
- A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate.Ames TD, Rodionov DA, Weinberg Z, Breaker RR. Chem Biol. 2010 Jul 30. PMID: 20659680.
- A bacterial ortholog of class II lysyl-tRNA synthetase activates lysine.Ambrogelly A, O'Donoghue P, Söll D, Moses S. FEBS Lett. 2010 Jul 16; 2010 May 24. PMID: 20580719.
- A tRNA-dependent cysteine biosynthesis enzyme recognizes the selenocysteine-specific tRNA in Escherichia coli.Yuan J, Hohn MJ, Sherrer RL, Palioura S, Su D, Söll D. FEBS Lett. 2010 Jul 2; 2010 May 21. PMID: 20493852.
- Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.Palioura S, Herkel J, Simonović M, Lohse AW, Söll D. Biol Chem. 2010 Jul. PMID: 20623998.
- Detection of bone marrow-derived lung epithelial cells.Kassmer SH, Krause DS. Exp Hematol. 2010 Jul; 2010 May 4. PMID: 20447442.
- Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB. Genome Res. 2010 Jul; 2010 Apr 29. PMID: 20430783.
- Are we studying what matters? Health priorities and NIH-funded biomedical engineering research.Rubin JB, Paltiel AD, Saltzman WM. Ann Biomed Eng. 2010 Jul; 2010 Mar 12. PMID: 20225125.
- Combining mathematics and empirical data to predict emergence of RNA viruses that differ in reservoir use.Ogbunugafor CB, Basu S, Morales NM, Turner PE. Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27. PMID: 20478887.
- A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity.Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. Science. 2010 Jun 25; 2010 May 6. PMID: 20448148.
- Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA.Cazalla D, Yario T, Steitz JA. Science. 2010 Jun 18. PMID: 20558719.
- Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M. BMC Genomics. 2010 Jun 17; 2010 Jun 17. PMID: 20565764.
- Using semantic web rules to reason on an ontology of pseudogenes.Holford ME, Khurana E, Cheung KH, Gerstein M. Bioinformatics. 2010 Jun 15. PMID: 20529940.
- From the structure and function of the ribosome to new antibiotics (Nobel Lecture).Steitz TA. Angew Chem Int Ed Engl. 2010 Jun 14. PMID: 20509130.
- SENP1-mediated GATA1 deSUMOylation is critical for definitive erythropoiesis.Yu L, Ji W, Zhang H, Renda MJ, He Y, Lin S, Cheng EC, Chen H, Krause DS, Min W. J Exp Med. 2010 Jun 7; 2010 May 10. PMID: 20457756.
- On the possible role of robustness in the evolution of infectious diseases.Ogbunugafor CB, Pease JB, Turner PE. Chaos. 2010 Jun. PMID: 20590337.
- The dual nature of T(H)17 cells: shifting the focus to function.O'Connor W Jr, Zenewicz LA, Flavell RA. Nat Immunol. 2010 Jun; 2010 May 18. PMID: 20485275.
- The tertiary structure of group II introns: implications for biological function and evolution.Pyle AM. Crit Rev Biochem Mol Biol. 2010 Jun. PMID: 20446804.
- MicroRNAs are necessary for vascular smooth muscle growth, differentiation, and function.Albinsson S, Suarez Y, Skoura A, Offermanns S, Miano JM, Sessa WC. Arterioscler Thromb Vasc Biol. 2010 Jun; 2010 Apr 8. PMID: 20378849.
- Cooperation between multiple microbial pattern recognition systems is important for host protection against the intracellular pathogen Legionella pneumophila.Archer KA, Ader F, Kobayashi KS, Flavell RA, Roy CR. Infect Immun. 2010 Jun; 2010 Mar 29. PMID: 20351139.
- Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development.Pan IL, McQuinn R, Giovannoni JJ, Irish VF. J Exp Bot. 2010 Jun; 2010 Mar 24. PMID: 20335407.
- Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB. PLoS Comput Biol. 2010 May 27; 2010 May 27. PMID: 20523742.
- A Yersinia effector protein promotes virulence by preventing inflammasome recognition of the type III secretion system.Brodsky IE, Palm NW, Sadanand S, Ryndak MB, Sutterwala FS, Flavell RA, Bliska JB, Medzhitov R. Cell Host Microbe. 2010 May 20. PMID: 20478539.
- Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18; 2010 May 3. PMID: 20439753.
- MOTIPS: automated motif analysis for predicting targets of modular protein domains.Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. BMC Bioinformatics. 2010 May 11; 2010 May 11. PMID: 20459839.
- Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects.Hiller DA, Zhong M, Singh V, Strobel SA. Biochemistry. 2010 May 11. PMID: 20359191.
- Semiautomated model building for RNA crystallography using a directed rotameric approach.Keating KS, Pyle AM. Proc Natl Acad Sci U S A. 2010 May 4; 2010 Apr 19. PMID: 20404211.
- c-Cbl deficiency leads to diminished lymphocyte development and functions in an age-dependent manner.Rathinam C, Flavell RA. Proc Natl Acad Sci U S A. 2010 May 4; 2010 Apr 19. PMID: 20404156.
- Catalytic importance of a protonated adenosine in the hairpin ribozyme active site.Suydam IT, Levandoski SD, Strobel SA. Biochemistry. 2010 May 4. PMID: 20373826.
- Influenza virus activates inflammasomes via its intracellular M2 ion channel.Ichinohe T, Pang IK, Iwasaki A. Nat Immunol. 2010 May; 2010 Apr 11. PMID: 20383149.
- Endothelin type A receptor (ETA) expression is regulated by HOXA10 in human endometrial stromal cells.Penna IA, Hongling Du, Kallen AN, Taylor HS. Reprod Sci. 2010 May. PMID: 20371740.
- Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.Riley KJ, Rabinowitz GS, Steitz JA. J Virol. 2010 May; 2010 Mar 10. PMID: 20219930.
- Caveolae, caveolins, and cavins: complex control of cellular signalling and inflammation.Chidlow JH Jr, Sessa WC. Cardiovasc Res. 2010 May 1; 2010 Mar 3. PMID: 20202978.
- Poly(lactide-co-glycolide) nanoparticle assembly for highly efficient delivery of potent therapeutic agents from medical devices.Lo CT, Van Tassel PR, Saltzman WM. Biomaterials. 2010 May; 2010 Feb 10. PMID: 20149428.
- Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.Bhardwaj N, Yan KK, Gerstein MB. Proc Natl Acad Sci U S A. 2010 Apr 13; 2010 Mar 29. PMID: 20351254.
- Variation in transcription factor binding among humans.Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. Science. 2010 Apr 9; 2010 Mar 18. PMID: 20299548.
- The NPH-II helicase displays efficient DNA x RNA helicase activity and a pronounced purine sequence bias.Taylor SD, Solem A, Kawaoka J, Pyle AM. J Biol Chem. 2010 Apr 9; 2010 Jan 28. PMID: 20110368.
- Protein-facilitated folding of group II intron ribozymes.Fedorova O, Solem A, Pyle AM. J Mol Biol. 2010 Apr 2; 2010 Feb 6. PMID: 20138894.
- An implantable vascularized protein gel construct that supports human fetal hepatoblast survival and infection by hepatitis C virus in mice.Harding MJ, Lepus CM, Gibson TF, Shepherd BR, Gerber SA, Graham M, Paturzo FX, Rahner C, Madri JA, Bothwell AL, Lindenbach BD, Pober JS. PLoS One. 2010 Apr 1; 2010 Apr 1. PMID: 20376322.
- Interchromosomal association and gene regulation in trans.Williams A, Spilianakis CG, Flavell RA. Trends Genet. 2010 Apr; 2010 Mar 16. PMID: 20236724.
- Plasticity of the RNA kink turn structural motif.Antonioli AH, Cochrane JC, Lipchock SV, Strobel SA. RNA. 2010 Apr; 2010 Feb 9. PMID: 20145044.
- Dual delivery of VEGF and MCP-1 to support endothelial cell transplantation for therapeutic vascularization.Jay SM, Shepherd BR, Andrejecsk JW, Kyriakides TR, Pober JS, Saltzman WM. Biomaterials. 2010 Apr; 2010 Jan 27. PMID: 20110124.
- Establishing a role for the GTPase Ypt1p at the late Golgi.Sclafani A, Chen S, Rivera-Molina F, Reinisch K, Novick P, Ferro-Novick S. Traffic. 2010 Apr; 2010 Jan 6. PMID: 20059749.
- Ligand-modified gene carriers increased uptake in target cells but reduced DNA release and transfection efficiency.Cu Y, LeMoëllic C, Caplan MJ, Saltzman WM. Nanomedicine. 2010 Apr; 2009 Oct 2. PMID: 19800989.
- Getting started in gene orthology and functional analysis.Fang G, Bhardwaj N, Robilotto R, Gerstein MB. PLoS Comput Biol. 2010 Mar 26; 2010 Mar 26. PMID: 20361041.
- Unraveling the genetics of autoimmunity.Zenewicz LA, Abraham C, Flavell RA, Cho JH. Cell. 2010 Mar 19. PMID: 20303870.
- The behavioral and biochemical effects of BDNF containing polymers implanted in the hippocampus of rats.Sirianni RW, Olausson P, Chiu AS, Taylor JR, Saltzman WM. Brain Res. 2010 Mar 19; 2010 Jan 21. PMID: 20096671.
- Parameter estimation methodology in a model of hydrophobic drug release from a polymer coating.Sirianni RW, Jang EH, Miller KM, Saltzman WM. J Control Release. 2010 Mar 19; 2009 Dec 1. PMID: 19958804.
- Tissue-engineered vascular grafts transform into mature blood vessels via an inflammation-mediated process of vascular remodeling.Roh JD, Sawh-Martinez R, Brennan MP, Jay SM, Devine L, Rao DA, Yi T, Mirensky TL, Nalbandian A, Udelsman B, Hibino N, Shinoka T, Saltzman WM, Snyder E, Kyriakides TR, Pober JS, Breuer CK. Proc Natl Acad Sci U S A. 2010 Mar 9; 2010 Mar 5. PMID: 20207947.
- Severe oxidative stress induces protein mistranslation through impairment of an aminoacyl-tRNA synthetase editing site.Ling J, Söll D. Proc Natl Acad Sci U S A. 2010 Mar 2; 2010 Feb 16. PMID: 20160114.
- The flowering of Arabidopsis flower development.Irish VF. Plant J. 2010 Mar. PMID: 20409275.
- The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling.Mara CD, Huang T, Irish VF. Plant Cell. 2010 Mar; 2010 Mar 19. PMID: 20305124.
- When ribosomes go bad: diseases of ribosome biogenesis.Freed EF, Bleichert F, Dutca LM, Baserga SJ. Mol Biosyst. 2010 Mar; 2010 Jan 11. PMID: 20174677.
- The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.Stanley RE, Blaha G, Grodzicki RL, Strickler MD, Steitz TA. Nat Struct Mol Biol. 2010 Mar; 2010 Feb 14. PMID: 20154709.
- The 2'-OH group at the group II intron terminus acts as a proton shuttle.Roitzsch M, Fedorova O, Pyle AM. Nat Chem Biol. 2010 Mar; 2010 Jan 31. PMID: 20118939.
- Adenosine inhibits chemotaxis and induces hepatocyte-specific genes in bone marrow mesenchymal stem cells.Mohamadnejad M, Sohail MA, Watanabe A, Krause DS, Swenson ES, Mehal WZ. Hepatology. 2010 Mar. PMID: 20044808.
- Overcoming the hurdles in using mouse genetic models that block TGF-beta signaling.Sanjabi S, Flavell RA. J Immunol Methods. 2010 Feb 28; 2010 Jan 11. PMID: 20060833.
- In vivo requirement for Atg5 in antigen presentation by dendritic cells.Lee HK, Mattei LM, Steinberg BE, Alberts P, Lee YH, Chervonsky A, Mizushima N, Grinstein S, Iwasaki A. Immunity. 2010 Feb 26; 2010 Feb 18. PMID: 20171125.
- Construction and genetic selection of small transmembrane proteins that activate the human erythropoietin receptor.Cammett TJ, Jun SJ, Cohen EB, Barrera FN, Engelman DM, Dimaio D. Proc Natl Acad Sci U S A. 2010 Feb 23; 2010 Feb 8. PMID: 20142506.
- Close association of RNA polymerase II and many transcription factors with Pol III genes.Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. Proc Natl Acad Sci U S A. 2010 Feb 23; 2010 Feb 5. PMID: 20139302.
- Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. PLoS Genet. 2010 Feb 19; 2010 Feb 19. PMID: 20174564.
- Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs.Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. Sci Signal. 2010 Feb 16; 2010 Feb 16. PMID: 20159853.
- Inhibition of poly(ADP-ribose) polymerase down-regulates BRCA1 and RAD51 in a pathway mediated by E2F4 and p130.Hegan DC, Lu Y, Stachelek GC, Crosby ME, Bindra RS, Glazer PM. Proc Natl Acad Sci U S A. 2010 Feb 2; 2010 Jan 19. PMID: 20133863.
- The role of NOD-like Receptors in shaping adaptive immunity.Williams A, Flavell RA, Eisenbarth SC. Curr Opin Immunol. 2010 Feb; 2010 Feb 9. PMID: 20149616.
- C/EBPepsilon directs granulocytic-vs-monocytic lineage determination and confers chemotactic function via Hlx.Halene S, Gaines P, Sun H, Zibello T, Lin S, Khanna-Gupta A, Williams SC, Perkins A, Krause D, Berliner N. Exp Hematol. 2010 Feb; 2009 Dec 5. PMID: 19925846.
- Partial correction of cystic fibrosis defects with PLGA nanoparticles encapsulating curcumin.Cartiera MS, Ferreira EC, Caputo C, Egan ME, Caplan MJ, Saltzman WM. Mol Pharm. 2010 Feb 1. PMID: 19886674.
- RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes.Abyzov A, Bjornson R, Felipe M, Gerstein M. Proteins. 2010 Feb 1. PMID: 19705487.
- Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.Yip KY, Alexander RP, Yan KK, Gerstein M. PLoS One. 2010 Jan 26; 2010 Jan 26. PMID: 20126643.
- Regulating human Th17 cells via differential expression of IL-1 receptor.Lee WW, Kang SW, Choi J, Lee SH, Shah K, Eynon EE, Flavell RA, Kang I. Blood. 2010 Jan 21; 2009 Nov 12. PMID: 19965648.
- Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems.Yuan J, O'Donoghue P, Ambrogelly A, Gundllapalli S, Sherrer RL, Palioura S, Simonović M, Söll D. FEBS Lett. 2010 Jan 21. PMID: 19903474.
- Transfer RNA processing in archaea: unusual pathways and enzymes.Heinemann IU, Söll D, Randau L. FEBS Lett. 2010 Jan 21. PMID: 19878676.
- Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.Bhardwaj N, Gerstein M, Lu H. BMC Bioinformatics. 2010 Jan 18; 2010 Jan 18. PMID: 20122235.
- RNA switches out in the cold.Breaker RR. Mol Cell. 2010 Jan 15. PMID: 20129048.
- Regulation of adaptive immunity by the innate immune system.Iwasaki A, Medzhitov R. Science. 2010 Jan 15. PMID: 20075244.
- FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. Genome Biol. 2010; 2010 Oct 21. PMID: 20964841.
- Emergence of rationally designed therapeutic strategies for breast cancer targeting DNA repair mechanisms.Rowe BP, Glazer PM. Breast Cancer Res. 2010; 2010 Apr 30. PMID: 20459590.
- Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR. Genome Biol. 2010; 2010 Mar 15. PMID: 20230605.
- Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Genome Biol. 2010; 2010 Mar 8. PMID: 20210993.
- Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. Nat Biotechnol. 2010 Jan; 2009 Dec 27. PMID: 20037582.
- Potentiation of temozolomide cytotoxicity by inhibition of DNA polymerase beta is accentuated by BRCA2 mutation.Stachelek GC, Dalal S, Donigan KA, Campisi Hegan D, Sweasy JB, Glazer PM. Cancer Res. 2010 Jan 1; 2009 Dec 22. PMID: 20028873.
- Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function.Pawlicki JM, Steitz JA. Trends Cell Biol. 2010 Jan; 2009 Dec 11. PMID: 20004579.
- Tertiary architecture of the Oceanobacillus iheyensis group II intron.Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. RNA. 2010 Jan; 2009 Dec 1. PMID: 19952115.
- Cutting edge: TNF-induced microRNAs regulate TNF-induced expression of E-selectin and intercellular adhesion molecule-1 on human endothelial cells: feedback control of inflammation.Suárez Y, Wang C, Manes TD, Pober JS. J Immunol. 2010 Jan 1; 2009 Nov 30. PMID: 19949084.
- A structural analysis of the group II intron active site and implications for the spliceosome.Keating KS, Toor N, Perlman PS, Pyle AM. RNA. 2010 Jan; 2009 Nov 30. PMID: 19948765.
- A novel class of meso-tetrakis-porphyrin derivatives exhibits potent activities against hepatitis C virus genotype 1b replicons in vitro.Cheng Y, Tsou LK, Cai J, Aya T, Dutschman GE, Gullen EA, Grill SP, Chen AP, Lindenbach BD, Hamilton AD, Cheng YC. Antimicrob Agents Chemother. 2010 Jan; 2009 Nov 9. PMID: 19901090.
2009
- EBNA1 regulates cellular gene expression by binding cellular promoters.Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM. Proc Natl Acad Sci U S A. 2009 Dec 29; 2009 Dec 22. PMID: 20080792.
- RNA interference in Trypanosoma brucei: role of the n-terminal RGG domain and the polyribosome association of argonaute.Shi H, Chamond N, Djikeng A, Tschudi C, Ullu E. J Biol Chem. 2009 Dec 25; 2009 Oct 30. PMID: 19880512.
- The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution.Heinemann IU, O'Donoghue P, Madinger C, Benner J, Randau L, Noren CJ, Söll D. Proc Natl Acad Sci U S A. 2009 Dec 15; 2009 Nov 24. PMID: 19965368.
- Structural basis of ligand binding by a c-di-GMP riboswitch.Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Nat Struct Mol Biol. 2009 Dec; 2009 Nov 8. PMID: 19898477.
- Defective survival of naive CD8+ T lymphocytes in the absence of the beta3 regulatory subunit of voltage-gated calcium channels.Jha MK, Badou A, Meissner M, McRory JE, Freichel M, Flockerzi V, Flavell RA. Nat Immunol. 2009 Dec; 2009 Oct 18. PMID: 19838200.
- Robust-linear-model normalization to reduce technical variability in functional protein microarrays.Sboner A, Karpikov A, Chen G, Smith M, Mattoon D, Freeman-Cook L, Schweitzer B, Gerstein MB. J Proteome Res. 2009 Dec. PMID: 19817483.
- The structural changes of T7 RNA polymerase from transcription initiation to elongation.Steitz TA. Curr Opin Struct Biol. 2009 Dec; 2009 Oct 5. PMID: 19811903.
- Absence of Akt1 reduces vascular smooth muscle cell migration and survival and induces features of plaque vulnerability and cardiac dysfunction during atherosclerosis.Fernández-Hernando C, József L, Jenkins D, Di Lorenzo A, Sessa WC. Arterioscler Thromb Vasc Biol. 2009 Dec; 2009 Sep 17. PMID: 19762778.
- Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.Gürel G, Blaha G, Steitz TA, Moore PB. Antimicrob Agents Chemother. 2009 Dec; 2009 Sep 8. PMID: 19738021.
- Computational analysis of membrane proteins: the largest class of drug targets.Arinaminpathy Y, Khurana E, Engelman DM, Gerstein MB. Drug Discov Today. 2009 Dec; 2009 Sep 3. PMID: 19733256.
- PEGylated PLGA nanoparticles for the improved delivery of doxorubicin.Park J, Fong PM, Lu J, Russell KS, Booth CJ, Saltzman WM, Fahmy TM. Nanomedicine. 2009 Dec; 2009 Mar 31. PMID: 19341815.
- Comorbidities and survival in a large cohort of patients with newly diagnosed myelodysplastic syndromes.Wang R, Gross CP, Halene S, Ma X. Leuk Res. 2009 Dec; 2009 Mar 25. PMID: 19324411.
- CD8(+) T lymphocyte mobilization to virus-infected tissue requires CD4(+) T-cell help.Nakanishi Y, Lu B, Gerard C, Iwasaki A. Nature. 2009 Nov 26; 2009 Nov 8. PMID: 19898495.
- Design and antimicrobial action of purine analogues that bind Guanine riboswitches.Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. ACS Chem Biol. 2009 Nov 20. PMID: 19739679.
- Bayesian Analysis of iTRAQ Data with Nonrandom Missingness: Identification of Differentially Expressed Proteins.Luo R, Colangelo CM, Sessa WC, Zhao H. Stat Biosci. 2009 Nov. PMID: 21927625.
- A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.Poiata E, Meyer MM, Ames TD, Breaker RR. RNA. 2009 Nov; 2009 Sep 23. PMID: 19776155.
- How to drive your helicase in a straight line.Pyle AM. Cell. 2009 Oct 30. PMID: 19879832.
- Endothelial and smooth muscle-derived neuropilin-like protein regulates platelet-derived growth factor signaling in human vascular smooth muscle cells by modulating receptor ubiquitination.Guo X, Nie L, Esmailzadeh L, Zhang J, Bender JR, Sadeghi MM. J Biol Chem. 2009 Oct 23; 2009 Aug 19. PMID: 19696027.
- Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.Patrick KL, Shi H, Kolev NG, Ersfeld K, Tschudi C, Ullu E. Proc Natl Acad Sci U S A. 2009 Oct 20; 2009 Oct 6. PMID: 19815526.
- Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. BMC Genomics. 2009 Oct 16; 2009 Oct 16. PMID: 19835609.
- Regulation of immature dendritic cell migration by RhoA guanine nucleotide exchange factor Arhgef5.Wang Z, Kumamoto Y, Wang P, Gan X, Lehmann D, Smrcka AV, Cohn L, Iwasaki A, Li L, Wu D. J Biol Chem. 2009 Oct 16; 2009 Aug 27. PMID: 19713215.
- Toll-like receptors 1 and 2 heterodimers alter Borrelia burgdorferi gene expression in mice and ticks.Fikrig E, Narasimhan S, Neelakanta G, Pal U, Chen M, Flavell R. J Infect Dis. 2009 Oct 15. PMID: 19754309.
- Reticulon 4B (Nogo-B) is necessary for macrophage infiltration and tissue repair.Yu J, Fernández-Hernando C, Suarez Y, Schleicher M, Hao Z, Wright PL, DiLorenzo A, Kyriakides TR, Sessa WC. Proc Natl Acad Sci U S A. 2009 Oct 13; 2009 Sep 25. PMID: 19805174.
- IL-10 signaling blockade controls murine West Nile virus infection.Bai F, Town T, Qian F, Wang P, Kamanaka M, Connolly TM, Gate D, Montgomery RR, Flavell RA, Fikrig E. PLoS Pathog. 2009 Oct; 2009 Oct 9. PMID: 19816558.
- miRNPs: versatile regulators of gene expression in vertebrate cells.Steitz JA, Vasudevan S. Biochem Soc Trans. 2009 Oct. PMID: 19754429.
- Thymic self-reactivity selects natural interleukin 17-producing T cells that can regulate peripheral inflammation.Marks BR, Nowyhed HN, Choi JY, Poholek AC, Odegard JM, Flavell RA, Craft J. Nat Immunol. 2009 Oct; 2009 Sep 6. PMID: 19734905.
- Poly(omega-pentadecalactone-co-butylene-co-succinate) nanoparticles as biodegradable carriers for camptothecin delivery.Liu J, Jiang Z, Zhang S, Saltzman WM. Biomaterials. 2009 Oct; 2009 Jul 25. PMID: 19632718.
- Dynamics of alpha-globin locus chromatin structure and gene expression during erythroid differentiation of human CD34(+) cells in culture.Mahajan MC, Karmakar S, Newburger PE, Krause DS, Weissman SM. Exp Hematol. 2009 Oct; 2009 Jul 14. PMID: 19607874.
- Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor.Talbert-Slagle K, Marlatt S, Barrera FN, Khurana E, Oates J, Gerstein M, Engelman DM, Dixon AM, Dimaio D. J Virol. 2009 Oct; 2009 Jul 15. PMID: 19605488.
- Simultaneous release of multiple molecules from poly(lactide-co-glycolide) nanoparticles assembled onto medical devices.Lo CT, Van Tassel PR, Saltzman WM. Biomaterials. 2009 Oct; 2009 Jul 9. PMID: 19592089.
- Neighborhood socioeconomic status influences the survival of elderly patients with myelodysplastic syndromes in the United States.Wang R, Gross CP, Halene S, Ma X. Cancer Causes Control. 2009 Oct; 2009 May 20. PMID: 19455395.
- E3 ubiquitin ligase GRAIL controls primary T cell activation and oral tolerance.Kriegel MA, Rathinam C, Flavell RA. Proc Natl Acad Sci U S A. 2009 Sep 29; 2009 Sep 17. PMID: 19805371.
- Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.Sharma H, Yu S, Kong J, Wang J, Steitz TA. Proc Natl Acad Sci U S A. 2009 Sep 29; 2009 Sep 16. PMID: 19805344.
- Membrane-initiated actions of estrogen on the endothelium.Kim KH, Bender JR. Mol Cell Endocrinol. 2009 Sep 24; 2009 Apr 9. PMID: 19549586.
- The relationship between the evolution of microRNA targets and the length of their UTRs.Cheng C, Bhardwaj N, Gerstein M. BMC Genomics. 2009 Sep 14; 2009 Sep 14. PMID: 19751524.
- A dimeric structure for archaeal box C/D small ribonucleoproteins.Bleichert F, Gagnon KT, Brown BA 2nd, Maxwell ES, Leschziner AE, Unger VM, Baserga SJ. Science. 2009 Sep 11. PMID: 19745151.
- Understanding the mysteries of iPS cells.Cohen JB, Krause DS. Yale J Biol Med. 2009 Sep. PMID: 19774121.
- Roles of Ca(v) channels and AHNAK1 in T cells: the beauty and the beast.Matza D, Flavell RA. Immunol Rev. 2009 Sep. PMID: 19754902.
- Nogo-B receptor stabilizes Niemann-Pick type C2 protein and regulates intracellular cholesterol trafficking.Harrison KD, Miao RQ, Fernandez-Hernándo C, Suárez Y, Dávalos A, Sessa WC. Cell Metab. 2009 Sep. PMID: 19723497.
- Mapping accessible chromatin regions using Sono-Seq.Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. Proc Natl Acad Sci U S A. 2009 Sep 1; 2009 Aug 18. PMID: 19706456.
- Hepatitis C virus NS2 protein contributes to virus particle assembly via opposing epistatic interactions with the E1-E2 glycoprotein and NS3-NS4A enzyme complexes.Phan T, Beran RK, Peters C, Lorenz IC, Lindenbach BD. J Virol. 2009 Sep; 2009 Jun 10. PMID: 19515772.
- Selective depletion of molecularly defined cortical interneurons in human holoprosencephaly with severe striatal hypoplasia.Fertuzinhos S, Krsnik Z, Kawasawa YI, Rasin MR, Kwan KY, Chen JG, Judas M, Hayashi M, Sestan N. Cereb Cortex. 2009 Sep; 2009 Feb 20. PMID: 19234067.
- Akt1 is critical for acute inflammation and histamine-mediated vascular leakage.Di Lorenzo A, Fernández-Hernando C, Cirino G, Sessa WC. Proc Natl Acad Sci U S A. 2009 Aug 25; 2009 Jul 21. PMID: 19622728.
- Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.Blaha G, Stanley RE, Steitz TA. Science. 2009 Aug 21. PMID: 19696344.
- Neocortical networks entrain neuronal circuits in cerebellar cortex.Ros H, Sachdev RN, Yu Y, Sestan N, McCormick DA. J Neurosci. 2009 Aug 19. PMID: 19692605.
- Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.Yip KY, Kim PM, McDermott D, Gerstein M. BMC Bioinformatics. 2009 Aug 5; 2009 Aug 5. PMID: 19656385.
- The Akt1-eNOS axis illustrates the specificity of kinase-substrate relationships in vivo.Schleicher M, Yu J, Murata T, Derakhshan B, Atochin D, Qian L, Kashiwagi S, Di Lorenzo A, Harrison KD, Huang PL, Sessa WC. Sci Signal. 2009 Aug 4; 2009 Aug 4. PMID: 19654415.
- Salmonella Typhimurium type III secretion effectors stimulate innate immune responses in cultured epithelial cells.Bruno VM, Hannemann S, Lara-Tejero M, Flavell RA, Kleinstein SH, Galán JE. PLoS Pathog. 2009 Aug; 2009 Aug 7. PMID: 19662166.
- Serial noninvasive targeted imaging of peripheral angiogenesis: validation and application of a semiautomated quantitative approach.Dobrucki LW, Dione DP, Kalinowski L, Dione D, Mendizabal M, Yu J, Papademetris X, Sessa WC, Sinusas AJ. J Nucl Med. 2009 Aug; 2009 Jul 17. PMID: 19617325.
- Anti-inflammatory and pro-inflammatory roles of TGF-beta, IL-10, and IL-22 in immunity and autoimmunity.Sanjabi S, Zenewicz LA, Kamanaka M, Flavell RA. Curr Opin Pharmacol. 2009 Aug; 2009 May 29. PMID: 19481975.
- Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests.Bascom-Slack CA, Ma C, Moore E, Babbs B, Fenn K, Greene JS, Hann BD, Keehner J, Kelley-Swift EG, Kembaiyan V, Lee SJ, Li P, Light DY, Lin EH, Schorn MA, Vekhter D, Boulanger LA, Hess WM, Vargas PN, Strobel GA, Strobel SA. Microb Ecol. 2009 Aug; 2009 Feb 28. PMID: 19252940.
- Understanding modularity in molecular networks requires dynamics.Alexander RP, Kim PM, Emonet T, Gerstein MB. Sci Signal. 2009 Jul 28; 2009 Jul 28. PMID: 19638611.
- An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.Sasidharan R, Agarwal A, Rozowsky J, Gerstein M. BMC Res Notes. 2009 Jul 24; 2009 Jul 24. PMID: 19630981.
- The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies.Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, Gerstein MB, Snyder M, Korenberg JR. Proc Natl Acad Sci U S A. 2009 Jul 21; 2009 Jul 13. PMID: 19597142.
- The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation.Palioura S, Sherrer RL, Steitz TA, Söll D, Simonovic M. Science. 2009 Jul 17. PMID: 19608919.
- Opposing effects of TGF-beta and IL-15 cytokines control the number of short-lived effector CD8+ T cells.Sanjabi S, Mosaheb MM, Flavell RA. Immunity. 2009 Jul 17. PMID: 19604492.
- Amino acid polymorphisms altering the glycosylation of IL-2 do not protect from type 1 diabetes in the NOD mouse.Kamanaka M, Rainbow D, Schuster-Gossler K, Eynon EE, Chervonsky AV, Wicker LS, Flavell RA. Proc Natl Acad Sci U S A. 2009 Jul 7; 2009 Jun 22. PMID: 19549859.
- Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. PLoS Comput Biol. 2009 Jul; 2009 Jul 10. PMID: 19593373.
- Genetic evidence supporting a critical role of endothelial caveolin-1 during the progression of atherosclerosis.Fernández-Hernando C, Yu J, Suárez Y, Rahner C, Dávalos A, Lasunción MA, Sessa WC. Cell Metab. 2009 Jul. PMID: 19583953.
- Autophagic control of RLR signaling.Tal MC, Iwasaki A. Autophagy. 2009 Jul. PMID: 19571662.
- A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics.Champion EA, Kundrat L, Regan L, Baserga SJ. Protein Eng Des Sel. 2009 Jul; 2009 Jun 10. PMID: 19515729.
- Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. BMC Genomics. 2009 Jun 16; 2009 Jun 16. PMID: 19531245.
- Requirement for AHNAK1-mediated calcium signaling during T lymphocyte cytolysis.Matza D, Badou A, Jha MK, Willinger T, Antov A, Sanjabi S, Kobayashi KS, Marchesi VT, Flavell RA. Proc Natl Acad Sci U S A. 2009 Jun 16; 2009 Jun 2. PMID: 19497879.
- Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei.Charrière F, O'Donoghue P, Helgadóttir S, Maréchal-Drouard L, Cristodero M, Horn EK, Söll D, Schneider A. J Biol Chem. 2009 Jun 12; 2009 Apr 22. PMID: 19386587.
- Kinetic analysis of the guanine nucleotide exchange activity of TRAPP, a multimeric Ypt1p exchange factor.Chin HF, Cai Y, Menon S, Ferro-Novick S, Reinisch KM, De La Cruz EM. J Mol Biol. 2009 Jun 5; 2009 Apr 8. PMID: 19361519.
- [Inflammasomes in viral infection].Ichinohe T, Iwasaki A. Uirusu. 2009 Jun. PMID: 19927984.
- Dynamic and complex transcription factor binding during an inducible response in yeast.Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. Genes Dev. 2009 Jun 1. PMID: 19487574.
- Relating protein conformational changes to packing efficiency and disorder.Bhardwaj N, Gerstein M. Protein Sci. 2009 Jun. PMID: 19472340.
- A protective function for interleukin 17A in T cell-mediated intestinal inflammation.O'Connor W Jr, Kamanaka M, Booth CJ, Town T, Nakae S, Iwakura Y, Kolls JK, Flavell RA. Nat Immunol. 2009 Jun. PMID: 19448631.
- Structural insights into RNA splicing.Toor N, Keating KS, Pyle AM. Curr Opin Struct Biol. 2009 Jun; 2009 May 13. PMID: 19443210.
- Intravaginal gene silencing using biodegradable polymer nanoparticles densely loaded with small-interfering RNA.Woodrow KA, Cu Y, Booth CJ, Saucier-Sawyer JK, Wood MJ, Saltzman WM. Nat Mater. 2009 Jun; 2009 May 3. PMID: 19404239.
- Targeted correction of a thalassemia-associated beta-globin mutation induced by pseudo-complementary peptide nucleic acids.Lonkar P, Kim KH, Kuan JY, Chin JY, Rogers FA, Knauert MP, Kole R, Nielsen PE, Glazer PM. Nucleic Acids Res. 2009 Jun; 2009 Apr 13. PMID: 19364810.
- Inflammasome-mediated regulation of hepatic stellate cells.Watanabe A, Sohail MA, Gomes DA, Hashmi A, Nagata J, Sutterwala FS, Mahmood S, Jhandier MN, Shi Y, Flavell RA, Mehal WZ. Am J Physiol Gastrointest Liver Physiol. 2009 Jun; 2009 Apr 9. PMID: 19359429.
- High-throughput cell-based screen for chemicals that inhibit infection by simian virus 40 and human polyomaviruses.Goodwin EC, Atwood WJ, DiMaio D. J Virol. 2009 Jun; 2009 Mar 18. PMID: 19297472.
- U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.Gürel G, Blaha G, Moore PB, Steitz TA. J Mol Biol. 2009 May 29; 2009 Apr 9. PMID: 19362093.
- Functional and evolutionary insights into human brain development through global transcriptome analysis.Johnson MB, Kawasawa YI, Mason CE, Krsnik Z, Coppola G, Bogdanović D, Geschwind DH, Mane SM, State MW, Sestan N. Neuron. 2009 May 28. PMID: 19477152.
- The structure of the ankyrin-binding site of beta-spectrin reveals how tandem spectrin-repeats generate unique ligand-binding properties.Stabach PR, Simonović I, Ranieri MA, Aboodi MS, Steitz TA, Simonović M, Morrow JS. Blood. 2009 May 28; 2009 Jan 23. PMID: 19168783.
- Inflammasome-activating nanoparticles as modular systems for optimizing vaccine efficacy.Demento SL, Eisenbarth SC, Foellmer HG, Platt C, Caplan MJ, Mark Saltzman W, Mellman I, Ledizet M, Fikrig E, Flavell RA, Fahmy TM. Vaccine. 2009 May 18; 2009 Apr 3. PMID: 19428913.
- Systematic identification of transcription factors associated with patient survival in cancers.Cheng C, Li LM, Alves P, Gerstein M. BMC Genomics. 2009 May 15; 2009 May 15. PMID: 19442316.
- Role of breast regression protein 39 (BRP-39)/chitinase 3-like-1 in Th2 and IL-13-induced tissue responses and apoptosis.Lee CG, Hartl D, Lee GR, Koller B, Matsuura H, Da Silva CA, Sohn MH, Cohn L, Homer RJ, Kozhich AA, Humbles A, Kearley J, Coyle A, Chupp G, Reed J, Flavell RA, Elias JA. J Exp Med. 2009 May 11; 2009 May 4. PMID: 19414556.
- Innate instruction of adaptive immunity revisited: the inflammasome.Eisenbarth SC, Flavell RA. EMBO Mol Med. 2009 May. PMID: 20049709.
- Hypoxic tumor microenvironment and cancer cell differentiation.Kim Y, Lin Q, Glazer PM, Yun Z. Curr Mol Med. 2009 May. PMID: 19519400.
- A cytidine deaminase edits C to U in transfer RNAs in Archaea.Randau L, Stanley BJ, Kohlway A, Mechta S, Xiong Y, Söll D. Science. 2009 May 1. PMID: 19407206.
- Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis.Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. Nat Struct Mol Biol. 2009 May; 2009 Apr 26. PMID: 19396172.
- A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs.Hammond MC, Wachter A, Breaker RR. Nat Struct Mol Biol. 2009 May; 2009 Apr 19. PMID: 19377483.
- DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans.Chi W, Reinke V. Mech Dev. 2009 May-Jun; 2009 Feb 6. PMID: 19368797.
- CD4 T-cell differentiation and inflammatory bowel disease.Zenewicz LA, Antov A, Flavell RA. Trends Mol Med. 2009 May; 2009 Apr 8. PMID: 19362058.
- The uptake and intracellular fate of PLGA nanoparticles in epithelial cells.Cartiera MS, Johnson KM, Rajendran V, Caplan MJ, Saltzman WM. Biomaterials. 2009 May; 2009 Feb 20. PMID: 19232712.
- Biodegradable meshes printed with extracellular matrix proteins support micropatterned hepatocyte cultures.Woodrow KA, Wood MJ, Saucier-Sawyer JK, Solbrig C, Saltzman WM. Tissue Eng Part A. 2009 May. PMID: 19072719.
- Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis.Wang J, Saxe JP, Tanaka T, Chuma S, Lin H. Curr Biol. 2009 Apr 28; 2009 Apr 2. PMID: 19345100.
- Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme.Cochrane JC, Lipchock SV, Smith KD, Strobel SA. Biochemistry. 2009 Apr 21. PMID: 19228039.
- Src-Induced cisplatin resistance mediated by cell-to-cell communication.Peterson-Roth E, Brdlik CM, Glazer PM. Cancer Res. 2009 Apr 15; 2009 Apr 7. PMID: 19351863.
- Acidic mammalian chitinase regulates epithelial cell apoptosis via a chitinolytic-independent mechanism.Hartl D, He CH, Koller B, Da Silva CA, Kobayashi Y, Lee CG, Flavell RA, Elias JA. J Immunol. 2009 Apr 15. PMID: 19342690.
- A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles.Tycowski KT, Shu MD, Kukoyi A, Steitz JA. Mol Cell. 2009 Apr 10; 2009 Mar 12. PMID: 19285445.
- Antigen presentation on artificial acellular substrates: modular systems for flexible, adaptable immunotherapy.Steenblock ER, Wrzesinski SH, Flavell RA, Fahmy TM. Expert Opin Biol Ther. 2009 Apr. PMID: 19344282.
- Nanotechnology for delivery of drugs to the brain for epilepsy.Bennewitz MF, Saltzman WM. Neurotherapeutics. 2009 Apr. PMID: 19332327.
- ICOS controls effector function but not trafficking receptor expression of kidney-infiltrating effector T cells in murine lupus.Odegard JM, DiPlacido LD, Greenwald L, Kashgarian M, Kono DH, Dong C, Flavell RA, Craft J. J Immunol. 2009 Apr 1. PMID: 19299705.
- Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression.Lee ER, Blount KF, Breaker RR. RNA Biol. 2009 Apr-Jun; 2009 Apr 30. PMID: 19246992.
- Germline expression influences operon organization in the Caenorhabditis elegans genome.Reinke V, Cutter AD. Genetics. 2009 Apr; 2009 Feb 9. PMID: 19204375.
- The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase.Beran RK, Lindenbach BD, Pyle AM. J Virol. 2009 Apr; 2009 Jan 19. PMID: 19153239.
- Repair of DNA lesions associated with triplex-forming oligonucleotides.Chin JY, Glazer PM. Mol Carcinog. 2009 Apr. PMID: 19072762.
- Role for MKL1 in megakaryocytic maturation.Cheng EC, Luo Q, Bruscia EM, Renda MJ, Troy JA, Massaro SA, Tuck D, Schulz V, Mane SM, Berliner N, Sun Y, Morris SW, Qiu C, Krause DS. Blood. 2009 Mar 19; 2009 Jan 9. PMID: 19136660.
- Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ. Genes Dev. 2009 Mar 1; 2009 Feb 24. PMID: 19240126.
- The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility.Roitzsch M, Pyle AM. RNA. 2009 Mar; 2009 Jan 23. PMID: 19168748.
- Developmentally regulated and evolutionarily conserved expression of SLITRK1 in brain circuits implicated in Tourette syndrome.Stillman AA, Krsnik Z, Sun J, Rasin MR, State MW, Sestan N, Louvi A. J Comp Neurol. 2009 Mar 1. PMID: 19105198.
- Macrophages directly contribute to the exaggerated inflammatory response in cystic fibrosis transmembrane conductance regulator-/- mice.Bruscia EM, Zhang PX, Ferreira E, Caputo C, Emerson JW, Tuck D, Krause DS, Egan ME. Am J Respir Cell Mol Biol. 2009 Mar; 2008 Sep 5. PMID: 18776130.
- Retrospective. Frederic M. Richards (1925-2009).Steitz TA. Science. 2009 Feb 27. PMID: 19251620.
- MicroRNAs as novel regulators of angiogenesis.Suárez Y, Sessa WC. Circ Res. 2009 Feb 27. PMID: 19246688.
- Mathematical modeling of molecular diffusion through mucus.Cu Y, Saltzman WM. Adv Drug Deliv Rev. 2009 Feb 27; 2008 Dec 16. PMID: 19135488.
- Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron.Borah S, Wong AC, Steitz JA. Proc Natl Acad Sci U S A. 2009 Feb 24; 2009 Feb 5. PMID: 19196985.
- Absence of autophagy results in reactive oxygen species-dependent amplification of RLR signaling.Tal MC, Sasai M, Lee HK, Yordy B, Shadel GS, Iwasaki A. Proc Natl Acad Sci U S A. 2009 Feb 24; 2009 Feb 5. PMID: 19196953.
- Toll-like receptor 7 mitigates lethal West Nile encephalitis via interleukin 23-dependent immune cell infiltration and homing.Town T, Bai F, Wang T, Kaplan AT, Qian F, Montgomery RR, Anderson JF, Flavell RA, Fikrig E. Immunity. 2009 Feb 20; 2009 Feb 5. PMID: 19200759.
- Controlled delivery of VEGF via modulation of alginate microparticle ionic crosslinking.Jay SM, Saltzman WM. J Control Release. 2009 Feb 20; 2008 Nov 8. PMID: 19027807.
- The bovine papillomavirus E5 protein and the PDGF beta receptor: it takes two to tango.Talbert-Slagle K, DiMaio D. Virology. 2009 Feb 20; 2008 Nov 6. PMID: 18990418.
- Differential roles of migratory and resident DCs in T cell priming after mucosal or skin HSV-1 infection.Lee HK, Zamora M, Linehan MM, Iijima N, Gonzalez D, Haberman A, Iwasaki A. J Exp Med. 2009 Feb 16; 2009 Jan 19. PMID: 19153243.
- Chimeric mice reveal clonal development of pancreatic acini, but not islets.Swenson ES, Xanthopoulos J, Nottoli T, McGrath J, Theise ND, Krause DS. Biochem Biophys Res Commun. 2009 Feb 6; 2008 Dec 29. PMID: 19116141.
- Quantifying environmental adaptation of metabolic pathways in metagenomics.Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Proc Natl Acad Sci U S A. 2009 Feb 3; 2009 Jan 22. PMID: 19164758.
- StoneHinge: hinge prediction by network analysis of individual protein structures.Keating KS, Flores SC, Gerstein MB, Kuhn LA. Protein Sci. 2009 Feb. PMID: 19180449.
- Subnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: processing at transcription sites or accumulation in SC35 foci.Pawlicki JM, Steitz JA. Cell Cycle. 2009 Feb 1; 2009 Feb 21. PMID: 19177009.
- MicroRNAs: key regulators of stem cells.Gangaraju VK, Lin H. Nat Rev Mol Cell Biol. 2009 Feb. PMID: 19165214.
- Acetaminophen-induced hepatotoxicity in mice is dependent on Tlr9 and the Nalp3 inflammasome.Imaeda AB, Watanabe A, Sohail MA, Mahmood S, Mohamadnejad M, Sutterwala FS, Flavell RA, Mehal WZ. J Clin Invest. 2009 Feb; 2009 Jan 26. PMID: 19164858.
- MicroRNA regulation of DNA repair gene expression in hypoxic stress.Crosby ME, Kulshreshtha R, Ivan M, Glazer PM. Cancer Res. 2009 Feb 1; 2009 Jan 13. PMID: 19141645.
- Establishing a mechanistic basis for the large kinetic steps of the NS3 helicase.Serebrov V, Beran RK, Pyle AM. J Biol Chem. 2009 Jan 23; 2008 Nov 14. PMID: 19010782.
- Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. BMC Genomics. 2009 Jan 21; 2009 Jan 21. PMID: 19159457.
- Inflammasome recognition of influenza virus is essential for adaptive immune responses.Ichinohe T, Lee HK, Ogura Y, Flavell R, Iwasaki A. J Exp Med. 2009 Jan 16; 2009 Jan 12. PMID: 19139171.
- Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer.Dong G, Wearsch PA, Peaper DR, Cresswell P, Reinisch KM. Immunity. 2009 Jan 16. PMID: 19119025.
- Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.Yip KY, Gerstein M. Bioinformatics. 2009 Jan 15; 2008 Nov 17. PMID: 19015141.
- Nucleotide analog interference mapping.Suydam IT, Strobel SA. Methods Enzymol. 2009. PMID: 20946762.
- Social networking and personal genomics: suggestions for optimizing the interaction.Greenbaum D, Gerstein M. Am J Bioeth. 2009. PMID: 19998104.
- Emerging roles of microRNAs in the molecular responses to hypoxia.Crosby ME, Devlin CM, Glazer PM, Calin GA, Ivan M. Curr Pharm Des. 2009. PMID: 19925433.
- Autophagy and innate recognition systems.Tal MC, Iwasaki A. Curr Top Microbiol Immunol. 2009. PMID: 19802562.
- mRNA expression profiles show differential regulatory effects of microRNAs between estrogen receptor-positive and estrogen receptor-negative breast cancer.Cheng C, Fu X, Alves P, Gerstein M. Genome Biol. 2009; 2009 Sep 1. PMID: 19723326.
- The biogenesis and function of PIWI proteins and piRNAs: progress and prospect.Thomson T, Lin H. Annu Rev Cell Dev Biol. 2009. PMID: 19575643.
- Evolution of petal identity.Irish VF. J Exp Bot. 2009; 2009 May 14. PMID: 19443615.
- In vitro selection of glmS ribozymes.Link KH, Breaker RR. Methods Mol Biol. 2009. PMID: 19381572.
- The structural and functional diversity of metabolite-binding riboswitches.Roth A, Breaker RR. Annu Rev Biochem. 2009. PMID: 19298181.
- [Mucosal immune defense against sexually transmitted diseases].Iijima N, Iwasaki A. Nihon Rinsho. 2009 Jan. PMID: 19177745.
- Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Genome Biol. 2009; 2009 Jan 5. PMID: 19123937.
- PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. Nat Biotechnol. 2009 Jan; 2009 Jan 4. PMID: 19122651.
- MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP. Genes Dev. 2009 Jan 1; 2008 Dec 18. PMID: 19095804.
- Controlled surface modification with poly(ethylene)glycol enhances diffusion of PLGA nanoparticles in human cervical mucus.Cu Y, Saltzman WM. Mol Pharm. 2009 Jan-Feb. PMID: 19053536.
- MSB: a mean-shift-based approach for the analysis of structural variation in the genome.Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. Genome Res. 2009 Jan; 2008 Nov 26. PMID: 19037015.
- Chimeric receptor mRNA transfection as a tool to generate antineoplastic lymphocytes.Rabinovich PM, Komarovskaya ME, Wrzesinski SH, Alderman JL, Budak-Alpdogan T, Karpikov A, Guo H, Flavell RA, Cheung NK, Weissman SM, Bahceci E. Hum Gene Ther. 2009 Jan. PMID: 19025415.
- RNA-Seq: a revolutionary tool for transcriptomics.Wang Z, Gerstein M, Snyder M. Nat Rev Genet. 2009 Jan. PMID: 19015660.
- Measuring HCV infectivity produced in cell culture and in vivo.Lindenbach BD. Methods Mol Biol. 2009. PMID: 19009272.
- Pseudofam: the pseudogene families database.Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Nucleic Acids Res. 2009 Jan; 2008 Oct 28. PMID: 18957444.
- How an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans.Su D, Hohn MJ, Palioura S, Sherrer RL, Yuan J, Söll D, O'Donoghue P. IUBMB Life. 2009 Jan. PMID: 18798524.
- Multiple MyD88-dependent responses contribute to pulmonary clearance of Legionella pneumophila.Archer KA, Alexopoulou L, Flavell RA, Roy CR. Cell Microbiol. 2009 Jan; 2008 Sep 8. PMID: 18782351.
- Human aortic smooth muscle cells promote arteriole formation by coengrafted endothelial cells.Shepherd BR, Jay SM, Saltzman WM, Tellides G, Pober JS. Tissue Eng Part A. 2009 Jan. PMID: 18620481.
2008
- Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M. BMC Genomics. 2008 Dec 31; 2008 Dec 31. PMID: 19117516.
- MyD88-dependent, superoxide-initiated inflammation is necessary for flow-mediated inward remodeling of conduit arteries.Tang PC, Qin L, Zielonka J, Zhou J, Matte-Martone C, Bergaya S, van Rooijen N, Shlomchik WD, Min W, Sessa WC, Pober JS, Tellides G. J Exp Med. 2008 Dec 22; 2008 Dec 8. PMID: 19064699.
- Dendritic cells and B cells maximize mucosal Th1 memory response to herpes simplex virus.Iijima N, Linehan MM, Zamora M, Butkus D, Dunn R, Kehry MR, Laufer TM, Iwasaki A. J Exp Med. 2008 Dec 22; 2008 Dec 1. PMID: 19047439.
- Innate and adaptive interleukin-22 protects mice from inflammatory bowel disease.Zenewicz LA, Yancopoulos GD, Valenzuela DM, Murphy AJ, Stevens S, Flavell RA. Immunity. 2008 Dec 19. PMID: 19100701.
- [MHC class II-presentation of antigen by autophagy].Kumamoto Y, Iwasaki A. Tanpakushitsu Kakusan Koso. 2008 Dec. PMID: 21038623.
- AIP1 functions as an endogenous inhibitor of VEGFR2-mediated signaling and inflammatory angiogenesis in mice.Zhang H, He Y, Dai S, Xu Z, Luo Y, Wan T, Luo D, Jones D, Tang S, Chen H, Sessa WC, Min W. J Clin Invest. 2008 Dec; 2008 Nov 3. PMID: 19033661.
- IL-22 and inflammation: leukin' through a glass onion.Zenewicz LA, Flavell RA. Eur J Immunol. 2008 Dec. PMID: 19016525.
- Flexibility in the site of exon junction complex deposition revealed by functional group and RNA secondary structure alterations in the splicing substrate.Mishler DM, Christ AB, Steitz JA. RNA. 2008 Dec; 2008 Oct 24. PMID: 18952819.
- Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history.Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. Genome Res. 2008 Dec; 2008 Oct 8. PMID: 18842824.
- ICOS-dependent extrafollicular helper T cells elicit IgG production via IL-21 in systemic autoimmunity.Odegard JM, Marks BR, DiPlacido LD, Poholek AC, Kono DH, Dong C, Flavell RA, Craft J. J Exp Med. 2008 Nov 24; 2008 Nov 3. PMID: 18981236.
- The GANC tetraloop: a novel motif in the group IIC intron structure.Keating KS, Toor N, Pyle AM. J Mol Biol. 2008 Nov 14; 2008 Aug 26. PMID: 18773908.
- Type IV secretion-dependent activation of host MAP kinases induces an increased proinflammatory cytokine response to Legionella pneumophila.Shin S, Case CL, Archer KA, Nogueira CV, Kobayashi KS, Flavell RA, Roy CR, Zamboni DS. PLoS Pathog. 2008 Nov; 2008 Nov 28. PMID: 19043549.
- Innate sensors of influenza virus: clues to developing better intranasal vaccines.Ichinohe T, Iwasaki A, Hasegawa H. Expert Rev Vaccines. 2008 Nov. PMID: 18980544.
- Structural basis for exon recognition by a group II intron.Toor N, Rajashankar K, Keating KS, Pyle AM. Nat Struct Mol Biol. 2008 Nov; 2008 Oct 26. PMID: 18953333.
- The hematopoiesis paradigm: clarity or ambiguity?Rathinam C, Flavell RA. Blood. 2008 Nov 1. PMID: 18948582.
- Amino-termini isoforms of the Slack K+ channel, regulated by alternative promoters, differentially modulate rhythmic firing and adaptation.Brown MR, Kronengold J, Gazula VR, Spilianakis CG, Flavell RA, von Hehn CA, Bhattacharjee A, Kaczmarek LK. J Physiol. 2008 Nov 1; 2008 Sep 11. PMID: 18787033.
- A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing.Champion EA, Lane BH, Jackrel ME, Regan L, Baserga SJ. Mol Cell Biol. 2008 Nov; 2008 Aug 25. PMID: 18725399.
- HingeMaster: normal mode hinge prediction approach and integration of complementary predictors.Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB. Proteins. 2008 Nov 1. PMID: 18433058.
- Hepatitis C viral NS3-4A protease activity is enhanced by the NS3 helicase.Beran RK, Pyle AM. J Biol Chem. 2008 Oct 31; 2008 Aug 22. PMID: 18723512.
- Quality control despite mistranslation caused by an ambiguous genetic code.Ruan B, Palioura S, Sabina J, Marvin-Guy L, Kochhar S, Larossa RA, Söll D. Proc Natl Acad Sci U S A. 2008 Oct 28; 2008 Oct 22. PMID: 18946032.
- The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation.Durniak KJ, Bailey S, Steitz TA. Science. 2008 Oct 24. PMID: 18948533.
- Interaction between Reelin and Notch signaling regulates neuronal migration in the cerebral cortex.Hashimoto-Torii K, Torii M, Sarkisian MR, Bartley CM, Shen J, Radtke F, Gridley T, Sestan N, Rakic P. Neuron. 2008 Oct 23. PMID: 18957219.
- Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.Wing RA, Bailey S, Steitz TA. J Mol Biol. 2008 Oct 17; 2008 Jul 27. PMID: 18691598.
- Fluorine substituted adenosines as probes of nucleobase protonation in functional RNAs.Suydam IT, Strobel SA. J Am Chem Soc. 2008 Oct 15; 2008 Sep 20. PMID: 18803382.
- Misacylation of pyrrolysine tRNA in vitro and in vivo.Gundllapalli S, Ambrogelly A, Umehara T, Li D, Polycarpo C, Söll D. FEBS Lett. 2008 Oct 15; 2008 Sep 5. PMID: 18775710.
- Gene regulation: a tale of germline mRNA tails.Reinke V. Curr Biol. 2008 Oct 14. PMID: 18957237.
- SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons.Kwan KY, Lam MM, Krsnik Z, Kawasawa YI, Lefebvre V, Sestan N. Proc Natl Acad Sci U S A. 2008 Oct 14; 2008 Oct 7. PMID: 18840685.
- Genomic anonymity: have we already lost it?Greenbaum D, Du J, Gerstein M. Am J Bioeth. 2008 Oct. PMID: 19003717.
- Effect of extracellular matrix elements on the transport of paclitaxel through an arterial wall tissue mimic.Sirianni RW, Kremer J, Guler I, Chen YL, Keeley FW, Saltzman WM. Biomacromolecules. 2008 Oct; 2008 Sep 12. PMID: 18785771.
- Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.Kolev NG, Yario TA, Benson E, Steitz JA. EMBO Rep. 2008 Oct; 2008 Aug 8. PMID: 18688255.
- Repression of the SUMO-specific protease Senp1 induces p53-dependent premature senescence in normal human fibroblasts.Yates KE, Korbel GA, Shtutman M, Roninson IB, DiMaio D. Aging Cell. 2008 Oct; 2008 Jul 24. PMID: 18616636.
- Vascular cell signaling by membrane estrogen receptors.Kim KH, Moriarty K, Bender JR. Steroids. 2008 Oct; 2008 Jan 18. PMID: 18325557.
- Dicer-dependent endothelial microRNAs are necessary for postnatal angiogenesis.Suárez Y, Fernández-Hernando C, Yu J, Gerber SA, Harrison KD, Pober JS, Iruela-Arispe ML, Merkenschlager M, Sessa WC. Proc Natl Acad Sci U S A. 2008 Sep 16; 2008 Sep 8. PMID: 18779589.
- Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids.Chin JY, Kuan JY, Lonkar PS, Krause DS, Seidman MM, Peterson KR, Nielsen PE, Kole R, Glazer PM. Proc Natl Acad Sci U S A. 2008 Sep 9; 2008 Aug 29. PMID: 18757759.
- Thrombospondin-2 modulates extracellular matrix remodeling during physiological angiogenesis.Krady MM, Zeng J, Yu J, MacLauchlan S, Skokos EA, Tian W, Bornstein P, Sessa WC, Kyriakides TR. Am J Pathol. 2008 Sep; 2008 Aug 7. PMID: 18688033.
- Transition state chirality and role of the vicinal hydroxyl in the ribosomal peptidyl transferase reaction.Huang KS, Carrasco N, Pfund E, Strobel SA. Biochemistry. 2008 Aug 26; 2008 Aug 2. PMID: 18672893.
- Bioactive endophytes warrant intensified exploration and conservation.Smith SA, Tank DC, Boulanger LA, Bascom-Slack CA, Eisenman K, Kingery D, Babbs B, Fenn K, Greene JS, Hann BD, Keehner J, Kelley-Swift EG, Kembaiyan V, Lee SJ, Li P, Light DY, Lin EH, Ma C, Moore E, Schorn MA, Vekhter D, Nunez PV, Strobel GA, Donoghue MJ, Strobel SA. PLoS One. 2008 Aug 25; 2008 Aug 25. PMID: 18725962.
- C. elegans nucleostemin is required for larval growth and germline stem cell division.Kudron MM, Reinke V. PLoS Genet. 2008 Aug 22; 2008 Aug 22. PMID: 18725931.
- Modeling ChIP sequencing in silico with applications.Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. PLoS Comput Biol. 2008 Aug 22; 2008 Aug 22. PMID: 18725927.
- Bone marrow-derived lung epithelial cells.Krause DS. Proc Am Thorac Soc. 2008 Aug 15. PMID: 18684720.
- Robustness promotes evolvability of thermotolerance in an RNA virus.McBride RC, Ogbunugafor CB, Turner PE. BMC Evol Biol. 2008 Aug 11; 2008 Aug 11. PMID: 18694497.
- TGF-beta signaling in dendritic cells is a prerequisite for the control of autoimmune encephalomyelitis.Laouar Y, Town T, Jeng D, Tran E, Wan Y, Kuchroo VK, Flavell RA. Proc Natl Acad Sci U S A. 2008 Aug 5; 2008 Jul 31. PMID: 18669656.
- Catalytic strategies of self-cleaving ribozymes.Cochrane JC, Strobel SA. Acc Chem Res. 2008 Aug; 2008 Jul 25. PMID: 18652494.
- Identification of initiator B cells, a novel subset of activation-induced deaminase-dependent B-1-like cells that mediate initiation of contact sensitivity.Kerfoot SM, Szczepanik M, Tung JW, Askenase PW. J Immunol. 2008 Aug 1. PMID: 18641308.
- The Arabidopsis petal: a model for plant organogenesis.Irish VF. Trends Plant Sci. 2008 Aug; 2008 Jul 5. PMID: 18603466.
- A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. Genome Res. 2008 Aug; 2008 May 16. PMID: 18487515.
- Engineering of multifunctional gels integrating highly efficient growth factor delivery with endothelial cell transplantation.Jay SM, Shepherd BR, Bertram JP, Pober JS, Saltzman WM. FASEB J. 2008 Aug; 2008 May 1. PMID: 18450813.
- Transmembrane protein oxygen content and compartmentalization of cells.Sasidharan R, Smith A, Gerstein M. PLoS One. 2008 Jul 16; 2008 Jul 16. PMID: 18628944.
- Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production.Pawlicki JM, Steitz JA. J Cell Biol. 2008 Jul 14. PMID: 18625843.
- High loading efficiency and tunable release of plasmid DNA encapsulated in submicron particles fabricated from PLGA conjugated with poly-L-lysine.Blum JS, Saltzman WM. J Control Release. 2008 Jul 2; 2008 Apr 16. PMID: 18511145.
- Amino acid modifications on tRNA.Yuan J, Sheppard K, Söll D. Acta Biochim Biophys Sin (Shanghai). 2008 Jul. PMID: 18604446.
- Transfer RNA genes in pieces.Randau L, Söll D. EMBO Rep. 2008 Jul; 2008 Jun 13. PMID: 18552771.
- Hepatocyte nuclear factor-1 as marker of epithelial phenotype reveals marrow-derived hepatocytes, but not duct cells, after liver injury in mice.Swenson ES, Guest I, Ilic Z, Mazzeo-Helgevold M, Lizardi P, Hardiman C, Sell S, Krause DS. Stem Cells. 2008 Jul; 2008 May 8. PMID: 18467658.
- The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.Cai Y, Chin HF, Lazarova D, Menon S, Fu C, Cai H, Sclafani A, Rodgers DW, De La Cruz EM, Ferro-Novick S, Reinisch KM. Cell. 2008 Jun 27. PMID: 18585354.
- Where in the cell is the minor spliceosome?Steitz JA, Dreyfuss G, Krainer AR, Lamond AI, Matera AG, Padgett RA. Proc Natl Acad Sci U S A. 2008 Jun 24; 2008 Jun 17. PMID: 18562285.
- A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis.Wang G, Reinke V. Curr Biol. 2008 Jun 24; 2008 May 22. PMID: 18501605.
- Crucial role for the Nalp3 inflammasome in the immunostimulatory properties of aluminium adjuvants.Eisenbarth SC, Colegio OR, O'Connor W, Sutterwala FS, Flavell RA. Nature. 2008 Jun 19; 2008 May 21. PMID: 18496530.
- Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.Blaha G, Gürel G, Schroeder SJ, Moore PB, Steitz TA. J Mol Biol. 2008 Jun 6; 2008 Apr 8. PMID: 18455733.
- The transcriptional landscape of the yeast genome defined by RNA sequencing.Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. Science. 2008 Jun 6; 2008 May 1. PMID: 18451266.
- Blocking TGF-beta-Smad2/3 innate immune signaling mitigates Alzheimer-like pathology.Town T, Laouar Y, Pittenger C, Mori T, Szekely CA, Tan J, Duman RS, Flavell RA. Nat Med. 2008 Jun; 2008 Jun 1. PMID: 18516051.
- The current excitement about copy-number variation: how it relates to gene duplications and protein families.Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. Curr Opin Struct Biol. 2008 Jun; 2008 May 27. PMID: 18511261.
- Design opportunities for actively targeted nanoparticle vaccines.Fahmy TM, Demento SL, Caplan MJ, Mellman I, Saltzman WM. Nanomedicine (Lond). 2008 Jun. PMID: 18510429.
- Cell-cycle control of microRNA-mediated translation regulation.Vasudevan S, Tong Y, Steitz JA. Cell Cycle. 2008 Jun 1; 2008 Mar 25. PMID: 18469529.
- A conserved element that stabilizes the group II intron active site.Fedorova O, Pyle AM. RNA. 2008 Jun; 2008 Apr 25. PMID: 18441048.
- Riboswitch effectors as protein enzyme cofactors.Cochrane JC, Strobel SA. RNA. 2008 Jun; 2008 Apr 22. PMID: 18430893.
- Two GATA transcription factors are downstream effectors of floral homeotic gene action in Arabidopsis.Mara CD, Irish VF. Plant Physiol. 2008 Jun; 2008 Apr 16. PMID: 18417639.
- An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.Kingery DA, Pfund E, Voorhees RM, Okuda K, Wohlgemuth I, Kitchen DE, Rodnina MV, Strobel SA. Chem Biol. 2008 May. PMID: 18482701.
- Life without RNase P.Randau L, Schröder I, Söll D. Nature. 2008 May 1. PMID: 18451863.
- Bioengineering approaches to controlled protein delivery.Kobsa S, Saltzman WM. Pediatr Res. 2008 May. PMID: 18427296.
- Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.Zhang ZD, Weinstock G, Gerstein M. J Mol Evol. 2008 May; 2008 Apr 15. PMID: 18414925.
- The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. RNA. 2008 May; 2008 Mar 27. PMID: 18369181.
- A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. Mol Microbiol. 2008 May; 2008 Mar 19. PMID: 18363797.
- Single-dose, therapeutic vaccination of mice with vesicular stomatitis virus expressing human papillomavirus type 16 E7 protein.Liao JB, Publicover J, Rose JK, DiMaio D. Clin Vaccine Immunol. 2008 May; 2008 Mar 12. PMID: 18337377.
- Toll-like receptors regulation of viral infection and disease.Thompson JM, Iwasaki A. Adv Drug Deliv Rev. 2008 Apr 29; 2007 Dec 28. PMID: 18280610.
- The E3 ubiquitin ligase c-Cbl restricts development and functions of hematopoietic stem cells.Rathinam C, Thien CB, Langdon WY, Gu H, Flavell RA. Genes Dev. 2008 Apr 15. PMID: 18413713.
- A relaxed active site after exon ligation by the group I intron.Lipchock SV, Strobel SA. Proc Natl Acad Sci U S A. 2008 Apr 15; 2008 Apr 11. PMID: 18408159.
- Bone marrow-derived cells and stem cells in lung repair.Krause DS. Proc Am Thorac Soc. 2008 Apr 15. PMID: 18403327.
- The role of CTCF in regulating nuclear organization.Williams A, Flavell RA. J Exp Med. 2008 Apr 14; 2008 Mar 17. PMID: 18347103.
- Piecing together the mosaic of early mammalian development through microRNAs.Blakaj A, Lin H. J Biol Chem. 2008 Apr 11; 2008 Feb 13. PMID: 18272516.
- Crystal structure of a self-spliced group II intron.Toor N, Keating KS, Taylor SD, Pyle AM. Science. 2008 Apr 4. PMID: 18388288.
- Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.Wang JX, Breaker RR. Biochem Cell Biol. 2008 Apr. PMID: 18443629.
- Defective p53 engagement after the induction of DNA damage in cells deficient in topoisomerase 3beta.Mohanty S, Town T, Yagi T, Scheidig C, Kwan KY, Allore HG, Flavell RA, Shaw AC. Proc Natl Acad Sci U S A. 2008 Apr 1; 2008 Mar 26. PMID: 18367668.
- Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria.Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR. RNA. 2008 Apr; 2008 Feb 27. PMID: 18305186.
- The candidate MAP kinase phosphorylation substrate DPL-1 (DP) promotes expression of the MAP kinase phosphatase LIP-1 in C. elegans germ cells.Lin B, Reinke V. Dev Biol. 2008 Apr 1; 2008 Jan 8. PMID: 18304523.
- An Arabidopsis F-box protein acts as a transcriptional co-factor to regulate floral development.Chae E, Tan QK, Hill TA, Irish VF. Development. 2008 Apr; 2008 Feb 20. PMID: 18287201.
- Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase.Sherrer RL, Ho JM, Söll D. Nucleic Acids Res. 2008 Apr; 2008 Feb 11. PMID: 18267971.
- From one amino acid to another: tRNA-dependent amino acid biosynthesis.Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Söll D. Nucleic Acids Res. 2008 Apr; 2008 Feb 5. PMID: 18252769.
- Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling.Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. Mol Cell. 2008 Mar 28. PMID: 18374645.
- Complex riboswitches.Breaker RR. Science. 2008 Mar 28. PMID: 18369140.
- Methanothermobacter thermautotrophicus tRNA Gln confines the amidotransferase GatCAB to asparaginyl-tRNA Asn formation.Sheppard K, Sherrer RL, Söll D. J Mol Biol. 2008 Mar 28; 2008 Jan 31. PMID: 18291416.
- On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE.Sheppard K, Söll D. J Mol Biol. 2008 Mar 28; 2008 Jan 16. PMID: 18279892.
- The structure of LepA, the ribosomal back translocase.Evans RN, Blaha G, Bailey S, Steitz TA. Proc Natl Acad Sci U S A. 2008 Mar 25; 2008 Mar 24. PMID: 18362332.
- A structural understanding of the dynamic ribosome machine.Steitz TA. Nat Rev Mol Cell Biol. 2008 Mar. PMID: 18292779.
- ICOS mediates the development of insulin-dependent diabetes mellitus in nonobese diabetic mice.Hawiger D, Tran E, Du W, Booth CJ, Wen L, Dong C, Flavell RA. J Immunol. 2008 Mar 1. PMID: 18292537.
- Physiological variations of stem cell factor and stromal-derived factor-1 in murine models of liver injury and regeneration.Swenson ES, Kuwahara R, Krause DS, Theise ND. Liver Int. 2008 Mar. PMID: 18290773.
- MEN1 and FANCD2 mediate distinct mechanisms of DNA crosslink repair.Marek LR, Kottemann MC, Glazer PM, Bale AE. DNA Repair (Amst). 2008 Mar 1; 2008 Feb 6. PMID: 18258493.
- Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.Sherrer RL, O'Donoghue P, Söll D. Nucleic Acids Res. 2008 Mar; 2008 Jan 3. PMID: 18174226.
- The stumpy gene is required for mammalian ciliogenesis.Town T, Breunig JJ, Sarkisian MR, Spilianakis C, Ayoub AE, Liu X, Ferrandino AF, Gallagher AR, Li MO, Rakic P, Flavell RA. Proc Natl Acad Sci U S A. 2008 Feb 26; 2008 Feb 19. PMID: 18287022.
- Replacement of bone marrow by bone in rat femurs: the bone bioreactor.Zhang Q, Cuartas E, Mehta N, Gilligan J, Ke HZ, Saltzman WM, Kotas M, Ma M, Rajan S, Chalouni C, Carlson J, Vignery A. Tissue Eng Part A. 2008 Feb. PMID: 18333776.
- Autophagy and antiviral immunity.Lee HK, Iwasaki A. Curr Opin Immunol. 2008 Feb; 2008 Feb 8. PMID: 18262399.
- Assays for transfer RNA-dependent amino acid biosynthesis.Sheppard K, Akochy PM, Söll D. Methods. 2008 Feb. PMID: 18241795.
- Uncovering trends in gene naming.Seringhaus MR, Cayting PD, Gerstein MB. Genome Biol. 2008 Jan 31; 2008 Jan 31. PMID: 18254929.
- Cell biology of stem cells: an enigma of asymmetry and self-renewal.Lin H. J Cell Biol. 2008 Jan 28. PMID: 18227277.
- Synthesis of isotopically labeled P-site substrates for the ribosomal peptidyl transferase reaction.Zhong M, Strobel SA. J Org Chem. 2008 Jan 18; 2007 Dec 15. PMID: 18081346.
- Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.Simonović M, Steitz TA. Proc Natl Acad Sci U S A. 2008 Jan 15; 2008 Jan 10. PMID: 18187576.
- An integrated system for studying residue coevolution in proteins.Yip KY, Patel P, Kim PM, Engelman DM, McDermott D, Gerstein M. Bioinformatics. 2008 Jan 15; 2007 Dec 1. PMID: 18056067.
- Prohibitin-1 maintains the angiogenic capacity of endothelial cells by regulating mitochondrial function and senescence.Schleicher M, Shepherd BR, Suarez Y, Fernandez-Hernando C, Yu J, Pan Y, Acevedo LM, Shadel GS, Sessa WC. J Cell Biol. 2008 Jan 14. PMID: 18195103.
- A kinetic intermediate that regulates proper folding of a group II intron RNA.Waldsich C, Pyle AM. J Mol Biol. 2008 Jan 11; 2007 Oct 24. PMID: 18022197.
- Required roles of Bax and JNKs in central and peripheral nervous system death of retinoblastoma-deficient mice.Keramaris E, Ruzhynsky VA, Callaghan SM, Wong E, Davis RJ, Flavell R, Slack RS, Park DS. J Biol Chem. 2008 Jan 4; 2007 Nov 5. PMID: 17984095.
- Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Genome Biol. 2008 Jan 3; 2008 Jan 3. PMID: 18173853.
- Protein-facilitated ribozyme folding and catalysis.Zingler N, Solem A, Pyle AM. Nucleic Acids Symp Ser (Oxf). 2008. PMID: 18776256.
- Approaches for studying angiogenesis-related signal transduction.Derakhshan B, Harrison KD, Miao QR, Sessa WC. Methods Enzymol. 2008. PMID: 18772008.
- Translocation and unwinding mechanisms of RNA and DNA helicases.Pyle AM. Annu Rev Biophys. 2008. PMID: 18573084.
- Triplex-mediated gene modification.Schleifman EB, Chin JY, Glazer PM. Methods Mol Biol. 2008. PMID: 18370076.
- In-line probing analysis of riboswitches.Regulski EE, Breaker RR. Methods Mol Biol. 2008. PMID: 18369975.
- The role of disorder in interaction networks: a structural analysis.Kim PM, Sboner A, Xia Y, Gerstein M. Mol Syst Biol. 2008; 2008 Mar 25. PMID: 18364713.
- MEG-1 and MEG-2 are embryo-specific P-granule components required for germline development in Caenorhabditis elegans.Leacock SW, Reinke V. Genetics. 2008 Jan. PMID: 18202375.
- A scaffold protein, AHNAK1, is required for calcium signaling during T cell activation.Matza D, Badou A, Kobayashi KS, Goldsmith-Pestana K, Masuda Y, Komuro A, McMahon-Pratt D, Marchesi VT, Flavell RA. Immunity. 2008 Jan. PMID: 18191595.
- Human papillomavirus in cervical and head-and-neck cancer.Psyrri A, DiMaio D. Nat Clin Pract Oncol. 2008 Jan. PMID: 18097454.
- Purine sensing by riboswitches.Kim JN, Breaker RR. Biol Cell. 2008 Jan. PMID: 18072940.
- Genomic rearrangements and transcriptional analysis of the spliced leader-associated retrotransposon in RNA interference-deficient Trypanosoma brucei.Patrick KL, Luz PM, Ruan JP, Shi H, Ullu E, Tschudi C. Mol Microbiol. 2008 Jan; 2007 Dec 5. PMID: 18067542.
- Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.Zhang ZD, Cayting P, Weinstock G, Gerstein M. Mol Biol Evol. 2008 Jan; 2007 Dec 7. PMID: 18065488.
- Rectal potential difference and the functional expression of CFTR in the gastrointestinal epithelia in cystic fibrosis mouse models.Weiner SA, Caputo C, Bruscia E, Ferreira EC, Price JE, Krause DS, Egan ME. Pediatr Res. 2008 Jan. PMID: 18043508.
- Chemical basis of glycine riboswitch cooperativity.Kwon M, Strobel SA. RNA. 2008 Jan; 2007 Nov 27. PMID: 18042658.
- Three essential and conserved regions of the group II intron are proximal to the 5'-splice site.de Lencastre A, Pyle AM. RNA. 2008 Jan; 2007 Nov 26. PMID: 18039742.
- c-Jun NH2-terminal kinase 2 inhibits gamma interferon production during Anaplasma phagocytophilum infection.Pedra JH, Mattner J, Tao J, Kerfoot SM, Davis RJ, Flavell RA, Askenase PW, Yin Z, Fikrig E. Infect Immun. 2008 Jan; 2007 Nov 12. PMID: 17998313.
- Dominant-negative Hsp90 reduces VEGF-stimulated nitric oxide release and migration in endothelial cells.Miao RQ, Fontana J, Fulton D, Lin MI, Harrison KD, Sessa WC. Arterioscler Thromb Vasc Biol. 2008 Jan; 2007 Nov 1. PMID: 17975117.
2007
- Immune recognition of Pseudomonas aeruginosa mediated by the IPAF/NLRC4 inflammasome.Sutterwala FS, Mijares LA, Li L, Ogura Y, Kazmierczak BI, Flavell RA. J Exp Med. 2007 Dec 24; 2007 Dec 10. PMID: 18070936.
- Switching from repression to activation: microRNAs can up-regulate translation.Vasudevan S, Tong Y, Steitz JA. Science. 2007 Dec 21; 2007 Nov 29. PMID: 18048652.
- Notch regulates cell fate and dendrite morphology of newborn neurons in the postnatal dentate gyrus.Breunig JJ, Silbereis J, Vaccarino FM, Sestan N, Rakic P. Proc Natl Acad Sci U S A. 2007 Dec 18; 2007 Dec 11. PMID: 18077357.
- Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.Kim PM, Korbel JO, Gerstein MB. Proc Natl Acad Sci U S A. 2007 Dec 18; 2007 Dec 12. PMID: 18077332.
- Optimal bacteriophage mutation rates for phage therapy.Kysela DT, Turner PE. J Theor Biol. 2007 Dec 7; 2007 Aug 25. PMID: 17904162.
- Collecting butterflies and the protein structure initiative: the right questions?Steitz TA. Structure. 2007 Dec. PMID: 18073100.
- Loss of Akt1 leads to severe atherosclerosis and occlusive coronary artery disease.Fernández-Hernando C, Ackah E, Yu J, Suárez Y, Murata T, Iwakiri Y, Prendergast J, Miao RQ, Birnbaum MJ, Sessa WC. Cell Metab. 2007 Dec. PMID: 18054314.
- Alloimmunity to human endothelial cells derived from cord blood progenitors.Suárez Y, Shepherd BR, Rao DA, Pober JS. J Immunol. 2007 Dec 1. PMID: 18025193.
- RNA catalysis: ribozymes, ribosomes, and riboswitches.Strobel SA, Cochrane JC. Curr Opin Chem Biol. 2007 Dec; 2007 Nov 5. PMID: 17981494.
- 'Yin-Yang' functions of transforming growth factor-beta and T regulatory cells in immune regulation.Wan YY, Flavell RA. Immunol Rev. 2007 Dec. PMID: 17979848.
- Functional analyses of genetic pathways controlling petal specification in poppy.Drea S, Hileman LC, de Martino G, Irish VF. Development. 2007 Dec; 2007 Oct 24. PMID: 17959716.
- Evidence for a capping enzyme with specificity for the trypanosome spliced leader RNA.Ruan JP, Shen S, Ullu E, Tschudi C. Mol Biochem Parasitol. 2007 Dec; 2007 Sep 15. PMID: 17949828.
- Development of PTH eluting microspheres for the treatment of hypoparathyroidism.Fong P, Goyal A, Brennan M, Park J, Moss L, Saltzman WM, Breuer CK. J Surg Res. 2007 Dec; 2007 Aug 27. PMID: 17720197.
- The commonly used beta-actin-GFP transgenic mouse strain develops a distinct type of glomerulosclerosis.Guo JK, Cheng EC, Wang L, Swenson ES, Ardito TA, Kashgarian M, Cantley LG, Krause DS. Transgenic Res. 2007 Dec; 2007 Jun 27. PMID: 17594530.
- The serine protease domain of hepatitis C viral NS3 activates RNA helicase activity by promoting the binding of RNA substrate.Beran RK, Serebrov V, Pyle AM. J Biol Chem. 2007 Nov 30; 2007 Oct 5. PMID: 17921146.
- Vaginal epithelial dendritic cells renew from bone marrow precursors.Iijima N, Linehan MM, Saeland S, Iwasaki A. Proc Natl Acad Sci U S A. 2007 Nov 27; 2007 Nov 15. PMID: 18006657.
- Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.Smith A, Cheung K, Krauthammer M, Schultz M, Gerstein M. Bioinformatics. 2007 Nov 15; 2007 Oct 7. PMID: 17923450.
- Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs.Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. Plant Cell. 2007 Nov; 2007 Nov 9. PMID: 17993623.
- Importance of the Debye screening length on nanowire field effect transistor sensors.Stern E, Wagner R, Sigworth FJ, Breaker R, Fahmy TM, Reed MA. Nano Lett. 2007 Nov; 2007 Oct 3. PMID: 17914853.
- Evolution of host specificity drives reproductive isolation among RNA viruses.Duffy S, Burch CL, Turner PE. Evolution. 2007 Nov; 2007 Oct 1. PMID: 17908251.
- COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor-induced entry into the cell cycle from quiescence.Menon S, Chi H, Zhang H, Deng XW, Flavell RA, Wei N. Nat Immunol. 2007 Nov; 2007 Sep 30. PMID: 17906629.
- Centrifugal seeding increases seeding efficiency and cellular distribution of bone marrow stromal cells in porous biodegradable scaffolds.Roh JD, Nelson GN, Udelsman BV, Brennan MP, Lockhart B, Fong PM, Lopez-Soler RI, Saltzman WM, Breuer CK. Tissue Eng. 2007 Nov. PMID: 17880269.
- Host density impacts relative fitness of bacteriophage Phi6 genotypes in structured habitats.Dennehy JJ, Abedon ST, Turner PE. Evolution. 2007 Nov; 2007 Aug 23. PMID: 17725627.
- Apoptotic hepatocyte DNA inhibits hepatic stellate cell chemotaxis via toll-like receptor 9.Watanabe A, Hashmi A, Gomes DA, Town T, Badou A, Flavell RA, Mehal WZ. Hepatology. 2007 Nov. PMID: 17705260.
- Autocrine/paracrine TGFbeta1 is required for the development of epidermal Langerhans cells.Kaplan DH, Li MO, Jenison MC, Shlomchik WD, Flavell RA, Shlomchik MJ. J Exp Med. 2007 Oct 29; 2007 Oct 15. PMID: 17938236.
- U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation.Friend K, Lovejoy AF, Steitz JA. Mol Cell. 2007 Oct 26. PMID: 17964263.
- Demethylation of a specific hypersensitive site in the Th2 locus control region.Kim ST, Fields PE, Flavell RA. Proc Natl Acad Sci U S A. 2007 Oct 23; 2007 Oct 12. PMID: 17940027.
- Structure of hexameric DnaB helicase and its complex with a domain of DnaG primase.Bailey S, Eliason WK, Steitz TA. Science. 2007 Oct 19. PMID: 17947583.
- Paired-end mapping reveals extensive structural variation in the human genome.Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. Science. 2007 Oct 19; 2007 Sep 27. PMID: 17901297.
- Myoferlin regulates vascular endothelial growth factor receptor-2 stability and function.Bernatchez PN, Acevedo L, Fernandez-Hernando C, Murata T, Chalouni C, Kim J, Erdjument-Bromage H, Shah V, Gratton JP, McNally EM, Tempst P, Sessa WC. J Biol Chem. 2007 Oct 19; 2007 Aug 16. PMID: 17702744.
- Variant estrogen receptor-c-Src molecular interdependence and c-Src structural requirements for endothelial NO synthase activation.Li L, Hisamoto K, Kim KH, Haynes MP, Bauer PM, Sanjay A, Collinge M, Baron R, Sessa WC, Bender JR. Proc Natl Acad Sci U S A. 2007 Oct 16; 2007 Oct 5. PMID: 17921256.
- Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine.Kim JN, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2007 Oct 9; 2007 Oct 2. PMID: 17911257.
- Interleukin-22 but not interleukin-17 provides protection to hepatocytes during acute liver inflammation.Zenewicz LA, Yancopoulos GD, Valenzuela DM, Murphy AJ, Karow M, Flavell RA. Immunity. 2007 Oct; 2007 Oct 4. PMID: 17919941.
- Evolving functions of endothelial cells in inflammation.Pober JS, Sessa WC. Nat Rev Immunol. 2007 Oct. PMID: 17893694.
- Reexpression of caveolin-1 in endothelium rescues the vascular, cardiac, and pulmonary defects in global caveolin-1 knockout mice.Murata T, Lin MI, Huang Y, Yu J, Bauer PM, Giordano FJ, Sessa WC. J Exp Med. 2007 Oct 1; 2007 Sep 24. PMID: 17893196.
- ASC/PYCARD and caspase-1 regulate the IL-18/IFN-gamma axis during Anaplasma phagocytophilum infection.Pedra JH, Sutterwala FS, Sukumaran B, Ogura Y, Qian F, Montgomery RR, Flavell RA, Fikrig E. J Immunol. 2007 Oct 1. PMID: 17878377.
- Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. Funct Integr Genomics. 2007 Oct; 2007 Jul 19. PMID: 17638031.
- Limitations of green fluorescent protein as a cell lineage marker.Swenson ES, Price JG, Brazelton T, Krause DS. Stem Cells. 2007 Oct; 2007 Jul 5. PMID: 17615263.
- Evaluating and learning from RNA pseudotorsional space: quantitative validation of a reduced representation for RNA structure.Wadley LM, Keating KS, Duarte CM, Pyle AM. J Mol Biol. 2007 Sep 28; 2007 Jun 27. PMID: 17707400.
- Transforming growth factor-beta and the immune response: implications for anticancer therapy.Wrzesinski SH, Wan YY, Flavell RA. Clin Cancer Res. 2007 Sep 15. PMID: 17875754.
- Structural metals in the group I intron: a ribozyme with a multiple metal ion core.Stahley MR, Adams PL, Wang J, Strobel SA. J Mol Biol. 2007 Sep 7; 2007 Jun 15. PMID: 17612557.
- Characterization of the Trypanosoma brucei cap hypermethylase Tgs1.Ruan JP, Ullu E, Tschudi C. Mol Biochem Parasitol. 2007 Sep; 2007 May 24. PMID: 17610965.
- The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication.Lindenbach BD, Prágai BM, Montserret R, Beran RK, Pyle AM, Penin F, Rice CM. J Virol. 2007 Sep; 2007 Jun 20. PMID: 17581983.
- PARE: a tool for comparing protein abundance and mRNA expression data.Yu EZ, Burba AE, Gerstein M. BMC Bioinformatics. 2007 Aug 24; 2007 Aug 24. PMID: 17718915.
- Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.Kavran JM, Steitz TA. J Mol Biol. 2007 Aug 24; 2007 Jun 4. PMID: 17599351.
- Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.Yu H, Jansen R, Stolovitzky G, Gerstein M. Bioinformatics. 2007 Aug 15; 2007 May 31. PMID: 17540677.
- Divergence of transcription factor binding sites across related yeast species.Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Science. 2007 Aug 10. PMID: 17690298.
- The long unwinding road of RNA helicases.Bleichert F, Baserga SJ. Mol Cell. 2007 Aug 3. PMID: 17679086.
- Engineering high-speed allosteric hammerhead ribozymes.Link KH, Guo L, Ames TD, Yen L, Mulligan RC, Breaker RR. Biol Chem. 2007 Aug. PMID: 17655496.
- The E295K DNA polymerase beta gastric cancer-associated variant interferes with base excision repair and induces cellular transformation.Lang T, Dalal S, Chikova A, DiMaio D, Sweasy JB. Mol Cell Biol. 2007 Aug; 2007 May 25. PMID: 17526740.
- IL-12/23p40-dependent clearance of Anaplasma phagocytophilum in the murine model of human anaplasmosis.Pedra JH, Tao J, Sutterwala FS, Sukumaran B, Berliner N, Bockenstedt LK, Flavell RA, Yin Z, Fikrig E. FEMS Immunol Med Microbiol. 2007 Aug; 2007 May 23. PMID: 17521390.
- The inflammasome in pathogen recognition and inflammation.Sutterwala FS, Ogura Y, Flavell RA. J Leukoc Biol. 2007 Aug; 2007 Apr 30. PMID: 17470531.
- Lung-specific nuclear reprogramming is accompanied by heterokaryon formation and Y chromosome loss following bone marrow transplantation and secondary inflammation.Herzog EL, Van Arnam J, Hu B, Zhang J, Chen Q, Haberman AM, Krause DS. FASEB J. 2007 Aug; 2007 Apr 20. PMID: 17449722.
- Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.Berman AJ, Kamtekar S, Goodman JL, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. EMBO J. 2007 Jul 25; 2007 Jul 5. PMID: 17611604.
- Packing contacts can mediate highly specific interactions between artificial transmembrane proteins and the PDGFbeta receptor.Ptacek JB, Edwards AP, Freeman-Cook LL, DiMaio D. Proc Natl Acad Sci U S A. 2007 Jul 17; 2007 Jul 3. PMID: 17609376.
- The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity.Herring S, Ambrogelly A, Gundllapalli S, O'Donoghue P, Polycarpo CR, Söll D. FEBS Lett. 2007 Jul 10; 2007 Jun 12. PMID: 17582401.
- Co-repression of mismatch repair gene expression by hypoxia in cancer cells: role of the Myc/Max network.Bindra RS, Glazer PM. Cancer Lett. 2007 Jul 8; 2007 Feb 1. PMID: 17275176.
- Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.Kavran JM, Gundllapalli S, O'Donoghue P, Englert M, Söll D, Steitz TA. Proc Natl Acad Sci U S A. 2007 Jul 3; 2007 Jun 25. PMID: 17592110.
- Direct regulation of Gata3 expression determines the T helper differentiation potential of Notch.Amsen D, Antov A, Jankovic D, Sher A, Radtke F, Souabni A, Busslinger M, McCright B, Gridley T, Flavell RA. Immunity. 2007 Jul; 2007 Jul 19. PMID: 17658279.
- Regulatory T cells, transforming growth factor-beta, and immune suppression.Wan YY, Flavell RA. Proc Am Thorac Soc. 2007 Jul. PMID: 17607012.
- Numb and Numbl are required for maintenance of cadherin-based adhesion and polarity of neural progenitors.Rasin MR, Gazula VR, Breunig JJ, Kwan KY, Johnson MB, Liu-Chen S, Li HS, Jan LY, Jan YN, Rakic P, Sestan N. Nat Neurosci. 2007 Jul; 2007 Jun 24. PMID: 17589506.
- Comparing classical pathways and modern networks: towards the development of an edge ontology.Lu LJ, Sboner A, Huang YJ, Lu HX, Gianoulis TA, Yip KY, Kim PM, Montelione GT, Gerstein MB. Trends Biochem Sci. 2007 Jul; 2007 Jun 20. PMID: 17583513.
- Plant endophytes as a platform for discovery-based undergraduate science education.Strobel SA, Strobel GA. Nat Chem Biol. 2007 Jul. PMID: 17576416.
- Depletion of newly synthesized Argonaute1 impairs the RNAi response in Trypanosoma brucei.Shi H, Tschudi C, Ullu E. RNA. 2007 Jul; 2007 May 25. PMID: 17526643.
- Venous identity is lost but arterial identity is not gained during vein graft adaptation.Kudo FA, Muto A, Maloney SP, Pimiento JM, Bergaya S, Fitzgerald TN, Westvik TS, Frattini JC, Breuer CK, Cha CH, Nishibe T, Tellides G, Sessa WC, Dardik A. Arterioscler Thromb Vasc Biol. 2007 Jul; 2007 Apr 26. PMID: 17463332.
- Role of autophagy in innate viral recognition.Iwasaki A. Autophagy. 2007 Jul-Aug; 2007 Jul 7. PMID: 17404496.
- FlexOracle: predicting flexible hinges by identification of stable domains.Flores SC, Gerstein MB. BMC Bioinformatics. 2007 Jun 22; 2007 Jun 22. PMID: 17587456.
- Mutational analysis of a viral RNA element that counteracts rapid RNA decay by interaction with the polyadenylate tail.Conrad NK, Shu MD, Uyhazi KE, Steitz JA. Proc Natl Acad Sci U S A. 2007 Jun 19; 2007 Jun 11. PMID: 17563387.
- Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome.Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. Proc Natl Acad Sci U S A. 2007 Jun 12; 2007 Jun 5. PMID: 17551006.
- Nanosystems for simultaneous imaging and drug delivery to T cells.Fahmy TM, Fong PM, Park J, Constable T, Saltzman WM. AAPS J. 2007 Jun 8; 2007 Jun 8. PMID: 17614359.
- An efficient pseudomedian filter for tiling microrrays.Royce TE, Carriero NJ, Gerstein MB. BMC Bioinformatics. 2007 Jun 7; 2007 Jun 7. PMID: 17555595.
- Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR.Lytle JR, Yario TA, Steitz JA. Proc Natl Acad Sci U S A. 2007 Jun 5; 2007 May 29. PMID: 17535905.
- Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. Genome Res. 2007 Jun. PMID: 17568005.
- Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Genome Res. 2007 Jun. PMID: 17568002.
- Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions.Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Genome Res. 2007 Jun. PMID: 17567997.
- The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. Genome Res. 2007 Jun. PMID: 17567993.
- What is a gene, post-ENCODE? History and updated definition.Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. Genome Res. 2007 Jun. PMID: 17567988.
- Genetic evidence supporting caveolae microdomain regulation of calcium entry in endothelial cells.Murata T, Lin MI, Stan RV, Bauer PM, Yu J, Sessa WC. J Biol Chem. 2007 Jun 1; 2007 Apr 6. PMID: 17416589.
- Regulation of DNA repair in hypoxic cancer cells.Bindra RS, Crosby ME, Glazer PM. Cancer Metastasis Rev. 2007 Jun. PMID: 17415527.
- The DNA binding domain of a papillomavirus E2 protein programs a chimeric nuclease to cleave integrated human papillomavirus DNA in HeLa cervical carcinoma cells.Horner SM, DiMaio D. J Virol. 2007 Jun; 2007 Mar 28. PMID: 17392356.
- Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. Genome Res. 2007 Jun; 2006 Nov 21. PMID: 17119069.
- Control of alternative RNA splicing and gene expression by eukaryotic riboswitches.Cheah MT, Wachter A, Sudarsan N, Breaker RR. Nature. 2007 May 24; 2007 Apr 29. PMID: 17468745.
- Hinge Atlas: relating protein sequence to sites of structural flexibility.Flores SC, Lu LJ, Yang J, Carriero N, Gerstein MB. BMC Bioinformatics. 2007 May 22; 2007 May 22. PMID: 17519025.
- LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.Smith AK, Cheung KH, Yip KY, Schultz M, Gerstein MK. BMC Bioinformatics. 2007 May 9; 2007 May 9. PMID: 17493288.
- Coats, tethers, Rabs, and SNAREs work together to mediate the intracellular destination of a transport vesicle.Cai H, Reinisch K, Ferro-Novick S. Dev Cell. 2007 May. PMID: 17488620.
- Repair and recombination induced by triple helix DNA.Chin JY, Schleifman EB, Glazer PM. Front Biosci. 2007 May 1; 2007 May 1. PMID: 17485375.
- T cell-produced transforming growth factor-beta1 controls T cell tolerance and regulates Th1- and Th17-cell differentiation.Li MO, Wan YY, Flavell RA. Immunity. 2007 May; 2007 May 3. PMID: 17481928.
- Getting connected: analysis and principles of biological networks.Zhu X, Gerstein M, Snyder M. Genes Dev. 2007 May 1. PMID: 17473168.
- The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?Zheng D, Gerstein MB. Trends Genet. 2007 May; 2007 Mar 26. PMID: 17382428.
- A selective activity-dependent requirement for dynamin 1 in synaptic vesicle endocytosis.Ferguson SM, Brasnjo G, Hayashi M, Wölfel M, Collesi C, Giovedi S, Raimondi A, Gong LW, Ariel P, Paradise S, O'toole E, Flavell R, Cremona O, Miesenböck G, Ryan TA, De Camilli P. Science. 2007 Apr 27. PMID: 17463283.
- Dicer dependent microRNAs regulate gene expression and functions in human endothelial cells.Suárez Y, Fernández-Hernando C, Pober JS, Sessa WC. Circ Res. 2007 Apr 27; 2007 Mar 22. PMID: 17379831.
- The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together.Lomakin IB, Xiong Y, Steitz TA. Cell. 2007 Apr 20. PMID: 17448991.
- miR-1-2 gets to the heart of the matter.Mishima Y, Stahlhut C, Giraldez AJ. Cell. 2007 Apr 20. PMID: 17448987.
- The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics.Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. PLoS Comput Biol. 2007 Apr 20; 2007 Feb 14. PMID: 17447836.
- piRNAs in the germ line.Lin H. Science. 2007 Apr 20. PMID: 17446387.
- The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln.Sheppard K, Akochy PM, Salazar JC, Söll D. J Biol Chem. 2007 Apr 20; 2007 Feb 28. PMID: 17329242.
- Assessing the need for sequence-based normalization in tiling microarray experiments.Royce TE, Rozowsky JS, Gerstein MB. Bioinformatics. 2007 Apr 15; 2007 Mar 25. PMID: 17387113.
- The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.Schroeder SJ, Blaha G, Tirado-Rives J, Steitz TA, Moore PB. J Mol Biol. 2007 Apr 13; 2007 Feb 7. PMID: 17321546.
- Toward ribosomal RNA catalytic activity in the absence of protein.Anderson RM, Kwon M, Strobel SA. J Mol Evol. 2007 Apr; 2007 Apr 5. PMID: 17417708.
- Emerging themes in non-coding RNA quality control.Reinisch KM, Wolin SL. Curr Opin Struct Biol. 2007 Apr; 2007 Mar 28. PMID: 17395456.
- Circulating stem cells in extremely preterm neonates.Bizzarro MJ, Bhandari V, Krause DS, Smith BR, Gross I. Acta Paediatr. 2007 Apr. PMID: 17391470.
- Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis.Welz R, Breaker RR. RNA. 2007 Apr; 2007 Feb 16. PMID: 17307816.
- Rbm15 modulates Notch-induced transcriptional activation and affects myeloid differentiation.Ma X, Renda MJ, Wang L, Cheng EC, Niu C, Morris SW, Chi AS, Krause DS. Mol Cell Biol. 2007 Apr; 2007 Feb 5. PMID: 17283045.
- Evidence supporting changes in Nogo-B levels as a marker of neointimal expansion but not adaptive arterial remodeling.Paszkowiak JJ, Maloney SP, Kudo FA, Muto A, Teso D, Rutland RC, Westvik TS, Pimiento JM, Tellides G, Sessa WC, Dardik A. Vascul Pharmacol. 2007 Apr; 2006 Nov 18. PMID: 17207665.
- AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2.Vasudevan S, Steitz JA. Cell. 2007 Mar 23. PMID: 17382880.
- Caveolin-1-deficient mice have increased tumor microvascular permeability, angiogenesis, and growth.Lin MI, Yu J, Murata T, Sessa WC. Cancer Res. 2007 Mar 15. PMID: 17363608.
- Global identification and characterization of transcriptionally active regions in the rice genome.Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW. PLoS One. 2007 Mar 14; 2007 Mar 14. PMID: 17372628.
- Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP. Proc Natl Acad Sci U S A. 2007 Mar 13; 2007 Feb 23. PMID: 17360592.
- Autophagy-dependent viral recognition by plasmacytoid dendritic cells.Lee HK, Lund JM, Ramanathan B, Mizushima N, Iwasaki A. Science. 2007 Mar 9; 2007 Feb 1. PMID: 17272685.
- Group II intron folding under near-physiological conditions: collapsing to the near-native state.Fedorova O, Waldsich C, Pyle AM. J Mol Biol. 2007 Mar 2; 2006 Dec 6. PMID: 17196976.
- A nanoscopic multivalent antigen-presenting carrier for sensitive detection and drug delivery to T cells.Fahmy TM, Schneck JP, Saltzman WM. Nanomedicine. 2007 Mar. PMID: 17379171.
- New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M, Snyder M. Genes Dev. 2007 Mar 1. PMID: 17344419.
- Endothelial-specific expression of mitochondrial thioredoxin improves endothelial cell function and reduces atherosclerotic lesions.Zhang H, Luo Y, Zhang W, He Y, Dai S, Zhang R, Huang Y, Bernatchez P, Giordano FJ, Shadel G, Sessa WC, Min W. Am J Pathol. 2007 Mar. PMID: 17322393.
- Epigenetic and transcriptional programs lead to default IFN-gamma production by gammadelta T cells.Chen L, He W, Kim ST, Tao J, Gao Y, Chi H, Intlekofer AM, Harvey B, Reiner SL, Yin Z, Flavell RA, Craft J. J Immunol. 2007 Mar 1. PMID: 17312115.
- Virus population extinction via ecological traps.Dennehy JJ, Friedenberg NA, Yang YW, Turner PE. Ecol Lett. 2007 Mar. PMID: 17305806.
- JNK2 negatively regulates CD8+ T cell effector function and anti-tumor immune response.Tao J, Gao Y, Li MO, He W, Chen L, Harvev B, Davis RJ, Flavell RA, Yin Z. Eur J Immunol. 2007 Mar. PMID: 17301952.
- Role of endothelial-derived nitric oxide in hypertension and renal disease.Marin E, Sessa WC. Curr Opin Nephrol Hypertens. 2007 Mar. PMID: 17293684.
- Folding of group II introns: a model system for large, multidomain RNAs?Pyle AM, Fedorova O, Waldsich C. Trends Biochem Sci. 2007 Mar; 2007 Feb 7. PMID: 17289393.
- Ribosome biogenesis is sensed at the Start cell cycle checkpoint.Bernstein KA, Bleichert F, Bean JM, Cross FR, Baserga SJ. Mol Biol Cell. 2007 Mar; 2006 Dec 27. PMID: 17192414.
- Human papillomavirus E7 repression in cervical carcinoma cells initiates a transcriptional cascade driven by the retinoblastoma family, resulting in senescence.Johung K, Goodwin EC, DiMaio D. J Virol. 2007 Mar; 2006 Dec 20. PMID: 17182682.
- Pyrrolysine is not hardwired for cotranslational insertion at UAG codons.Ambrogelly A, Gundllapalli S, Herring S, Polycarpo C, Frauer C, Söll D. Proc Natl Acad Sci U S A. 2007 Feb 27; 2007 Feb 20. PMID: 17360621.
- TRAPPI tethers COPII vesicles by binding the coat subunit Sec23.Cai H, Yu S, Menon S, Cai Y, Lazarova D, Fu C, Reinisch K, Hay JC, Ferro-Novick S. Nature. 2007 Feb 22; 2007 Feb 7. PMID: 17287728.
- Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.Kamtekar S, Hohn MJ, Park HS, Schnitzbauer M, Sauerwald A, Söll D, Steitz TA. Proc Natl Acad Sci U S A. 2007 Feb 20; 2007 Feb 14. PMID: 17301225.
- Regulatory T-cell functions are subverted and converted owing to attenuated Foxp3 expression.Wan YY, Flavell RA. Nature. 2007 Feb 15; 2007 Jan 14. PMID: 17220876.
- A catalytic coiled coil: structural insights into the activation of the Rab GTPase Sec4p by Sec2p.Dong G, Medkova M, Novick P, Reinisch KM. Mol Cell. 2007 Feb 9. PMID: 17289591.
- Division of labor by dendritic cells.Iwasaki A. Cell. 2007 Feb 9. PMID: 17289563.
- Innate control of adaptive immunity: dendritic cells and beyond.Lee HK, Iwasaki A. Semin Immunol. 2007 Feb; 2007 Feb 5. PMID: 17276695.
- Antiviral peptides targeting the west nile virus envelope protein.Bai F, Town T, Pradhan D, Cox J, Ashish, Ledizet M, Anderson JF, Flavell RA, Krueger JK, Koski RA, Fikrig E. J Virol. 2007 Feb; 2006 Dec 6. PMID: 17151121.
- Fibronectin terminated multilayer films: protein adsorption and cell attachment studies.Wittmer CR, Phelps JA, Saltzman WM, Van Tassel PR. Biomaterials. 2007 Feb; 2006 Oct 23. PMID: 17056106.
- An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.Gerstein M, Greenbaum D, Cheung K, Miller PL. J Biomed Inform. 2007 Feb; 2006 Mar 6. PMID: 16650809.
- Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNA(Asn).Namgoong S, Sheppard K, Sherrer RL, Söll D. FEBS Lett. 2007 Jan 23; 2007 Jan 2. PMID: 17214986.
- Publishing perishing? Towards tomorrow's information architecture.Seringhaus MR, Gerstein MB. BMC Bioinformatics. 2007 Jan 19; 2007 Jan 19. PMID: 17239245.
- The genetic code revisited--four decades after Francis Crick.Söll D. Nucleic Acids Symp Ser (Oxf). 2007. PMID: 18029562.
- The distributions, mechanisms, and structures of metabolite-binding riboswitches.Barrick JE, Breaker RR. Genome Biol. 2007. PMID: 17997835.
- Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids.Kim KH, Nielsen PE, Glazer PM. Nucleic Acids Res. 2007; 2007 Oct 30. PMID: 17977869.
- In vitro selection and characterization of cellulose-binding DNA aptamers.Boese BJ, Breaker RR. Nucleic Acids Res. 2007; 2007 Sep 18. PMID: 17881365.
- Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution.Wagner GP, Pyle AM. Novartis Found Symp. 2007. PMID: 17710850.
- Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.Royce TE, Rozowsky JS, Gerstein MB. Nucleic Acids Res. 2007; 2007 Aug 7. PMID: 17686789.
- Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Nucleic Acids Res. 2007; 2007 Jul 9. PMID: 17621584.
- The crystal structure of the Thermus aquaticus DnaB helicase monomer.Bailey S, Eliason WK, Steitz TA. Nucleic Acids Res. 2007; 2007 Jul 1. PMID: 17606462.
- Tilescope: online analysis pipeline for high-density tiling microarray data.Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Genome Biol. 2007. PMID: 17501994.
- Mucosal dendritic cells.Iwasaki A. Annu Rev Immunol. 2007. PMID: 17378762.
- Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase.Herring S, Ambrogelly A, Polycarpo CR, Söll D. Nucleic Acids Res. 2007; 2007 Jan 31. PMID: 17267409.
- Activated alphavbeta3 integrin targeting in injury-induced vascular remodeling.Sadeghi MM, Bender JR. Trends Cardiovasc Med. 2007 Jan. PMID: 17210471.
- Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor.Cochrane JC, Lipchock SV, Strobel SA. Chem Biol. 2007 Jan; 2006 Dec 28. PMID: 17196404.
- The power of riboswitches.Barrick JE, Breaker RR. Sci Am. 2007 Jan. PMID: 17186833.
- Natural expansion of the genetic code.Ambrogelly A, Palioura S, Söll D. Nat Chem Biol. 2007 Jan. PMID: 17173027.
- Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. Nucleic Acids Res. 2007; 2006 Dec 7. PMID: 17158151.
- A folding control element for tertiary collapse of a group II intron ribozyme.Waldsich C, Pyle AM. Nat Struct Mol Biol. 2007 Jan; 2006 Dec 3. PMID: 17143279.
- Antibacterial lysine analogs that target lysine riboswitches.Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR. Nat Chem Biol. 2007 Jan; 2006 Dec 3. PMID: 17143270.
- IL9 leads to airway inflammation by inducing IL13 expression in airway epithelial cells.Temann UA, Laouar Y, Eynon EE, Homer R, Flavell RA. Int Immunol. 2007 Jan; 2006 Nov 13. PMID: 17101709.
- Biosynthesis of phosphoserine in the Methanococcales.Helgadóttir S, Rosas-Sandoval G, Söll D, Graham DE. J Bacteriol. 2007 Jan; 2006 Oct 27. PMID: 17071763.
2006
- Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element.Conrad NK, Mili S, Marshall EL, Shu MD, Steitz JA. Mol Cell. 2006 Dec 28. PMID: 17189195.
- Nitric oxide synthase generates nitric oxide locally to regulate compartmentalized protein S-nitrosylation and protein trafficking.Iwakiri Y, Satoh A, Chatterjee S, Toomre DK, Chalouni CM, Fulton D, Groszmann RJ, Shah VH, Sessa WC. Proc Natl Acad Sci U S A. 2006 Dec 26; 2006 Dec 14. PMID: 17170139.
- Relating three-dimensional structures to protein networks provides evolutionary insights.Kim PM, Lu LJ, Xia Y, Gerstein MB. Science. 2006 Dec 22. PMID: 17185604.
- Identification of a large noncoding RNA in extremophilic eubacteria.Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR. Proc Natl Acad Sci U S A. 2006 Dec 19; 2006 Dec 12. PMID: 17164334.
- A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. Bioinformatics. 2006 Dec 15; 2006 Oct 12. PMID: 17038339.
- RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea.Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Söll D. Proc Natl Acad Sci U S A. 2006 Dec 12; 2006 Dec 1. PMID: 17142313.
- Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase.Polycarpo CR, Herring S, Bérubé A, Wood JL, Söll D, Ambrogelly A. FEBS Lett. 2006 Dec 11; 2006 Nov 20. PMID: 17126325.
- Overexpression of the DNA mismatch repair factor, PMS2, confers hypermutability and DNA damage tolerance.Gibson SL, Narayanan L, Hegan DC, Buermeyer AB, Liskay RM, Glazer PM. Cancer Lett. 2006 Dec 8; 2006 Jan 19. PMID: 16426742.
- MEKK4 signaling regulates filamin expression and neuronal migration.Sarkisian MR, Bartley CM, Chi H, Nakamura F, Hashimoto-Torii K, Torii M, Flavell RA, Rakic P. Neuron. 2006 Dec 7. PMID: 17145501.
- Thirty years into the genomics era: tumor viruses led the way.DiMaio D, Miller G. Yale J Biol Med. 2006 Dec. PMID: 17940630.
- New methods for direct delivery of chemotherapy for treating brain tumors.Sawyer AJ, Piepmeier JM, Saltzman WM. Yale J Biol Med. 2006 Dec. PMID: 17940624.
- Riboswitches as antibacterial drug targets.Blount KF, Breaker RR. Nat Biotechnol. 2006 Dec. PMID: 17160062.
- Expression of interleukin-10 in intestinal lymphocytes detected by an interleukin-10 reporter knockin tiger mouse.Kamanaka M, Kim ST, Wan YY, Sutterwala FS, Lara-Tejero M, Galán JE, Harhaj E, Flavell RA. Immunity. 2006 Dec; 2006 Nov 30. PMID: 17137799.
- Cutting Edge: Plasmacytoid dendritic cells provide innate immune protection against mucosal viral infection in situ.Lund JM, Linehan MM, Iijima N, Iwasaki A. J Immunol. 2006 Dec 1. PMID: 17114418.
- An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei.Shi H, Tschudi C, Ullu E. RNA. 2006 Dec; 2006 Oct 19. PMID: 17053086.
- The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.Yip KY, Yu H, Kim PM, Schultz M, Gerstein M. Bioinformatics. 2006 Dec 1; 2006 Oct 4. PMID: 17021160.
- Differing patterns of genetic instability in mice deficient in the mismatch repair genes Pms2, Mlh1, Msh2, Msh3 and Msh6.Hegan DC, Narayanan L, Jirik FR, Edelmann W, Liskay RM, Glazer PM. Carcinogenesis. 2006 Dec; 2006 May 25. PMID: 16728433.
- Emergence of the universal genetic code imprinted in an RNA record.Hohn MJ, Park HS, O'Donoghue P, Schnitzbauer M, Söll D. Proc Natl Acad Sci U S A. 2006 Nov 28; 2006 Nov 16. PMID: 17110438.
- mBET3 is required for the organization of the TRAPP complexes.Menon S, Cai H, Lu H, Dong G, Cai Y, Reinisch K, Ferro-Novick S. Biochem Biophys Res Commun. 2006 Nov 24; 2006 Sep 28. PMID: 17027922.
- A DEAD protein that activates intron self-splicing without unwinding RNA.Solem A, Zingler N, Pyle AM. Mol Cell. 2006 Nov 17. PMID: 17188036.
- Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.Burba AE, Lehnert U, Yu EZ, Gerstein M. Bioinformatics. 2006 Nov 15; 2006 Oct 23. PMID: 17060355.
- Dual recognition of herpes simplex viruses by TLR2 and TLR9 in dendritic cells.Sato A, Linehan MM, Iwasaki A. Proc Natl Acad Sci U S A. 2006 Nov 14; 2006 Nov 3. PMID: 17085599.
- Expression profiling of MAP kinase-mediated meiotic progression in Caenorhabditis elegans.Leacock SW, Reinke V. PLoS Genet. 2006 Nov 10. PMID: 17096596.
- Structure of the calmodulin alphaII-spectrin complex provides insight into the regulation of cell plasticity.Simonovic M, Zhang Z, Cianci CD, Steitz TA, Morrow JS. J Biol Chem. 2006 Nov 10; 2006 Aug 31. PMID: 16945920.
- Differential functions of tumor necrosis factor receptor 1 and 2 signaling in ischemia-mediated arteriogenesis and angiogenesis.Luo D, Luo Y, He Y, Zhang H, Zhang R, Li X, Dobrucki WL, Sinusas AJ, Sessa WC, Min W. Am J Pathol. 2006 Nov. PMID: 17071609.
- Engraftment of marrow-derived epithelial cells: the role of fusion.Herzog EL, Krause DS. Proc Am Thorac Soc. 2006 Nov. PMID: 17065375.
- Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen.Fuchs G, Stein AJ, Fu C, Reinisch KM, Wolin SL. Nat Struct Mol Biol. 2006 Nov; 2006 Oct 15. PMID: 17041599.
- Molecular and phylogenetic analyses of the MADS-box gene family in tomato.Hileman LC, Sundstrom JF, Litt A, Chen M, Shumba T, Irish VF. Mol Biol Evol. 2006 Nov; 2006 Aug 22. PMID: 16926244.
- Critical role for the beta regulatory subunits of Cav channels in T lymphocyte function.Badou A, Jha MK, Matza D, Mehal WZ, Freichel M, Flockerzi V, Flavell RA. Proc Natl Acad Sci U S A. 2006 Oct 17; 2006 Oct 6. PMID: 17028169.
- Tandem riboswitch architectures exhibit complex gene control functions.Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. Science. 2006 Oct 13. PMID: 17038623.
- Characteristics of ligand recognition by a glmS self-cleaving ribozyme.Lim J, Grove BC, Roth A, Breaker RR. Angew Chem Int Ed Engl. 2006 Oct 13. PMID: 16986193.
- Integration of curated databases to identify genotype-phenotype associations.Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M. BMC Genomics. 2006 Oct 12; 2006 Oct 12. PMID: 17038185.
- Modulation of cell adhesion and motility in the immune system by Myo1f.Kim SV, Mehal WZ, Dong X, Heinrich V, Pypaert M, Mellman I, Dembo M, Mooseker MS, Wu D, Flavell RA. Science. 2006 Oct 6. PMID: 17023661.
- Genomic analysis of the hierarchical structure of regulatory networks.Yu H, Gerstein M. Proc Natl Acad Sci U S A. 2006 Oct 3; 2006 Sep 26. PMID: 17003135.
- The genetic code - thawing the 'frozen accident'.Söll D, RajBhandary UL. J Biosci. 2006 Oct. PMID: 17206066.
- Basal repression of BRCA1 by multiple E2Fs and pocket proteins at adjacent E2F sites.Bindra RS, Glazer PM. Cancer Biol Ther. 2006 Oct; 2006 Oct 30. PMID: 17106239.
- CHK2-dependent phosphorylation of BRCA1 in hypoxia.Gibson SL, Bindra RS, Glazer PM. Radiat Res. 2006 Oct. PMID: 17007555.
- Wnk4 controls blood pressure and potassium homeostasis via regulation of mass and activity of the distal convoluted tubule.Lalioti MD, Zhang J, Volkman HM, Kahle KT, Hoffmann KE, Toka HR, Nelson-Williams C, Ellison DH, Flavell R, Booth CJ, Lu Y, Geller DS, Lifton RP. Nat Genet. 2006 Oct; 2006 Sep 10. PMID: 16964266.
- Engraftment of donor-derived epithelial cells in multiple organs following bone marrow transplantation into newborn mice.Bruscia EM, Ziegler EC, Price JE, Weiner S, Egan ME, Krause DS. Stem Cells. 2006 Oct; 2006 Jun 22. PMID: 16794262.
- The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.Bailey S, Wing RA, Steitz TA. Cell. 2006 Sep 8. PMID: 16959569.
- Inactivation of JNK1 enhances innate IL-10 production and dampens autoimmune inflammation in the brain.Tran EH, Azuma YT, Chen M, Weston C, Davis RJ, Flavell RA. Proc Natl Acad Sci U S A. 2006 Sep 5; 2006 Aug 28. PMID: 16938889.
- Toll-like receptor 7 and TLR9 dictate autoantibody specificity and have opposing inflammatory and regulatory roles in a murine model of lupus.Christensen SR, Shupe J, Nickerson K, Kashgarian M, Flavell RA, Shlomchik MJ. Immunity. 2006 Sep. PMID: 16973389.
- Transforming growth factor-beta controls development, homeostasis, and tolerance of T cells by regulatory T cell-dependent and -independent mechanisms.Li MO, Sanjabi S, Flavell RA. Immunity. 2006 Sep. PMID: 16973386.
- DNA secretion and gene-level selection in bacteria.Draghi JA, Turner PE. Microbiology (Reading). 2006 Sep. PMID: 16946263.
- Critical function of Bmx/Etk in ischemia-mediated arteriogenesis and angiogenesis.He Y, Luo Y, Tang S, Rajantie I, Salven P, Heil M, Zhang R, Luo D, Li X, Chi H, Yu J, Carmeliet P, Schaper W, Sinusas AJ, Sessa WC, Alitalo K, Min W. J Clin Invest. 2006 Sep; 2006 Aug 24. PMID: 16932810.
- Predicting essential genes in fungal genomes.Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. Genome Res. 2006 Sep; 2006 Aug 9. PMID: 16899653.
- Prevention of mesangial sclerosis by bone marrow transplantation.Guo JK, Ardito TA, Kashgarian M, Krause DS. Kidney Int. 2006 Sep; 2006 Jul 19. PMID: 16850025.
- Triplex-stimulated intermolecular recombination at a single-copy genomic target.Knauert MP, Kalish JM, Hegan DC, Glazer PM. Mol Ther. 2006 Sep; 2006 May 30. PMID: 16731047.
- The inflammasome: first line of the immune response to cell stress.Ogura Y, Sutterwala FS, Flavell RA. Cell. 2006 Aug 25. PMID: 16923387.
- Visualizing polynucleotide polymerase machines at work.Steitz TA. EMBO J. 2006 Aug 9. PMID: 16900098.
- The roles for cytokines in the generation and maintenance of regulatory T cells.Wan YY, Flavell RA. Immunol Rev. 2006 Aug. PMID: 16903910.
- A crucial role for plasmacytoid dendritic cells in antiviral protection by CpG ODN-based vaginal microbicide.Shen H, Iwasaki A. J Clin Invest. 2006 Aug; 2006 Jul 27. PMID: 16878177.
- Threshold of lung injury required for the appearance of marrow-derived lung epithelia.Herzog EL, Van Arnam J, Hu B, Krause DS. Stem Cells. 2006 Aug. PMID: 16868209.
- The real life of pseudogenes.Gerstein M, Zheng D. Sci Am. 2006 Aug. PMID: 16866288.
- Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB).Chi W, Reinke V. Development. 2006 Aug; 2006 Jul 19. PMID: 16854972.
- Functional analyses of two tomato APETALA3 genes demonstrate diversification in their roles in regulating floral development.de Martino G, Pan I, Emmanuel E, Levy A, Irish VF. Plant Cell. 2006 Aug; 2006 Jul 14. PMID: 16844904.
- Vascularization and engraftment of a human skin substitute using circulating progenitor cell-derived endothelial cells.Shepherd BR, Enis DR, Wang F, Suarez Y, Pober JS, Schechner JS. FASEB J. 2006 Aug; 2006 Jun 28. PMID: 16807367.
- The kinase TAK1 integrates antigen and cytokine receptor signaling for T cell development, survival and function.Wan YY, Chi H, Xie M, Schneider MD, Flavell RA. Nat Immunol. 2006 Aug; 2006 Jun 25. PMID: 16799562.
- Identification of Golgi-localized acyl transferases that palmitoylate and regulate endothelial nitric oxide synthase.Fernández-Hernando C, Fukata M, Bernatchez PN, Fukata Y, Lin MI, Bredt DS, Sessa WC. J Cell Biol. 2006 Jul 31; 2006 Jul 24. PMID: 16864653.
- Identification of a receptor necessary for Nogo-B stimulated chemotaxis and morphogenesis of endothelial cells.Miao RQ, Gao Y, Harrison KD, Prendergast J, Acevedo LM, Yu J, Hu F, Strittmatter SM, Sessa WC. Proc Natl Acad Sci U S A. 2006 Jul 18; 2006 Jul 11. PMID: 16835300.
- Essential role of nitric oxide in VEGF-induced, asthma-like angiogenic, inflammatory, mucus, and physiologic responses in the lung.Bhandari V, Choo-Wing R, Chapoval SP, Lee CG, Tang C, Kim YK, Ma B, Baluk P, Lin MI, McDonald DM, Homer RJ, Sessa WC, Elias JA. Proc Natl Acad Sci U S A. 2006 Jul 18; 2006 Jul 10. PMID: 16832062.
- Implications of structures of synaptic tetramers of gamma delta resolvase for the mechanism of recombination.Kamtekar S, Ho RS, Cocco MJ, Li W, Wenwieser SV, Boocock MR, Grindley ND, Steitz TA. Proc Natl Acad Sci U S A. 2006 Jul 11; 2006 Jun 28. PMID: 16807292.
- The Ro 60 kDa autoantigen comes into focus: interpreting epitope mapping experiments on the basis of structure.Wolin SL, Reinisch KM. Autoimmun Rev. 2006 Jul; 2005 Nov 15. PMID: 16890888.
- FAT10/diubiquitin-like protein-deficient mice exhibit minimal phenotypic differences.Canaan A, Yu X, Booth CJ, Lian J, Lazar I, Gamfi SL, Castille K, Kohya N, Nakayama Y, Liu YC, Eynon E, Flavell R, Weissman SM. Mol Cell Biol. 2006 Jul. PMID: 16782901.
- The PINc domain protein Utp24, a putative nuclease, is required for the early cleavage steps in 18S rRNA maturation.Bleichert F, Granneman S, Osheim YN, Beyer AL, Baserga SJ. Proc Natl Acad Sci U S A. 2006 Jun 20; 2006 Jun 12. PMID: 16769905.
- The nucleolar protein Esf2 interacts directly with the DExD/H box RNA helicase, Dbp8, to stimulate ATP hydrolysis.Granneman S, Lin C, Champion EA, Nandineni MR, Zorca C, Baserga SJ. Nucleic Acids Res. 2006; 2006 Jun 13. PMID: 16772403.
- Role of the caspase-1 inflammasome in Salmonella typhimurium pathogenesis.Lara-Tejero M, Sutterwala FS, Ogura Y, Grant EP, Bertin J, Coyle AJ, Flavell RA, Galán JE. J Exp Med. 2006 Jun 12; 2006 May 22. PMID: 16717117.
- Midline radial glia translocation and corpus callosum formation require FGF signaling.Smith KM, Ohkubo Y, Maragnoli ME, Rasin MR, Schwartz ML, Sestan N, Vaccarino FM. Nat Neurosci. 2006 Jun; 2006 May 21. PMID: 16715082.
- RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis.Stahley MR, Strobel SA. Curr Opin Struct Biol. 2006 Jun; 2006 May 11. PMID: 16697179.
- Functional replacement of Trypanosoma brucei Argonaute by the human slicer Argonaute2.Shi H, Tschudi C, Ullu E. RNA. 2006 Jun; 2006 Apr 12. PMID: 16611939.
- Participation of the tRNA A76 hydroxyl groups throughout translation.Weinger JS, Strobel SA. Biochemistry. 2006 May 16. PMID: 16681365.
- Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track.Beran RK, Bruno MM, Bowers HA, Jankowsky E, Pyle AM. J Mol Biol. 2006 May 12; 2006 Mar 20. PMID: 16569413.
- Epstein-Barr virus noncoding RNAs are confined to the nucleus, whereas their partner, the human La protein, undergoes nucleocytoplasmic shuttling.Fok V, Friend K, Steitz JA. J Cell Biol. 2006 May 8. PMID: 16682524.
- TGF-beta signaling is required for the function of insulin-reactive T regulatory cells.Du W, Wong FS, Li MO, Peng J, Qi H, Flavell RA, Sherwin R, Wen L. J Clin Invest. 2006 May. PMID: 16670772.
- Direct evidence for the role of caveolin-1 and caveolae in mechanotransduction and remodeling of blood vessels.Yu J, Bergaya S, Murata T, Alp IF, Bauer MP, Lin MI, Drab M, Kurzchalia TV, Stan RV, Sessa WC. J Clin Invest. 2006 May. PMID: 16670769.
- Adenosine metabolism and murine strain-specific IL-4-induced inflammation, emphysema, and fibrosis.Ma B, Blackburn MR, Lee CG, Homer RJ, Liu W, Flavell RA, Boyden L, Lifton RP, Sun CX, Young HW, Elias JA. J Clin Invest. 2006 May. PMID: 16670768.
- Direct regulation of the floral homeotic APETALA1 gene by APETALA3 and PISTILLATA in Arabidopsis.Sundström JF, Nakayama N, Glimelius K, Irish VF. Plant J. 2006 May. PMID: 16640596.
- Multiple domains of EBER 1, an Epstein-Barr virus noncoding RNA, recruit human ribosomal protein L22.Fok V, Mitton-Fry RM, Grech A, Steitz JA. RNA. 2006 May; 2006 Mar 23. PMID: 16556938.
- 2'-O-methylation of position 2 of the trypanosome spliced leader cap 4 is mediated by a 48 kDa protein related to vaccinia virus VP39.Arhin GK, Ullu E, Tschudi C. Mol Biochem Parasitol. 2006 May; 2006 Feb 17. PMID: 16516986.
- Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. Nucleic Acids Res. 2006 Apr 28; 2006 Apr 28. PMID: 16648358.
- Molecular biology. Managing associations between different chromosomes.Spilianakis CG, Flavell RA. Science. 2006 Apr 14. PMID: 16614205.
- Development and application of a high-throughput assay for glmS riboswitch activators.Blount K, Puskarz I, Penchovsky R, Breaker R. RNA Biol. 2006 Apr; 2006 Apr 14. PMID: 17114942.
- T helper cell differentiation: regulation by cis elements and epigenetics.Lee GR, Kim ST, Spilianakis CG, Fields PE, Flavell RA. Immunity. 2006 Apr. PMID: 16618596.
- Transforming growth factor-beta: recent advances on its role in immune tolerance.Kriegel MA, Li MO, Sanjabi S, Wan YY, Flavell RA. Curr Rheumatol Rep. 2006 Apr. PMID: 16569373.
- Development of a model system for preliminary evaluation of tissue-engineered vascular conduits.Goyal A, Wang Y, Su H, Dobrucki LW, Brennan M, Fong P, Dardik A, Tellides G, Sinusas A, Pober JS, Saltzman WM, Breuer CK. J Pediatr Surg. 2006 Apr. PMID: 16567194.
- Interleukin-4-dependent innate collaboration between iNKT cells and B-1 B cells controls adaptative contact sensitivity.Campos RA, Szczepanik M, Itakura A, Lisbonne M, Dey N, Leite-de-Moraes MC, Askenase PW. Immunology. 2006 Apr. PMID: 16556268.
- In vivo assembly of functional U7 snRNP requires RNA backbone flexibility within the Sm-binding site.Kolev NG, Steitz JA. Nat Struct Mol Biol. 2006 Apr; 2006 Mar 19. PMID: 16547514.
- Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.Roth A, Nahvi A, Lee M, Jona I, Breaker RR. RNA. 2006 Apr; 2006 Feb 16. PMID: 16484375.
- Predicting interactions in protein networks by completing defective cliques.Yu H, Paccanaro A, Trifonov V, Gerstein M. Bioinformatics. 2006 Apr 1; 2006 Feb 2. PMID: 16455753.
- The phi29 DNA polymerase:protein-primer structure suggests a model for the initiation to elongation transition.Kamtekar S, Berman AJ, Wang J, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. EMBO J. 2006 Mar 22; 2006 Mar 2. PMID: 16511564.
- High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays.Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. Proc Natl Acad Sci U S A. 2006 Mar 21; 2006 Mar 14. PMID: 16537408.
- Integrated prediction of the helical membrane protein interactome in yeast.Xia Y, Lu LJ, Gerstein M. J Mol Biol. 2006 Mar 17; 2006 Jan 5. PMID: 16413578.
- The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine formation.Sabina J, Söll D. J Biol Chem. 2006 Mar 17; 2006 Jan 10. PMID: 16407303.
- Regiospecificity of the peptidyl tRNA ester within the ribosomal P site.Huang KS, Weinger JS, Butler EB, Strobel SA. J Am Chem Soc. 2006 Mar 15. PMID: 16522067.
- Microglia recognize double-stranded RNA via TLR3.Town T, Jeng D, Alexopoulou L, Tan J, Flavell RA. J Immunol. 2006 Mar 15. PMID: 16517751.
- TGF-beta, T-cell tolerance and immunotherapy of autoimmune diseases and cancer.Li MO, Flavell RA. Expert Rev Clin Immunol. 2006 Mar. PMID: 20477076.
- Viral ecology and the maintenance of novel host use.Dennehy JJ, Friedenberg NA, Holt RD, Turner PE. Am Nat. 2006 Mar. PMID: 16673350.
- Critical role for NALP3/CIAS1/Cryopyrin in innate and adaptive immunity through its regulation of caspase-1.Sutterwala FS, Ogura Y, Szczepanik M, Lara-Tejero M, Lichtenberger GS, Grant EP, Bertin J, Coyle AJ, Galán JE, Askenase PW, Flavell RA. Immunity. 2006 Mar. PMID: 16546100.
- Sustained remission from angioimmunoblastic T-cell lymphoma induced by alemtuzumab.Halene S, Zieske A, Berliner N. Nat Clin Pract Oncol. 2006 Mar. PMID: 16520806.
- Bacteriophage migration via nematode vectors: host-parasite-consumer interactions in laboratory microcosms.Dennehy JJ, Friedenberg NA, Yang YW, Turner PE. Appl Environ Microbiol. 2006 Mar. PMID: 16517645.
- The Birc1e cytosolic pattern-recognition receptor contributes to the detection and control of Legionella pneumophila infection.Zamboni DS, Kobayashi KS, Kohlsdorf T, Ogura Y, Long EM, Vance RE, Kuida K, Mariathasan S, Dixit VM, Flavell RA, Dietrich WF, Roy CR. Nat Immunol. 2006 Mar; 2006 Jan 29. PMID: 16444259.
- The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development.Tan QK, Irish VF. Plant Physiol. 2006 Mar; 2006 Jan 20. PMID: 16428600.
- An engineered VEGF-activating zinc finger protein transcription factor improves blood flow and limb salvage in advanced-age mice.Yu J, Lei L, Liang Y, Hinh L, Hickey RP, Huang Y, Liu D, Yeh JL, Rebar E, Case C, Spratt K, Sessa WC, Giordano FJ. FASEB J. 2006 Mar; 2006 Jan 19. PMID: 16423874.
- Assessment of cystic fibrosis transmembrane conductance regulator (CFTR) activity in CFTR-null mice after bone marrow transplantation.Bruscia EM, Price JE, Cheng EC, Weiner S, Caputo C, Ferreira EC, Egan ME, Krause DS. Proc Natl Acad Sci U S A. 2006 Feb 21; 2006 Feb 15. PMID: 16481627.
- LFA-1-dependent HuR nuclear export and cytokine mRNA stabilization in T cell activation.Wang JG, Collinge M, Ramgolam V, Ayalon O, Fan XC, Pardi R, Bender JR. J Immunol. 2006 Feb 15. PMID: 16455966.
- Target hub proteins serve as master regulators of development in yeast.Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. Genes Dev. 2006 Feb 15; 2006 Jan 31. PMID: 16449570.
- Dynamic regulation of pro- and anti-inflammatory cytokines by MAPK phosphatase 1 (MKP-1) in innate immune responses.Chi H, Barry SP, Roth RJ, Wu JJ, Jones EA, Bennett AM, Flavell RA. Proc Natl Acad Sci U S A. 2006 Feb 14; 2006 Feb 6. PMID: 16461893.
- Caspases 3 and 7: key mediators of mitochondrial events of apoptosis.Lakhani SA, Masud A, Kuida K, Porter GA Jr, Booth CJ, Mehal WZ, Inayat I, Flavell RA. Science. 2006 Feb 10. PMID: 16469926.
- Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved in large ribosomal subunit biogenesis.Bernstein KA, Granneman S, Lee AV, Manickam S, Baserga SJ. Mol Cell Biol. 2006 Feb. PMID: 16449635.
- Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis.Granneman S, Bernstein KA, Bleichert F, Baserga SJ. Mol Cell Biol. 2006 Feb. PMID: 16449634.
- Is base excision repair a tumor suppressor mechanism?Sweasy JB, Lang T, DiMaio D. Cell Cycle. 2006 Feb; 2006 Feb 14. PMID: 16418580.
- Design optimization methods for genomic DNA tiling arrays.Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. Genome Res. 2006 Feb; 2005 Dec 19. PMID: 16365382.
- A story with a good ending: tRNA 3'-end maturation by CCA-adding enzymes.Xiong Y, Steitz TA. Curr Opin Struct Biol. 2006 Feb; 2005 Dec 20. PMID: 16364630.
- Pleiotropic costs of niche expansion in the RNA bacteriophage phi 6.Duffy S, Turner PE, Burch CL. Genetics. 2006 Feb; 2005 Nov 19. PMID: 16299384.
- Bone marrow transplantation can attenuate the progression of mesangial sclerosis.Guo JK, Schedl A, Krause DS. Stem Cells. 2006 Feb; 2005 Sep 8. PMID: 16150922.
- Molecular-recognition characteristics of SAM-binding riboswitches.Lim J, Winkler WC, Nakamura S, Scott V, Breaker RR. Angew Chem Int Ed Engl. 2006 Jan 30. PMID: 16381055.
- Germline genomics.Reinke V. WormBook. 2006 Jan 20; 2006 Jan 20. PMID: 18050476.
- Metazoan oocyte and early embryo development program: a progression through translation regulatory cascades.Vasudevan S, Seli E, Steitz JA. Genes Dev. 2006 Jan 15. PMID: 16418480.
- Site-specific gene modification by PNAs conjugated to psoralen.Kim KH, Nielsen PE, Glazer PM. Biochemistry. 2006 Jan 10. PMID: 16388608.
- Synthesis of the ribosomal P-site substrate CCA-pcb.Zhong M, Strobel SA. Org Lett. 2006 Jan 5. PMID: 16381566.
- ProCAT: a data analysis approach for protein microarrays.Zhu X, Gerstein M, Snyder M. Genome Biol. 2006. PMID: 17109749.
- The use of bone marrow-chimeric mice in elucidating immune mechanisms.Iwasaki A. Methods Mol Med. 2006. PMID: 16988461.
- Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection.Link KH, Guo L, Breaker RR. Nucleic Acids Res. 2006; 2006 Sep 18. PMID: 16982640.
- NALP3: a key player in caspase-1 activation.Sutterwala FS, Ogura Y, Zamboni DS, Roy CR, Flavell RA. J Endotoxin Res. 2006. PMID: 16953978.
- Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex.Gill ML, Strobel SA, Loria JP. Nucleic Acids Res. 2006; 2006 Aug 31. PMID: 16945956.
- Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. Methods Enzymol. 2006. PMID: 16939796.
- A computational approach for identifying pseudogenes in the ENCODE regions.Zheng D, Gerstein MB. Genome Biol. 2006; 2006 Aug 7. PMID: 16925835.
- Human papillomaviruses and cervical cancer.DiMaio D, Liao JB. Adv Virus Res. 2006. PMID: 16877060.
- Design principles of molecular networks revealed by global comparisons and composite motifs.Yu H, Xia Y, Trifonov V, Gerstein M. Genome Biol. 2006. PMID: 16859507.
- Transforming growth factor-beta regulation of immune responses.Li MO, Wan YY, Sanjabi S, Robertson AK, Flavell RA. Annu Rev Immunol. 2006. PMID: 16551245.
- Enhanced and prolonged cross-presentation following endosomal escape of exogenous antigens encapsulated in biodegradable nanoparticles.Shen H, Ackerman AL, Cody V, Giodini A, Hinson ER, Cresswell P, Edelson RL, Saltzman WM, Hanlon DJ. Immunology. 2006 Jan. PMID: 16423043.
- The Database of Macromolecular Motions: new features added at the decade mark.Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M. Nucleic Acids Res. 2006 Jan 1. PMID: 16381870.
- A protein related to the vaccinia virus cap-specific methyltransferase VP39 is involved in cap 4 modification in Trypanosoma brucei.Arhin GK, Li H, Ullu E, Tschudi C. RNA. 2006 Jan; 2005 Nov 21. PMID: 16301606.
2005
- Hypoxia-induced down-regulation of BRCA1 expression by E2Fs.Bindra RS, Gibson SL, Meng A, Westermark U, Jasin M, Pierce AJ, Bristow RG, Classon MK, Glazer PM. Cancer Res. 2005 Dec 15. PMID: 16357170.
- Global changes in STAT target selection and transcription regulation upon interferon treatments.Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. Genes Dev. 2005 Dec 15; 2005 Nov 30. PMID: 16319195.
- The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves.Randau L, Calvin K, Hall M, Yuan J, Podar M, Li H, Söll D. Proc Natl Acad Sci U S A. 2005 Dec 13; 2005 Dec 5. PMID: 16330750.
- Zfp312 is required for subcortical axonal projections and dendritic morphology of deep-layer pyramidal neurons of the cerebral cortex.Chen JG, Rasin MR, Kwan KY, Sestan N. Proc Natl Acad Sci U S A. 2005 Dec 6; 2005 Nov 28. PMID: 16314561.
- Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine.Sudarsan N, Cohen-Chalamish S, Nakamura S, Emilsson GM, Breaker RR. Chem Biol. 2005 Dec. PMID: 16356850.
- Twisting the Th1/Th2 immune response via the retinoid X receptor: lessons from a genetic approach.Spilianakis CG, Lee GR, Flavell RA. Eur J Immunol. 2005 Dec. PMID: 16331704.
- Hypoxia-induced phosphorylation of Chk2 in an ataxia telangiectasia mutated-dependent manner.Gibson SL, Bindra RS, Glazer PM. Cancer Res. 2005 Dec 1. PMID: 16322218.
- Global analysis of protein phosphorylation in yeast.Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. Nature. 2005 Dec 1. PMID: 16319894.
- Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster.Jones EA, Flavell RA. J Immunol. 2005 Dec 1. PMID: 16301651.
- An hour after immunization peritoneal B-1 cells are activated to migrate to lymphoid organs where within 1 day they produce IgM antibodies that initiate elicitation of contact sensitivity.Itakura A, Szczepanik M, Campos RA, Paliwal V, Majewska M, Matsuda H, Takatsu K, Askenase PW. J Immunol. 2005 Dec 1. PMID: 16301620.
- The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14.Granneman S, Nandineni MR, Baserga SJ. Mol Cell Biol. 2005 Dec. PMID: 16287850.
- The structures of exocyst subunit Exo70p and the Exo84p C-terminal domains reveal a common motif.Dong G, Hutagalung AH, Fu C, Novick P, Reinisch KM. Nat Struct Mol Biol. 2005 Dec; 2005 Oct 26. PMID: 16249794.
- Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted.Tu D, Blaha G, Moore PB, Steitz TA. Extremophiles. 2005 Dec; 2005 Jun 22. PMID: 15970993.
- 205Tl NMR methods for the characterization of monovalent cation binding to nucleic acids.Gill ML, Strobel SA, Loria JP. J Am Chem Soc. 2005 Nov 30. PMID: 16305263.
- An obligate intermediate along the slow folding pathway of a group II intron ribozyme.Su LJ, Waldsich C, Pyle AM. Nucleic Acids Res. 2005; 2005 Nov 27. PMID: 16314300.
- An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.Schmeing TM, Huang KS, Strobel SA, Steitz TA. Nature. 2005 Nov 24. PMID: 16306996.
- Modulation of cell function by small transmembrane proteins modeled on the bovine papillomavirus E5 protein.Freeman-Cook LL, Dimaio D. Oncogene. 2005 Nov 21. PMID: 16299535.
- Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3.Fedorova O, Pyle AM. EMBO J. 2005 Nov 16; 2005 Oct 27. PMID: 16252007.
- TLR-dependent IL-4 production by invariant Valpha14+Jalpha18+ NKT cells to initiate contact sensitivity in vivo.Askenase PW, Itakura A, Leite-de-Moraes MC, Lisbonne M, Roongapinun S, Goldstein DR, Szczepanik M. J Immunol. 2005 Nov 15. PMID: 16272291.
- Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. Mol Cell. 2005 Nov 11. PMID: 16285925.
- Innate control of adaptive immunity via remodeling of lymph node feed arteriole.Soderberg KA, Payne GW, Sato A, Medzhitov R, Segal SS, Iwasaki A. Proc Natl Acad Sci U S A. 2005 Nov 8; 2005 Oct 31. PMID: 16260739.
- Asymmetric behavior of archaeal prolyl-tRNA synthetase.Ambrogelly A, Kamtekar S, Stathopoulos C, Kennedy D, Söll D. FEBS Lett. 2005 Nov 7; 2005 Oct 5. PMID: 16226256.
- Targeted genome modification via triple helix formation.Kalish JM, Glazer PM. Ann N Y Acad Sci. 2005 Nov. PMID: 16394134.
- Alterations in DNA repair gene expression under hypoxia: elucidating the mechanisms of hypoxia-induced genetic instability.Bindra RS, Schaffer PJ, Meng A, Woo J, Måseide K, Roth ME, Lizardi P, Hedley DW, Bristow RG, Glazer PM. Ann N Y Acad Sci. 2005 Nov. PMID: 16382054.
- Evolution of mutational robustness in an RNA virus.Montville R, Froissart R, Remold SK, Tenaillon O, Turner PE. PLoS Biol. 2005 Nov; 2005 Nov 1. PMID: 16248678.
- Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.Penchovsky R, Breaker RR. Nat Biotechnol. 2005 Nov; 2005 Oct 23. PMID: 16244657.
- JNK1 is essential for CD8+ T cell-mediated tumor immune surveillance.Gao Y, Tao J, Li MO, Zhang D, Chi H, Henegariu O, Kaech SM, Davis RJ, Flavell RA, Yin Z. J Immunol. 2005 Nov 1. PMID: 16237070.
- Symplekin and multiple other polyadenylation factors participate in 3'-end maturation of histone mRNAs.Kolev NG, Steitz JA. Genes Dev. 2005 Nov 1; 2005 Oct 17. PMID: 16230528.
- Alphavbeta3-targeted detection of arteriopathy in transplanted human coronary arteries: an autoradiographic study.Zhang J, Krassilnikova S, Gharaei AA, Fassaei HR, Esmailzadeh L, Asadi A, Edwards DS, Harris TD, Azure M, Tellides G, Sinusas AJ, Zaret BL, Bender JR, Sadeghi MM. FASEB J. 2005 Nov; 2005 Sep 8. PMID: 16150802.
- Repression of gene expression by the coliphage MS2 coat protein in Trypanosoma brucei.Shi H, Djikeng A, Chamond N, Ngô H, Tschudi C, Ullu E. Mol Biochem Parasitol. 2005 Nov. PMID: 16139377.
- Downregulation of the essential Trypanosoma brucei La protein affects accumulation of elongator methionyl-tRNA.Arhin GK, Shen S, Pérez IF, Tschudi C, Ullu E. Mol Biochem Parasitol. 2005 Nov. PMID: 16055205.
- Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.Coric T, Zheng D, Gerstein M, Canessa CM. J Physiol. 2005 Nov 1; 2005 Jul 7. PMID: 16002453.
- Integration of engrafted Schwann cells into injured peripheral nerve: axonal association and nodal formation on regenerated axons.Radtke C, Akiyama Y, Lankford KL, Vogt PM, Krause DS, Kocsis JD. Neurosci Lett. 2005 Oct 21. PMID: 16084645.
- Sequence variants in SLITRK1 are associated with Tourette's syndrome.Abelson JF, Kwan KY, O'Roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LS 4th, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW. Science. 2005 Oct 14. PMID: 16224024.
- The kinetics of ligand binding by an adenine-sensing riboswitch.Wickiser JK, Cheah MT, Breaker RR, Crothers DM. Biochemistry. 2005 Oct 11. PMID: 16201765.
- Expression of DNA polymerase {beta} cancer-associated variants in mouse cells results in cellular transformation.Sweasy JB, Lang T, Starcevic D, Sun KW, Lai CC, Dimaio D, Dalal S. Proc Natl Acad Sci U S A. 2005 Oct 4; 2005 Sep 22. PMID: 16179390.
- Virus-induced gene silencing is an effective tool for assaying gene function in the basal eudicot species Papaver somniferum (opium poppy).Hileman LC, Drea S, Martino G, Litt A, Irish VF. Plant J. 2005 Oct. PMID: 16212610.
- Cytokines and cardiovascular disease.Mehra VC, Ramgolam VS, Bender JR. J Leukoc Biol. 2005 Oct; 2005 Jul 8. PMID: 16006537.
- Structural evidence for a two-metal-ion mechanism of group I intron splicing.Stahley MR, Strobel SA. Science. 2005 Sep 2. PMID: 16141079.
- Capping by branching: a new ribozyme makes tiny lariats.Pyle AM. Science. 2005 Sep 2. PMID: 16141065.
- A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW. Plant Mol Biol. 2005 Sep. PMID: 16217608.
- Molecular basis for RNA kink-turn recognition by the h15.5K small RNP protein.Szewczak LB, Gabrielsen JS, Degregorio SJ, Strobel SA, Steitz JA. RNA. 2005 Sep. PMID: 16120832.
- Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.Nakayama N, Arroyo JM, Simorowski J, May B, Martienssen R, Irish VF. Plant Cell. 2005 Sep; 2005 Jul 29. PMID: 16055634.
- Structure of a synaptic gammadelta resolvase tetramer covalently linked to two cleaved DNAs.Li W, Kamtekar S, Xiong Y, Sarkis GJ, Grindley ND, Steitz TA. Science. 2005 Aug 19; 2005 Jun 30. PMID: 15994378.
- Selective inhibition of divergent seryl-tRNA synthetases by serine analogues.Ahel D, Slade D, Mocibob M, Söll D, Weygand-Durasevic I. FEBS Lett. 2005 Aug 15. PMID: 16054140.
- Endothelial nitric oxide synthase is critical for ischemic remodeling, mural cell recruitment, and blood flow reserve.Yu J, deMuinck ED, Zhuang Z, Drinane M, Kauser K, Rubanyi GM, Qian HS, Murata T, Escalante B, Sessa WC. Proc Natl Acad Sci U S A. 2005 Aug 2; 2005 Jul 25. PMID: 16043715.
- The importance of National Blood Foundation funding.Krause DS. Transfusion. 2005 Aug. PMID: 16086791.
- Akt1/protein kinase Balpha is critical for ischemic and VEGF-mediated angiogenesis.Ackah E, Yu J, Zoellner S, Iwakiri Y, Skurk C, Shibata R, Ouchi N, Easton RM, Galasso G, Birnbaum MJ, Walsh K, Sessa WC. J Clin Invest. 2005 Aug. PMID: 16075056.
- Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Trends Genet. 2005 Aug. PMID: 15979196.
- Flower development and evolution: gene duplication, diversification and redeployment.Irish VF, Litt A. Curr Opin Genet Dev. 2005 Aug. PMID: 15964755.
- Toll-like receptor 9 controls anti-DNA autoantibody production in murine lupus.Christensen SR, Kashgarian M, Alexopoulou L, Flavell RA, Akira S, Shlomchik MJ. J Exp Med. 2005 Jul 18. PMID: 16027240.
- Sugar-coated regulation of T cells.Eynon EE, Zenewicz LA, Flavell RA. Cell. 2005 Jul 15. PMID: 16009124.
- The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase.Ruan B, Söll D. J Biol Chem. 2005 Jul 8; 2005 May 10. PMID: 15886196.
- Triplex-forming oligonucleotides as potential tools for modulation of gene expression.Rogers FA, Lloyd JA, Glazer PM. Curr Med Chem Anticancer Agents. 2005 Jul. PMID: 16101484.
- Assessing the limits of genomic data integration for predicting protein networks.Lu LJ, Xia Y, Paccanaro A, Yu H, Gerstein M. Genome Res. 2005 Jul. PMID: 15998909.
- Triplex-induced recombination and repair in the pyrimidine motif.Kalish JM, Seidman MM, Weeks DL, Glazer PM. Nucleic Acids Res. 2005; 2005 Jun 16. PMID: 15961731.
- Role of cathepsin S-dependent epithelial cell apoptosis in IFN-gamma-induced alveolar remodeling and pulmonary emphysema.Zheng T, Kang MJ, Crothers K, Zhu Z, Liu W, Lee CG, Rabach LA, Chapman HA, Homer RJ, Aldous D, De Sanctis GT, Underwood S, Graupe M, Flavell RA, Schmidt JA, Elias JA. J Immunol. 2005 Jun 15. PMID: 15944319.
- Rapid, estrogen receptor-mediated signaling: why is the endothelium so special?Kim KH, Bender JR. Sci STKE. 2005 Jun 14; 2005 Jun 14. PMID: 15956360.
- Interchromosomal associations between alternatively expressed loci.Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. Nature. 2005 Jun 2; 2005 May 8. PMID: 15880101.
- Hsp90-Akt phosphorylates ASK1 and inhibits ASK1-mediated apoptosis.Zhang R, Luo D, Miao R, Bai L, Ge Q, Sessa WC, Min W. Oncogene. 2005 Jun 2. PMID: 15782121.
- YeastHub: a semantic web use case for integrating data in the life sciences domain.Cheung KH, Yip KY, Smith A, Deknikker R, Masiar A, Gerstein M. Bioinformatics. 2005 Jun. PMID: 15961502.
- Engraftment of bone marrow-derived epithelial cells.Krause DS. Ann N Y Acad Sci. 2005 Jun. PMID: 15958704.
- Small sense and antisense RNAs derived from a telomeric retroposon family in Giardia intestinalis.Ullu E, Lujan HD, Tschudi C. Eukaryot Cell. 2005 Jun. PMID: 15947207.
- Riboswitches as versatile gene control elements.Tucker BJ, Breaker RR. Curr Opin Struct Biol. 2005 Jun. PMID: 15919195.
- Activation of NF-kappaB promotes the transition of large, CD43+ pre-B cells to small, CD43- pre-B cells.Jimi E, Phillips RJ, Rincon M, Voll R, Karasuyama H, Flavell R, Ghosh S. Int Immunol. 2005 Jun; 2005 May 20. PMID: 15908447.
- Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing.Granneman S, Baserga SJ. Curr Opin Cell Biol. 2005 Jun. PMID: 15901498.
- Transforming growth factor-beta controls T helper type 1 cell development through regulation of natural killer cell interferon-gamma.Laouar Y, Sutterwala FS, Gorelik L, Flavell RA. Nat Immunol. 2005 Jun; 2005 Apr 24. PMID: 15852008.
- Integrated pseudogene annotation for human chromosome 22: evidence for transcription.Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. J Mol Biol. 2005 May 27; 2005 Apr 2. PMID: 15876366.
- Aspartyl-tRNA synthetase requires a conserved proline in the anticodon-binding loop for tRNA(Asn) recognition in vivo.Feng L, Yuan J, Toogood H, Tumbula-Hansen D, Söll D. J Biol Chem. 2005 May 27; 2005 Mar 21. PMID: 15781458.
- Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the expression of genes linked to T cell activation in virally transformed T cells.Cook HL, Lytle JR, Mischo HE, Li MJ, Rossi JJ, Silva DP, Desrosiers RC, Steitz JA. Curr Biol. 2005 May 24. PMID: 15916956.
- N6-Acetyladenosine: a new modified nucleoside from Methanopyrus kandleri tRNA.Sauerwald A, Sitaramaiah D, McCloskey JA, Söll D, Crain PF. FEBS Lett. 2005 May 23; 2005 Apr 21. PMID: 15907485.
- The complete set of tRNA species in Nanoarchaeum equitans.Randau L, Pearson M, Söll D. FEBS Lett. 2005 May 23. PMID: 15893316.
- Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity.Stein AJ, Fuchs G, Fu C, Wolin SL, Reinisch KM. Cell. 2005 May 20. PMID: 15907467.
- A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts.Conrad NK, Steitz JA. EMBO J. 2005 May 18; 2005 Apr 28. PMID: 15861127.
- Uncovering the enzymatic pKa of the ribosomal peptidyl transferase reaction utilizing a fluorinated puromycin derivative.Okuda K, Seila AC, Strobel SA. Biochemistry. 2005 May 3. PMID: 15850401.
- Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles.Gilad Y, Rifkin SA, Bertone P, Gerstein M, White KP. Genome Res. 2005 May. PMID: 15867429.
- Vascular cell signaling by membrane estrogen receptors.Hisamoto K, Bender JR. Steroids. 2005 May-Jun; 2005 Mar 16. PMID: 15862821.
- TGF-beta signaling regulates CD8+ T cell responses to high- and low-affinity TCR interactions.Mehal WZ, Sheikh SZ, Gorelik L, Flavell RA. Int Immunol. 2005 May; 2005 Apr 11. PMID: 15824070.
- 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. RNA. 2005 May; 2005 Apr 5. PMID: 15811922.
- Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.Tu D, Blaha G, Moore PB, Steitz TA. Cell. 2005 Apr 22. PMID: 15851032.
- Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter.Wan YY, Flavell RA. Proc Natl Acad Sci U S A. 2005 Apr 5; 2005 Mar 28. PMID: 15795373.
- IL-1 receptor-associated kinase M is a central regulator of osteoclast differentiation and activation.Li H, Cuartas E, Cui W, Choi Y, Crawford TD, Ke HZ, Kobayashi KS, Flavell RA, Vignery A. J Exp Med. 2005 Apr 4. PMID: 15809356.
- The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch.Wickiser JK, Winkler WC, Breaker RR, Crothers DM. Mol Cell. 2005 Apr 1. PMID: 15808508.
- RNA-dependent cysteine biosynthesis in archaea.Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR 3rd, Ibba M, Söll D. Science. 2005 Mar 25. PMID: 15790858.
- Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms.Balasubramanian S, Xia Y, Freinkman E, Gerstein M. Nucleic Acids Res. 2005; 2005 Mar 22. PMID: 15784611.
- Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction.Seila AC, Okuda K, Núñez S, Seila AF, Strobel SA. Biochemistry. 2005 Mar 15. PMID: 15751978.
- Distance and affinity dependence of triplex-induced recombination.Knauert MP, Lloyd JA, Rogers FA, Datta HJ, Bennett ML, Weeks DL, Glazer PM. Biochemistry. 2005 Mar 15. PMID: 15751961.
- Loss of mitogen-activated protein kinase kinase kinase 4 (MEKK4) results in enhanced apoptosis and defective neural tube development.Chi H, Sarkisian MR, Rakic P, Flavell RA. Proc Natl Acad Sci U S A. 2005 Mar 8; 2005 Feb 24. PMID: 15731347.
- SRprises along a messenger's journey.Huang Y, Steitz JA. Mol Cell. 2005 Mar 4. PMID: 15749011.
- Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.Feng L, Sheppard K, Tumbula-Hansen D, Söll D. J Biol Chem. 2005 Mar 4; 2004 Dec 16. PMID: 15611111.
- Regulation of endothelial derived nitric oxide in health and disease.Sessa WC. Mem Inst Oswaldo Cruz. 2005 Mar; 2005 Jun 14. PMID: 15962093.
- Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei.Li H, Tschudi C. Mol Cell Biol. 2005 Mar. PMID: 15743819.
- The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans.Grosshans H, Johnson T, Reinert KL, Gerstein M, Slack FJ. Dev Cell. 2005 Mar. PMID: 15737928.
- Cutting edge: regulation of T cell trafficking and primary immune responses by sphingosine 1-phosphate receptor 1.Chi H, Flavell RA. J Immunol. 2005 Mar 1. PMID: 15728452.
- Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M. Protein Sci. 2005 Mar. PMID: 15722444.
- Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion.Rinehart J, Krett B, Rubio MA, Alfonzo JD, Söll D. Genes Dev. 2005 Mar 1; 2005 Feb 10. PMID: 15706032.
- T cells from epicutaneously immunized mice are prone to T cell receptor revision.Bynoe MS, Viret C, Flavell RA, Janeway CA Jr. Proc Natl Acad Sci U S A. 2005 Feb 22; 2005 Feb 11. PMID: 15708975.
- On the structural basis of peptide-bond formation and antibiotic resistance from atomic structures of the large ribosomal subunit.Steitz TA. FEBS Lett. 2005 Feb 7. PMID: 15680981.
- Nod2-dependent regulation of innate and adaptive immunity in the intestinal tract.Kobayashi KS, Chamaillard M, Ogura Y, Henegariu O, Inohara N, Nuñez G, Flavell RA. Science. 2005 Feb 4. PMID: 15692051.
- Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves.Randau L, Münch R, Hohn MJ, Jahn D, Söll D. Nature. 2005 Feb 3. PMID: 15690044.
- Productive interaction between transmembrane mutants of the bovine papillomavirus E5 protein and the platelet-derived growth factor beta receptor.Lai CC, Edwards AP, DiMaio D. J Virol. 2005 Feb. PMID: 15650217.
- Engineered allosteric ribozymes that respond to specific divalent metal ions.Zivarts M, Liu Y, Breaker RR. Nucleic Acids Res. 2005; 2005 Jan 28. PMID: 15681614.
- Specific locations of hydrophilic amino acids in constructed transmembrane ligands of the platelet-derived growth factor beta receptor.Freeman-Cook LL, Edwards AP, Dixon AM, Yates KE, Ely L, Engelman DM, Dimaio D. J Mol Biol. 2005 Jan 28. PMID: 15588835.
- Dissecting the molecular control of endothelial NO synthase by caveolin-1 using cell-permeable peptides.Bernatchez PN, Bauer PM, Yu J, Prendergast JS, He P, Sessa WC. Proc Natl Acad Sci U S A. 2005 Jan 18; 2005 Jan 6. PMID: 15637154.
- An embryonic poly(A)-binding protein (ePAB) is expressed in mouse oocytes and early preimplantation embryos.Seli E, Lalioti MD, Flaherty SM, Sakkas D, Terzi N, Steitz JA. Proc Natl Acad Sci U S A. 2005 Jan 11; 2005 Jan 3. PMID: 15630085.
- Requirement of voltage-gated calcium channel beta4 subunit for T lymphocyte functions.Badou A, Basavappa S, Desai R, Peng YQ, Matza D, Mehal WZ, Kaczmarek LK, Boulpaep EL, Flavell RA. Science. 2005 Jan 7. PMID: 15637280.
- A unique hydrophobic cluster near the active site contributes to differences in borrelidin inhibition among threonyl-tRNA synthetases.Ruan B, Bovee ML, Sacher M, Stathopoulos C, Poralla K, Francklyn CS, Söll D. J Biol Chem. 2005 Jan 7; 2004 Oct 26. PMID: 15507440.
- Genetic instability and the tumor microenvironment: towards the concept of microenvironment-induced mutagenesis.Bindra RS, Glazer PM. Mutat Res. 2005 Jan 6. PMID: 15603753.
- Endothelial-specific expression of caveolin-1 impairs microvascular permeability and angiogenesis.Bauer PM, Yu J, Chen Y, Hickey R, Bernatchez PN, Looft-Wilson R, Huang Y, Giordano F, Stan RV, Sessa WC. Proc Natl Acad Sci U S A. 2005 Jan 4; 2004 Dec 22. PMID: 15615855.
- Engraftment of bone marrow-derived epithelial cells.Van Arnam JS, Herzog E, Grove J, Bruscia E, Ziegler E, Swenson S, Krause DS. Stem Cell Rev. 2005. PMID: 17132871.
- T-cells in Alzheimer's disease.Town T, Tan J, Flavell RA, Mullan M. Neuromolecular Med. 2005. PMID: 16247185.
- A weed for all reasons.Irish VF, Day CD. Genome Biol. 2005; 2005 Sep 28. PMID: 16207368.
- Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.Smith A, Greenbaum D, Douglas SM, Long M, Gerstein M. Genome Biol. 2005; 2005 Aug 30. PMID: 16168090.
- PubNet: a flexible system for visualizing literature derived networks.Douglas SM, Montelione GT, Gerstein M. Genome Biol. 2005; 2005 Aug 16. PMID: 16168087.
- Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Genome Biol. 2005; 2005 Aug 1. PMID: 16086852.
- Development of a parathyroid hormone-controlled release system as a potential surgical treatment for hypoparathyroidism.Anthony T, Fong P, Goyal A, Saltzman WM, Moss RL, Breuer C. J Pediatr Surg. 2005 Jan. PMID: 15868563.
- Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery.Bertone P, Gerstein M, Snyder M. Chromosome Res. 2005. PMID: 15868420.
- Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions.Lee GR, Spilianakis CG, Flavell RA. Nat Immunol. 2005 Jan; 2004 Dec 19. PMID: 15608641.
- Correction of X-ray intensities from single crystals containing lattice-translocation defects.Wang J, Kamtekar S, Berman AJ, Steitz TA. Acta Crystallogr D Biol Crystallogr. 2005 Jan; 2004 Dec 17. PMID: 15608377.
- A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. J Am Med Inform Assoc. 2005 Jan-Feb; 2004 Oct 18. PMID: 15492032.
2004
- Splicing of U12-type introns deposits an exon junction complex competent to induce nonsense-mediated mRNA decay.Hirose T, Shu MD, Steitz JA. Proc Natl Acad Sci U S A. 2004 Dec 28; 2004 Dec 17. PMID: 15608055.
- Global identification of human transcribed sequences with genome tiling arrays.Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Science. 2004 Dec 24; 2004 Nov 11. PMID: 15539566.
- DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D. Proc Natl Acad Sci U S A. 2004 Dec 21; 2004 Dec 10. PMID: 15591350.
- Natural and engineered nucleic acids as tools to explore biology.Breaker RR. Nature. 2004 Dec 16. PMID: 15602549.
- Peptide conjugates for chromosomal gene targeting by triplex-forming oligonucleotides.Rogers FA, Manoharan M, Rabinovitch P, Ward DC, Glazer PM. Nucleic Acids Res. 2004; 2004 Dec 15. PMID: 15602001.
- Involvement of dendritic cell subsets in the induction of oral tolerance and immunity.Fleeton M, Contractor N, Leon F, He J, Wetzel D, Dermody T, Iwasaki A, Kelsall B. Ann N Y Acad Sci. 2004 Dec. PMID: 15681744.
- Antiangiogenic therapy: creating a unique "window" of opportunity.Lin MI, Sessa WC. Cancer Cell. 2004 Dec. PMID: 15607955.
- The small-subunit processome is a ribosome assembly intermediate.Bernstein KA, Gallagher JE, Mitchell BM, Granneman S, Baserga SJ. Eukaryot Cell. 2004 Dec. PMID: 15590835.
- Selection and characterization of RNA interference-deficient trypanosomes impaired in target mRNA degradation.Shi H, Chamond N, Tschudi C, Ullu E. Eukaryot Cell. 2004 Dec. PMID: 15590819.
- Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region.Fields PE, Lee GR, Kim ST, Bartsevich VV, Flavell RA. Immunity. 2004 Dec. PMID: 15589174.
- Toll-like receptor 3 mediates West Nile virus entry into the brain causing lethal encephalitis.Wang T, Town T, Alexopoulou L, Anderson JF, Fikrig E, Flavell RA. Nat Med. 2004 Dec; 2004 Nov 21. PMID: 15558055.
- Crystal structure of a group I intron splicing intermediate.Adams PL, Stahley MR, Gill ML, Kosek AB, Wang J, Strobel SA. RNA. 2004 Dec. PMID: 15547134.
- RNA kink turns to the left and to the right.Strobel SA, Adams PL, Stahley MR, Wang J. RNA. 2004 Dec. PMID: 15547133.
- Function of the Trypanosome Argonaute 1 protein in RNA interference requires the N-terminal RGG domain and arginine 735 in the Piwi domain.Shi H, Ullu E, Tschudi C. J Biol Chem. 2004 Nov 26; 2004 Sep 21. PMID: 15383544.
- Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa.Tycowski KT, Aab A, Steitz JA. Curr Biol. 2004 Nov 23. PMID: 15556860.
- Stromal cell-derived factor-1alpha plays a critical role in stem cell recruitment to the heart after myocardial infarction but is not sufficient to induce homing in the absence of injury.Abbott JD, Huang Y, Liu D, Hickey R, Krause DS, Giordano FJ. Circulation. 2004 Nov 23; 2004 Nov 8. PMID: 15533866.
- Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29.Kamtekar S, Berman AJ, Wang J, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. Mol Cell. 2004 Nov 19. PMID: 15546620.
- Differential modes of transfer RNASer recognition in Methanosarcina barkeri.Korencic D, Polycarpo C, Weygand-Durasevic I, Söll D. J Biol Chem. 2004 Nov 19; 2004 Sep 13. PMID: 15364939.
- Induction of antiviral immunity requires Toll-like receptor signaling in both stromal and dendritic cell compartments.Sato A, Iwasaki A. Proc Natl Acad Sci U S A. 2004 Nov 16; 2004 Nov 8. PMID: 15534227.
- Reduced fecundity is the cost of cheating in RNA virus phi6.Dennehy JJ, Turner PE. Proc Biol Sci. 2004 Nov 7. PMID: 15539353.
- Bone marrow-derived cells contribute to epithelial engraftment during wound healing.Borue X, Lee S, Grove J, Herzog EL, Harris R, Diflo T, Glusac E, Hyman K, Theise ND, Krause DS. Am J Pathol. 2004 Nov. PMID: 15509544.
- Functional characterization of a Trypanosoma brucei TATA-binding protein-related factor points to a universal regulator of transcription in trypanosomes.Ruan JP, Arhin GK, Ullu E, Tschudi C. Mol Cell Biol. 2004 Nov. PMID: 15485927.
- Substrate-assisted catalysis of peptide bond formation by the ribosome.Weinger JS, Parnell KM, Dorner S, Green R, Strobel SA. Nat Struct Mol Biol. 2004 Nov; 2004 Oct 10. PMID: 15475967.
- Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses.Mili S, Steitz JA. RNA. 2004 Nov; 2004 Sep 23. PMID: 15388877.
- The small subunit processome is required for cell cycle progression at G1.Bernstein KA, Baserga SJ. Mol Biol Cell. 2004 Nov; 2004 Sep 8. PMID: 15356263.
- RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components.Gallagher JE, Dunbar DA, Granneman S, Mitchell BM, Osheim Y, Beyer AL, Baserga SJ. Genes Dev. 2004 Oct 15. PMID: 15489292.
- Regulation of gene expression by a metabolic enzyme.Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. Science. 2004 Oct 15. PMID: 15486299.
- A glycine-dependent riboswitch that uses cooperative binding to control gene expression.Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. Science. 2004 Oct 8. PMID: 15472076.
- Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon.Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M. Genome Res. 2004 Oct. PMID: 15466296.
- Toll-like receptor control of the adaptive immune responses.Iwasaki A, Medzhitov R. Nat Immunol. 2004 Oct. PMID: 15454922.
- Airway hyper-reactivity mediated by B-1 cell immunoglobulin M antibody generating complement C5a at 1 day post-immunization in a murine hapten model of non-atopic asthma.Kawikova I, Paliwal V, Szczepanik M, Itakura A, Fukui M, Campos RA, Geba GP, Homer RJ, Iliopoulou BP, Pober JS, Tsuji RF, Askenase PW. Immunology. 2004 Oct. PMID: 15379984.
- Long-range intrachromosomal interactions in the T helper type 2 cytokine locus.Spilianakis CG, Flavell RA. Nat Immunol. 2004 Oct; 2004 Sep 19. PMID: 15378057.
- Down-regulation of Rad51 and decreased homologous recombination in hypoxic cancer cells.Bindra RS, Schaffer PJ, Meng A, Woo J, Måseide K, Roth ME, Lizardi P, Hedley DW, Bristow RG, Glazer PM. Mol Cell Biol. 2004 Oct. PMID: 15367671.
- Impaired PtdIns(4,5)P2 synthesis in nerve terminals produces defects in synaptic vesicle trafficking.Di Paolo G, Moskowitz HS, Gipson K, Wenk MR, Voronov S, Obayashi M, Flavell R, Fitzsimonds RM, Ryan TA, De Camilli P. Nature. 2004 Sep 23. PMID: 15386003.
- Genomic analysis of regulatory network dynamics reveals large topological changes.Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Nature. 2004 Sep 16. PMID: 15372033.
- Probing RNA structure and function by nucleotide analog interference mapping.Cochrane JC, Strobel SA. Curr Protoc Nucleic Acid Chem. 2004 Sep. PMID: 18428931.
- Co-infection weakens selection against epistatic mutations in RNA viruses.Froissart R, Wilke CO, Montville R, Remold SK, Chao L, Turner PE. Genetics. 2004 Sep. PMID: 15454523.
- T cell-mediated vascular dysfunction of human allografts results from IFN-gamma dysregulation of NO synthase.Koh KP, Wang Y, Yi T, Shiao SL, Lorber MI, Sessa WC, Tellides G, Pober JS. J Clin Invest. 2004 Sep. PMID: 15372109.
- The contribution of metal ions to the structural stability of the large ribosomal subunit.Klein DJ, Moore PB, Steitz TA. RNA. 2004 Sep. PMID: 15317974.
- An aminoacyl-tRNA synthetase that specifically activates pyrrolysine.Polycarpo C, Ambrogelly A, Bérubé A, Winbush SM, McCloskey JA, Crain PF, Wood JL, Söll D. Proc Natl Acad Sci U S A. 2004 Aug 24; 2004 Aug 16. PMID: 15314242.
- Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template.Xiong Y, Steitz TA. Nature. 2004 Aug 5. PMID: 15295590.
- Early growth response gene 1-mediated apoptosis is essential for transforming growth factor beta1-induced pulmonary fibrosis.Lee CG, Cho SJ, Kang MJ, Chapoval SP, Lee PJ, Noble PW, Yehualaeshet T, Lu B, Flavell RA, Milbrandt J, Homer RJ, Elias JA. J Exp Med. 2004 Aug 2. PMID: 15289506.
- Role of a 300-kilodalton nuclear complex in the maturation of Trypanosoma brucei initiator methionyl-tRNA.Arhin GK, Shen S, Irmer H, Ullu E, Tschudi C. Eukaryot Cell. 2004 Aug. PMID: 15302822.
- Extravascular T-cell recruitment requires initiation begun by Valpha14+ NKT cells and B-1 B cells.Askenase PW, Szczepanik M, Itakura A, Kiener C, Campos RA. Trends Immunol. 2004 Aug. PMID: 15275644.
- MAdCAM-1 expressing sacral lymph node in the lymphotoxin beta-deficient mouse provides a site for immune generation following vaginal herpes simplex virus-2 infection.Soderberg KA, Linehan MM, Ruddle NH, Iwasaki A. J Immunol. 2004 Aug 1. PMID: 15265924.
- Large-scale analysis of pseudogenes in the human genome.Zhang Z, Gerstein M. Curr Opin Genet Dev. 2004 Aug. PMID: 15261647.
- Transgenic mice which overproduce Th2 cytokines develop spontaneous atopic dermatitis and asthma.Lee GR, Flavell RA. Int Immunol. 2004 Aug; 2004 Jun 28. PMID: 15226271.
- Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase.Serebrov V, Pyle AM. Nature. 2004 Jul 22. PMID: 15269774.
- Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors.Pata JD, Stirtan WG, Goldstein SW, Steitz TA. Proc Natl Acad Sci U S A. 2004 Jul 20; 2004 Jul 12. PMID: 15249669.
- Targeting of endothelial nitric-oxide synthase to the cytoplasmic face of the Golgi complex or plasma membrane regulates Akt- versus calcium-dependent mechanisms for nitric oxide release.Fulton D, Babbitt R, Zoellner S, Fontana J, Acevedo L, McCabe TJ, Iwakiri Y, Sessa WC. J Biol Chem. 2004 Jul 16; 2004 May 10. PMID: 15136572.
- Exploration of the conserved A+C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes.Hesslein AE, Katunin VI, Beringer M, Kosek AB, Rodnina MV, Strobel SA. Nucleic Acids Res. 2004; 2004 Jul 15. PMID: 15256541.
- A freestanding proofreading domain is required for protein synthesis quality control in Archaea.Korencic D, Ahel I, Schelert J, Sacher M, Ruan B, Stathopoulos C, Blum P, Ibba M, Söll D. Proc Natl Acad Sci U S A. 2004 Jul 13; 2004 Jul 6. PMID: 15240874.
- Detection of injury-induced vascular remodeling by targeting activated alphavbeta3 integrin in vivo.Sadeghi MM, Krassilnikova S, Zhang J, Gharaei AA, Fassaei HR, Esmailzadeh L, Kooshkabadi A, Edwards S, Yalamanchili P, Harris TD, Sinusas AJ, Zaret BL, Bender JR. Circulation. 2004 Jul 6; 2004 Jun 21. PMID: 15210600.
- Lack of a fusion requirement for development of bone marrow-derived epithelia.Harris RG, Herzog EL, Bruscia EM, Grove JE, Van Arnam JS, Krause DS. Science. 2004 Jul 2. PMID: 15232107.
- Crystal structure of a self-splicing group I intron with both exons.Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. Nature. 2004 Jul 1; 2004 Jun 2. PMID: 15175762.
- A molecular link between SR protein dephosphorylation and mRNA export.Huang Y, Yario TA, Steitz JA. Proc Natl Acad Sci U S A. 2004 Jun 29; 2004 Jun 21. PMID: 15210956.
- Beyond Arabidopsis. Translational biology meets evolutionary developmental biology.Irish VF, Benfey PN. Plant Physiol. 2004 Jun. PMID: 15208409.
- Major molecular differences between mammalian sexes are involved in drug metabolism and renal function.Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. Dev Cell. 2004 Jun. PMID: 15177028.
- Computer security in academia-a potential roadblock to distributed annotation of the human genome.Greenbaum D, Douglas SM, Smith A, Lim J, Fischer M, Schultz M, Gerstein M. Nat Biotechnol. 2004 Jun. PMID: 15175700.
- Gene regulation by riboswitches.Mandal M, Breaker RR. Nat Rev Mol Cell Biol. 2004 Jun. PMID: 15173824.
- Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Genome Res. 2004 Jun. PMID: 15173116.
- Genomic analysis of essentiality within protein networks.Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Trends Genet. 2004 Jun. PMID: 15145574.
- RNA interference in protozoan parasites.Ullu E, Tschudi C, Chakraborty T. Cell Microbiol. 2004 Jun. PMID: 15104593.
- A truncated aminoacyl-tRNA synthetase modifies RNA.Salazar JC, Ambrogelly A, Crain PF, McCloskey JA, Söll D. Proc Natl Acad Sci U S A. 2004 May 18; 2004 Apr 19. PMID: 15096612.
- eNOS at a glance.Sessa WC. J Cell Sci. 2004 May 15. PMID: 15159447.
- Ribosome biogenesis: of knobs and RNA processing.Granneman S, Baserga SJ. Exp Cell Res. 2004 May 15. PMID: 15120992.
- Instruction of distinct CD4 T helper cell fates by different notch ligands on antigen-presenting cells.Amsen D, Blander JM, Lee GR, Tanigaki K, Honjo T, Flavell RA. Cell. 2004 May 14. PMID: 15137944.
- Selection and characterization of small random transmembrane proteins that bind and activate the platelet-derived growth factor beta receptor.Freeman-Cook LL, Dixon AM, Frank JB, Xia Y, Ely L, Gerstein M, Engelman DM, DiMaio D. J Mol Biol. 2004 May 14. PMID: 15111056.
- Aminoacyl-tRNA synthesis by pre-translational amino acid modification.Feng L, Sheppard K, Namgoong S, Ambrogelly A, Polycarpo C, Randau L, Tumbula-Hansen D, Söll D. RNA Biol. 2004 May; 2004 May 28. PMID: 17194933.
- Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu H, Zhang ZL, Engelman DM, Gerstein M. Q Rev Biophys. 2004 May. PMID: 15999419.
- Phenotypic plasticity in bacterial plasmids.Turner PE. Genetics. 2004 May. PMID: 15166133.
- Role of the retinoblastoma pathway in senescence triggered by repression of the human papillomavirus E7 protein in cervical carcinoma cells.Psyrri A, DeFilippis RA, Edwards AP, Yates KE, Manuelidis L, DiMaio D. Cancer Res. 2004 May 1. PMID: 15126344.
- The Herpesvirus saimiri small nuclear RNAs recruit AU-rich element-binding proteins but do not alter host AU-rich element-containing mRNA levels in virally transformed T cells.Cook HL, Mischo HE, Steitz JA. Mol Cell Biol. 2004 May. PMID: 15121869.
- CREB binds to multiple loci on human chromosome 22.Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. Mol Cell Biol. 2004 May. PMID: 15082775.
- New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. Proc Natl Acad Sci U S A. 2004 Apr 27; 2004 Apr 19. PMID: 15096624.
- Immunology. CD8alphaalpha and T cell memory.Kim SV, Flavell RA. Science. 2004 Apr 23. PMID: 15105485.
- Cell-interdependent cisplatin killing by Ku/DNA-dependent protein kinase signaling transduced through gap junctions.Jensen R, Glazer PM. Proc Natl Acad Sci U S A. 2004 Apr 20; 2004 Apr 6. PMID: 15069205.
- Recognition of single-stranded RNA viruses by Toll-like receptor 7.Lund JM, Alexopoulou L, Sato A, Karow M, Adams NC, Gale NW, Iwasaki A, Flavell RA. Proc Natl Acad Sci U S A. 2004 Apr 13; 2004 Mar 19. PMID: 15034168.
- GADD45beta/GADD45gamma and MEKK4 comprise a genetic pathway mediating STAT4-independent IFNgamma production in T cells.Chi H, Lu B, Takekawa M, Davis RJ, Flavell RA. EMBO J. 2004 Apr 7; 2004 Mar 25. PMID: 15044949.
- Repression of the human papillomavirus E6 gene initiates p53-dependent, telomerase-independent senescence and apoptosis in HeLa cervical carcinoma cells.Horner SM, DeFilippis RA, Manuelidis L, DiMaio D. J Virol. 2004 Apr. PMID: 15047823.
- A preclinical xenotransplantation animal model to assess human hematopoietic stem cell engraftment.Angelopoulou MK, Rinder H, Wang C, Burtness B, Cooper DL, Krause DS. Transfusion. 2004 Apr. PMID: 15043572.
- Premature termination codons do not affect the rate of splicing of neighboring introns.Lytle JR, Steitz JA. RNA. 2004 Apr. PMID: 15037775.
- Transportins 1 and 2 are redundant nuclear import factors for hnRNP A1 and HuR.Rebane A, Aab A, Steitz JA. RNA. 2004 Apr. PMID: 15037768.
- A new role for Nogo as a regulator of vascular remodeling.Acevedo L, Yu J, Erdjument-Bromage H, Miao RQ, Kim JE, Fulton D, Tempst P, Strittmatter SM, Sessa WC. Nat Med. 2004 Apr; 2004 Mar 21. PMID: 15034570.
- TGF-beta regulates in vivo expansion of Foxp3-expressing CD4+CD25+ regulatory T cells responsible for protection against diabetes.Peng Y, Laouar Y, Li MO, Green EA, Flavell RA. Proc Natl Acad Sci U S A. 2004 Mar 30; 2004 Mar 18. PMID: 15070759.
- Ligating DNA with DNA.Sreedhara A, Li Y, Breaker RR. J Am Chem Soc. 2004 Mar 24. PMID: 15025472.
- The AHNAKs are a class of giant propeller-like proteins that associate with calcium channel proteins of cardiomyocytes and other cells.Komuro A, Masuda Y, Kobayashi K, Babbitt R, Gunel M, Flavell RA, Marchesi VT. Proc Natl Acad Sci U S A. 2004 Mar 23; 2004 Mar 8. PMID: 15007166.
- Control of gene expression by a natural metabolite-responsive ribozyme.Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. Nature. 2004 Mar 18. PMID: 15029187.
- Overexpression of IL-7R alpha provides a competitive advantage during early T-cell development.Laouar Y, Crispe IN, Flavell RA. Blood. 2004 Mar 15; 2003 Oct 30. PMID: 14592827.
- Structure of the La motif: a winged helix domain mediates RNA binding via a conserved aromatic patch.Dong G, Chakshusmathi G, Wolin SL, Reinisch KM. EMBO J. 2004 Mar 10; 2004 Feb 19. PMID: 14976553.
- Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism.Liu Y, Gerstein M, Engelman DM. Proc Natl Acad Sci U S A. 2004 Mar 9; 2004 Mar 1. PMID: 14993608.
- A toll-like receptor that prevents infection by uropathogenic bacteria.Zhang D, Zhang G, Hayden MS, Greenblatt MB, Bussey C, Flavell RA, Ghosh S. Science. 2004 Mar 5. PMID: 15001781.
- Solid phase synthesis and binding affinity of peptidyl transferase transition state mimics containing 2'-OH at P-site position A76.Weinger JS, Kitchen D, Scaringe SA, Strobel SA, Muth GW. Nucleic Acids Res. 2004; 2004 Mar 3. PMID: 14999092.
- The voltage-gated potassium channel Kv1.3 regulates peripheral insulin sensitivity.Xu J, Wang P, Li Y, Li G, Kaczmarek LK, Wu Y, Koni PA, Flavell RA, Desir GV. Proc Natl Acad Sci U S A. 2004 Mar 2; 2004 Feb 23. PMID: 14981264.
- Kinetic analysis of genomewide gene expression reveals molecule circuitries that control T cell activation and Th1/2 differentiation.Lu B, Zagouras P, Fischer JE, Lu J, Li B, Flavell RA. Proc Natl Acad Sci U S A. 2004 Mar 2; 2004 Feb 20. PMID: 14978277.
- Virus induced gene silencing of a DEFICIENS ortholog in Nicotiana benthamiana.Liu Y, Nakayama N, Schiff M, Litt A, Irish VF, Dinesh-Kumar SP. Plant Mol Biol. 2004 Mar. PMID: 15356389.
- Early delayed-type hypersensitivity eosinophil infiltrates depend on T helper 2 cytokines and interferon-gamma via CXCR3 chemokines.Akahira-Azuma M, Szczepanik M, Tsuji RF, Campos RA, Itakura A, Mobini N, McNiff J, Kawikova I, Lu B, Gerard C, Pober JS, Askenase PW. Immunology. 2004 Mar. PMID: 15009431.
- Preferential presence of decorin-binding protein B (BBA25) and BBA50 antibodies in cerebrospinal fluid of patients with neurologic Lyme disease.Fikrig E, Coyle PK, Schutzer SE, Chen M, Deng Z, Flavell RA. J Clin Microbiol. 2004 Mar. PMID: 15004083.
- OspB antibody prevents Borrelia burgdorferi colonization of Ixodes scapularis.Fikrig E, Pal U, Chen M, Anderson JF, Flavell RA. Infect Immun. 2004 Mar. PMID: 14977984.
- An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes.Scamborova P, Wong A, Steitz JA. Mol Cell Biol. 2004 Mar. PMID: 14966268.
- In vivo role of nectin-1 in entry of herpes simplex virus type 1 (HSV-1) and HSV-2 through the vaginal mucosa.Linehan MM, Richman S, Krummenacher C, Eisenberg RJ, Cohen GH, Iwasaki A. J Virol. 2004 Mar. PMID: 14963155.
- Interferon-gamma plays a nonredundant role in mediating T cell-dependent outward vascular remodeling of allogeneic human coronary arteries.Wang Y, Burns WR, Tang PC, Yi T, Schechner JS, Zerwes HG, Sessa WC, Lorber MI, Pober JS, Tellides G. FASEB J. 2004 Mar; 2004 Jan 20. PMID: 14734640.
- Shielding the double-edged sword: negative regulation of the innate immune system.Kobayashi KS, Flavell RA. J Leukoc Biol. 2004 Mar; 2003 Nov 3. PMID: 14597727.
- Two-hybrid Mpp10p interaction-defective Imp4 proteins are not interaction defective in vivo but do confer specific pre-rRNA processing defects in Saccharomyces cerevisiae.Gallagher JE, Baserga SJ. Nucleic Acids Res. 2004; 2004 Feb 27. PMID: 14990745.
- The structural mechanism of translocation and helicase activity in T7 RNA polymerase.Yin YW, Steitz TA. Cell. 2004 Feb 6. PMID: 15016374.
- Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M. J Mol Biol. 2004 Feb 6. PMID: 14741208.
- Disruption of Ixodes scapularis anticoagulation by using RNA interference.Narasimhan S, Montgomery RR, DePonte K, Tschudi C, Marcantonio N, Anderson JF, Sauer JR, Cappello M, Kantor FS, Fikrig E. Proc Natl Acad Sci U S A. 2004 Feb 3; 2004 Jan 26. PMID: 14745044.
- Innate immunity and apoptosis in IBD.Lichtenberger GS, Flavell RA, Alexopoulou L. Inflamm Bowel Dis. 2004 Feb. PMID: 15168833.
- Conformational changes associated with protein-protein interactions.Goh CS, Milburn D, Gerstein M. Curr Opin Struct Biol. 2004 Feb. PMID: 15102456.
- The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase.Steitz TA. Curr Opin Struct Biol. 2004 Feb. PMID: 15102443.
- Exploring the range of protein flexibility, from a structural proteomics perspective.Gerstein M, Echols N. Curr Opin Chem Biol. 2004 Feb. PMID: 15036151.
- Histamine inhibits conducted vasodilation through endothelium-derived NO production in arterioles of mouse skeletal muscle.Payne GW, Madri JA, Sessa WC, Segal SS. FASEB J. 2004 Feb. PMID: 14769822.
- Comparative analysis of processed pseudogenes in the mouse and human genomes.Zhang Z, Carriero N, Gerstein M. Trends Genet. 2004 Feb. PMID: 14746985.
- Vanadate is a potent activator of endothelial nitric-oxide synthase: evidence for the role of the serine/threonine kinase Akt and the 90-kDa heat shock protein.Papapetropoulos A, Fulton D, Lin MI, Fontana J, McCabe TJ, Zoellner S, García-Cardeña G, Zhou Z, Gratton JP, Sessa WC. Mol Pharmacol. 2004 Feb. PMID: 14742683.
- Roles of caspase-1 in Listeria infection in mice.Tsuji NM, Tsutsui H, Seki E, Kuida K, Okamura H, Nakanishi K, Flavell RA. Int Immunol. 2004 Feb. PMID: 14734619.
- Role of L-selectin in the development of autoimmune diabetes in non-obese diabetic mice.Mora C, Grewal IS, Wong FS, Flavell RA. Int Immunol. 2004 Feb. PMID: 14734611.
- Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.Steitz TA, Yin YW. Philos Trans R Soc Lond B Biol Sci. 2004 Jan 29. PMID: 15065652.
- TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics.Yu H, Zhu X, Greenbaum D, Karro J, Gerstein M. Nucleic Acids Res. 2004; 2004 Jan 14. PMID: 14724320.
- JNK-mediated induction of cyclooxygenase 2 is required for neurodegeneration in a mouse model of Parkinson's disease.Hunot S, Vila M, Teismann P, Davis RJ, Hirsch EC, Przedborski S, Rakic P, Flavell RA. Proc Natl Acad Sci U S A. 2004 Jan 13; 2004 Jan 2. PMID: 14704277.
- Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.Alexandrov V, Gerstein M. BMC Bioinformatics. 2004 Jan 9; 2004 Jan 9. PMID: 14715091.
- Non-canonical eukaryotic glutaminyl- and glutamyl-tRNA synthetases form mitochondrial aminoacyl-tRNA in Trypanosoma brucei.Rinehart J, Horn EK, Wei D, Soll D, Schneider A. J Biol Chem. 2004 Jan 9; 2003 Oct 16. PMID: 14563839.
- Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes.Nahvi A, Barrick JE, Breaker RR. Nucleic Acids Res. 2004; 2004 Jan 2. PMID: 14704351.
- Aminoacyl-tRNA tRNA formation: an essential function in protein synthesis and its quality control.Söll D. Nucleic Acids Symp Ser (Oxf). 2004. PMID: 17150589.
- Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.Liu Y, Harrison PM, Kunin V, Gerstein M. Genome Biol. 2004; 2004 Aug 26. PMID: 15345048.
- Plasticity of bone marrow-derived stem cells.Grove JE, Bruscia E, Krause DS. Stem Cells. 2004. PMID: 15277695.
- Analyzing cellular biochemistry in terms of molecular networks.Xia Y, Yu H, Jansen R, Seringhaus M, Baxter S, Greenbaum D, Zhao H, Gerstein M. Annu Rev Biochem. 2004. PMID: 15189167.
- Analysis of gene function in Trypanosoma brucei using RNA interference.Djikeng A, Shen S, Tschudi C, Ullu E. Methods Mol Biol. 2004. PMID: 15153635.
- A PCR-based method for gene deletion and protein tagging in Trypanosoma brucei.Arhin GK, Shen S, Ullu E, Tschudi C. Methods Mol Biol. 2004. PMID: 15153634.
- Analysis of gene function in Trypanosoma brucei using RNA interference.Djikeng A, Shen S, Tschudi C, Ullu E. Methods Mol Biol. 2004. PMID: 15103069.
- Selection in vitro of allosteric ribozymes.Roth A, Breaker RR. Methods Mol Biol. 2004. PMID: 15017047.
- Targeted gene modification using triplex-forming oligonucleotides.Kuan JY, Glazer PM. Methods Mol Biol. 2004. PMID: 14769962.
- OspC facilitates Borrelia burgdorferi invasion of Ixodes scapularis salivary glands.Pal U, Yang X, Chen M, Bockenstedt LK, Anderson JF, Flavell RA, Norgard MV, Fikrig E. J Clin Invest. 2004 Jan. PMID: 14722614.
- Adenine riboswitches and gene activation by disruption of a transcription terminator.Mandal M, Breaker RR. Nat Struct Mol Biol. 2004 Jan; 2003 Dec 29. PMID: 14718920.
- Gadd45beta is important for perpetuating cognate and inflammatory signals in T cells.Lu B, Ferrandino AF, Flavell RA. Nat Immunol. 2004 Jan; 2003 Dec 14. PMID: 14691480.
- Cysteinyl-tRNA(Cys) formation in Methanocaldococcus jannaschii: the mechanism is still unknown.Ruan B, Nakano H, Tanaka M, Mills JA, DeVito JA, Min B, Low KB, Battista JR, Söll D. J Bacteriol. 2004 Jan. PMID: 14679218.
- Argonaute protein in the early divergent eukaryote Trypanosoma brucei: control of small interfering RNA accumulation and retroposon transcript abundance.Shi H, Djikeng A, Tschudi C, Ullu E. Mol Cell Biol. 2004 Jan. PMID: 14673174.
- Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans.Reinke V, Gil IS, Ward S, Kazmer K. Development. 2004 Jan; 2003 Dec 10. PMID: 14668411.
2003
- Trans-editing of mischarged tRNAs.Ahel I, Korencic D, Ibba M, Söll D. Proc Natl Acad Sci U S A. 2003 Dec 23; 2003 Dec 8. PMID: 14663147.
- The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation.Chen X, Smith JD, Shi H, Yang DD, Flavell RA, Wolin SL. Curr Biol. 2003 Dec 16. PMID: 14680639.
- Cutaneous immunization rapidly activates liver invariant Valpha14 NKT cells stimulating B-1 B cells to initiate T cell recruitment for elicitation of contact sensitivity.Campos RA, Szczepanik M, Itakura A, Akahira-Azuma M, Sidobre S, Kronenberg M, Askenase PW. J Exp Med. 2003 Dec 15. PMID: 14676294.
- Relationship between gene co-expression and probe localization on microarray slides.Kluger Y, Yu H, Qian J, Gerstein M. BMC Genomics. 2003 Dec 10; 2003 Dec 10. PMID: 14667251.
- A Salmonella protein causes macrophage cell death by inducing autophagy.Hernandez LD, Pypaert M, Flavell RA, Galán JE. J Cell Biol. 2003 Dec 8. PMID: 14662750.
- Splicing double: insights from the second spliceosome.Patel AA, Steitz JA. Nat Rev Mol Cell Biol. 2003 Dec. PMID: 14685174.
- STAT3 is required for Flt3L-dependent dendritic cell differentiation.Laouar Y, Welte T, Fu XY, Flavell RA. Immunity. 2003 Dec. PMID: 14670306.
- Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.Zhang Z, Harrison PM, Liu Y, Gerstein M. Genome Res. 2003 Dec. PMID: 14656962.
- MKK3 mitogen-activated protein kinase pathway mediates carbon monoxide-induced protection against oxidant-induced lung injury.Otterbein LE, Otterbein SL, Ifedigbo E, Liu F, Morse DE, Fearns C, Ulevitch RJ, Knickelbein R, Flavell RA, Choi AM. Am J Pathol. 2003 Dec. PMID: 14633627.
- A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, Gerstein M, Zhao H, Qu LJ, Deng XW. Plant Physiol. 2003 Dec; 2003 Nov 6. PMID: 14605227.
- Phosphatidylserine receptor is required for clearance of apoptotic cells.Li MO, Sarkisian MR, Mehal WZ, Rakic P, Flavell RA. Science. 2003 Nov 28. PMID: 14645847.
- Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates.Salazar JC, Ahel I, Orellana O, Tumbula-Hansen D, Krieger R, Daniels L, Söll D. Proc Natl Acad Sci U S A. 2003 Nov 25; 2003 Nov 13. PMID: 14615592.
- Endothelial cells require STAT3 for protection against endotoxin-induced inflammation.Kano A, Wolfgang MJ, Gao Q, Jacoby J, Chai GX, Hansen W, Iwamoto Y, Pober JS, Flavell RA, Fu XY. J Exp Med. 2003 Nov 17. PMID: 14623907.
- Plasticity of marrow-derived stem cells.Herzog EL, Chai L, Krause DS. Blood. 2003 Nov 15; 2003 Jul 31. PMID: 12893756.
- A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.Harrison PM, Carriero N, Liu Y, Gerstein M. J Mol Biol. 2003 Nov 7. PMID: 14583187.
- Phosphorylation of threonine 497 in endothelial nitric-oxide synthase coordinates the coupling of L-arginine metabolism to efficient nitric oxide production.Lin MI, Fulton D, Babbitt R, Fleming I, Busse R, Pritchard KA Jr, Sessa WC. J Biol Chem. 2003 Nov 7; 2003 Sep 2. PMID: 12952971.
- The role of dendritic cells in immune responses against vaginal infection by herpes simplex virus type 2.Iwasaki A. Microbes Infect. 2003 Nov. PMID: 14623018.
- An mRNA structure in bacteria that controls gene expression by binding lysine.Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR. Genes Dev. 2003 Nov 1. PMID: 14597663.
- Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.Schmeing TM, Moore PB, Steitz TA. RNA. 2003 Nov. PMID: 14561884.
- A Bayesian networks approach for predicting protein-protein interactions from genomic data.Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. Science. 2003 Oct 17. PMID: 14564010.
- Distribution of NF-kappaB-binding sites across human chromosome 22.Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Proc Natl Acad Sci U S A. 2003 Oct 14; 2003 Oct 3. PMID: 14527995.
- Genetic control by metabolite-binding riboswitches.Winkler WC, Breaker RR. Chembiochem. 2003 Oct 6. PMID: 14523920.
- HIS & HERS, magic magnesium and the ballet of protein synthesis.Parnell KM, Strobel SA. Curr Opin Chem Biol. 2003 Oct. PMID: 14580554.
- Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development.Litt A, Irish VF. Genetics. 2003 Oct. PMID: 14573491.
- A novel method of determining the number of macromolecules per asymmetric unit from accurate crystal-volume measurements.Li F, Steitz TA. Acta Crystallogr D Biol Crystallogr. 2003 Oct; 2003 Sep 19. PMID: 14501119.
- Quantitation of free energy profiles in RNA-ligand interactions by nucleotide analog interference mapping.Cochrane JC, Batey RT, Strobel SA. RNA. 2003 Oct. PMID: 13130142.
- CCL9 is secreted by the follicle-associated epithelium and recruits dome region Peyer's patch CD11b+ dendritic cells.Zhao X, Sato A, Dela Cruz CS, Linehan M, Luegering A, Kucharzik T, Shirakawa AK, Marquez G, Farber JM, Williams I, Iwasaki A. J Immunol. 2003 Sep 15. PMID: 12960300.
- Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.Zhang Z, Gerstein M. Nucleic Acids Res. 2003 Sep 15. PMID: 12954770.
- A universal legal framework as a prerequisite for database interoperability.Greenbaum D, Gerstein M. Nat Biotechnol. 2003 Sep. PMID: 12949555.
- Molecular markers in clinical radiation oncology.Haffty BG, Glazer PM. Oncogene. 2003 Sep 1. PMID: 12947398.
- An mRNA structure that controls gene expression by binding S-adenosylmethionine.Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. Nat Struct Biol. 2003 Sep; 2003 Aug 10. PMID: 12910260.
- Impaired membrane resealing and autoimmune myositis in synaptotagmin VII-deficient mice.Chakrabarti S, Kobayashi KS, Flavell RA, Marks CB, Miyake K, Liston DR, Fowler KT, Gorelick FS, Andrews NW. J Cell Biol. 2003 Aug 18. PMID: 12925704.
- Toll-like receptor 9-mediated recognition of Herpes simplex virus-2 by plasmacytoid dendritic cells.Lund J, Sato A, Akira S, Medzhitov R, Iwasaki A. J Exp Med. 2003 Aug 4. PMID: 12900525.
- Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases.Polycarpo C, Ambrogelly A, Ruan B, Tumbula-Hansen D, Ataide SF, Ishitani R, Yokoyama S, Nureki O, Ibba M, Söll D. Mol Cell. 2003 Aug. PMID: 14536069.
- RNA, the first macromolecular catalyst: the ribosome is a ribozyme.Steitz TA, Moore PB. Trends Biochem Sci. 2003 Aug. PMID: 12932729.
- The potential for gene repair via triple helix formation.Seidman MM, Glazer PM. J Clin Invest. 2003 Aug. PMID: 12925687.
- Genomic analysis of gene expression relationships in transcriptional regulatory networks.Yu H, Luscombe NM, Qian J, Gerstein M. Trends Genet. 2003 Aug. PMID: 12902159.
- A common speed limit for RNA-cleaving ribozymes and deoxyribozymes.Breaker RR, Emilsson GM, Lazarev D, Nakamura S, Puskarz IJ, Roth A, Sudarsan N. RNA. 2003 Aug. PMID: 12869706.
- Ribozyme speed limits.Emilsson GM, Nakamura S, Roth A, Breaker RR. RNA. 2003 Aug. PMID: 12869701.
- In vivo analysis of the RNA interference mechanism in Trypanosoma brucei.Tschudi C, Djikeng A, Shi H, Ullu E. Methods. 2003 Aug. PMID: 12828944.
- Abolition of arteriolar dilation but not constriction to histamine in cremaster muscle of eNOS-/- mice.Payne GW, Madri JA, Sessa WC, Segal SS. Am J Physiol Heart Circ Physiol. 2003 Aug; 2003 Apr 10. PMID: 12689855.
- Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.Hansen JL, Moore PB, Steitz TA. J Mol Biol. 2003 Jul 25. PMID: 12860128.
- The importance of CD11b+ dendritic cells in CD4+ T cell activation in vivo: with help from interleukin 1.Iwasaki A. J Exp Med. 2003 Jul 21; 2003 Jul 14. PMID: 12860934.
- The human genome has 49 cytochrome c pseudogenes, including a relic of a primordial gene that still functions in mouse.Zhang Z, Gerstein M. Gene. 2003 Jul 17. PMID: 12909341.
- Domains 2 and 3 interact to form critical elements of the group II intron active site.Fedorova O, Mitros T, Pyle AM. J Mol Biol. 2003 Jul 4. PMID: 12823961.
- Selective inhibition of tumor microvascular permeability by cavtratin blocks tumor progression in mice.Gratton JP, Lin MI, Yu J, Weiss ED, Jiang ZL, Fairchild TA, Iwakiri Y, Groszmann R, Claffey KP, Cheng YC, Sessa WC. Cancer Cell. 2003 Jul. PMID: 12892711.
- Commentary: Bio2010--new challenges for biology educators.Steitz JA. Cell Biol Educ. 2003 Summer. PMID: 12888841.
- Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells.Hirose T, Shu MD, Steitz JA. Mol Cell. 2003 Jul. PMID: 12887897.
- Regulation of the Th2 cytokine locus by a locus control region.Lee GR, Fields PE, Griffin TJ, Flavell RA. Immunity. 2003 Jul. PMID: 12871646.
- Identification and correction of spurious spatial correlations in microarray data.Qian J, Kluger Y, Yu H, Gerstein M. Biotechniques. 2003 Jul. PMID: 12866403.
- Bone marrow stem cells contribute to repair of the ischemically injured renal tubule.Kale S, Karihaloo A, Clark PR, Kashgarian M, Krause DS, Cantley LG. J Clin Invest. 2003 Jul; 2003 Jun 16. PMID: 12824456.
- ExpressYourself: A modular platform for processing and visualizing microarray data.Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. Nucleic Acids Res. 2003 Jul 1. PMID: 12824348.
- The evolution of floral homeotic gene function.Irish VF. Bioessays. 2003 Jul. PMID: 12815719.
- An siRNA ribonucleoprotein is found associated with polyribosomes in Trypanosoma brucei.Djikeng A, Shi H, Tschudi C, Shen S, Ullu E. RNA. 2003 Jul. PMID: 12810914.
- CD154-CD40-independent up-regulation of B7-2 on splenic antigen-presenting cells and efficient T cell priming by staphylococcal enterotoxin A.Eshima K, Choi Y, Flavell RA. Int Immunol. 2003 Jul. PMID: 12807820.
- A lupus-like syndrome develops in mice lacking the Ro 60-kDa protein, a major lupus autoantigen.Xue D, Shi H, Smith JD, Chen X, Noe DA, Cedervall T, Yang DD, Eynon E, Brash DE, Kashgarian M, Flavell RA, Wolin SL. Proc Natl Acad Sci U S A. 2003 Jun 24; 2003 Jun 3. PMID: 12788971.
- Carbon monoxide modulates Fas/Fas ligand, caspases, and Bcl-2 family proteins via the p38alpha mitogen-activated protein kinase pathway during ischemia-reperfusion lung injury.Zhang X, Shan P, Alam J, Davis RJ, Flavell RA, Lee PJ. J Biol Chem. 2003 Jun 13; 2003 Apr 10. PMID: 12690100.
- Protein synthesis in Escherichia coli with mischarged tRNA.Min B, Kitabatake M, Polycarpo C, Pelaschier J, Raczniak G, Ruan B, Kobayashi H, Namgoong S, Söll D. J Bacteriol. 2003 Jun. PMID: 12775689.
- SPINE 2: a system for collaborative structural proteomics within a federated database framework.Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M. Nucleic Acids Res. 2003 Jun 1. PMID: 12771210.
- Substrate specificity and reaction kinetics of an X-motif ribozyme.Lazarev D, Puskarz I, Breaker RR. RNA. 2003 Jun. PMID: 12756327.
- Caspases and T lymphocytes: a flip of the coin?Lakhani S, Flavell RA. Immunol Rev. 2003 Jun. PMID: 12752667.
- Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria.Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Cell. 2003 May 30. PMID: 12787499.
- Functional divergence within the APETALA3/PISTILLATA floral homeotic gene lineages.Lamb RS, Irish VF. Proc Natl Acad Sci U S A. 2003 May 27; 2003 May 13. PMID: 12746493.
- The phosphorylation of caveolin-2 on serines 23 and 36 modulates caveolin-1-dependent caveolae formation.Sowa G, Pypaert M, Fulton D, Sessa WC. Proc Natl Acad Sci U S A. 2003 May 27; 2003 May 12. PMID: 12743374.
- Expanding tRNA recognition of a tRNA synthetase by a single amino acid change.Feng L, Tumbula-Hansen D, Toogood H, Soll D. Proc Natl Acad Sci U S A. 2003 May 13; 2003 May 1. PMID: 12730374.
- Activation of CD4 T cells by Raf-independent effectors of Ras.Czyzyk J, Brogdon JL, Badou A, Henegariu O, Preston Hurlburt P, Flavell R, Bottomly K. Proc Natl Acad Sci U S A. 2003 May 13; 2003 Apr 29. PMID: 12721365.
- Cotransplantation of human mesenchymal stem cells enhances human myelopoiesis and megakaryocytopoiesis in NOD/SCID mice.Angelopoulou M, Novelli E, Grove JE, Rinder HM, Civin C, Cheng L, Krause DS. Exp Hematol. 2003 May. PMID: 12763140.
- The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development.Wang X, Feng S, Nakayama N, Crosby WL, Irish V, Deng XW, Wei N. Plant Cell. 2003 May. PMID: 12724534.
- Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.Zhang Z, Gerstein M. Genomics. 2003 May. PMID: 12706105.
- Decreased expression of the DNA mismatch repair gene Mlh1 under hypoxic stress in mammalian cells.Mihaylova VT, Bindra RS, Yuan J, Campisi D, Narayanan L, Jensen R, Giordano F, Johnson RS, Rockwell S, Glazer PM. Mol Cell Biol. 2003 May. PMID: 12697826.
- Compensatory phosphorylation and protein-protein interactions revealed by loss of function and gain of function mutants of multiple serine phosphorylation sites in endothelial nitric-oxide synthase.Bauer PM, Fulton D, Boo YC, Sorescu GP, Kemp BE, Jo H, Sessa WC. J Biol Chem. 2003 Apr 25; 2003 Feb 18. PMID: 12591925.
- Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.Jansen R, Bussemaker HJ, Gerstein M. Nucleic Acids Res. 2003 Apr 15. PMID: 12682375.
- Plasma membrane localization and function of the estrogen receptor alpha variant (ER46) in human endothelial cells.Li L, Haynes MP, Bender JR. Proc Natl Acad Sci U S A. 2003 Apr 15; 2003 Apr 7. PMID: 12682286.
- Ionization of a critical adenosine residue in the neurospora Varkud Satellite ribozyme active site.Jones FD, Strobel SA. Biochemistry. 2003 Apr 15. PMID: 12680781.
- Genomics. Defining genes in the genomics era.Snyder M, Gerstein M. Science. 2003 Apr 11. PMID: 12690176.
- Spectral biclustering of microarray data: coclustering genes and conditions.Kluger Y, Basri R, Chang JT, Gerstein M. Genome Res. 2003 Apr. PMID: 12671006.
- A group II intron inserted into a bacterial heat-shock operon shows autocatalytic activity and unusual thermostability.Adamidi C, Fedorova O, Pyle AM. Biochemistry. 2003 Apr 1. PMID: 12653544.
- The tyrphostin AG1024 accelerates the degradation of phosphorylated forms of retinoblastoma protein (pRb) and restores pRb tumor suppressive function in melanoma cells.von Willebrand M, Zacksenhaus E, Cheng E, Glazer P, Halaban R. Cancer Res. 2003 Mar 15. PMID: 12649208.
- A pool of central memory-like CD4 T cells contains effector memory precursors.Blander JM, Sant'Angelo DB, Metz D, Kim SW, Flavell RA, Bottomly K, Janeway CA Jr. J Immunol. 2003 Mar 15. PMID: 12626545.
- Escape from Prisoner's Dilemma in RNA phage phi6.Turner PE, Chao L. Am Nat. 2003 Mar. PMID: 12699226.
- SR splicing factors serve as adapter proteins for TAP-dependent mRNA export.Huang Y, Gattoni R, Stévenin J, Steitz JA. Mol Cell. 2003 Mar. PMID: 12667464.
- A crucial role of CD4 T cells as a functional source of CD154 in the initiation of insulin-dependent diabetes mellitus in the non-obese diabetic mouse.Eshima K, Mora C, Wong FS, Green EA, Grewal IS, Flavell RA. Int Immunol. 2003 Mar. PMID: 12618479.
- Cell-permeable peptides improve cellular uptake and therapeutic gene delivery of replication-deficient viruses in cells and in vivo.Gratton JP, Yu J, Griffith JW, Babbitt RW, Scotland RS, Hickey R, Giordano FJ, Sessa WC. Nat Med. 2003 Mar; 2003 Feb 24. PMID: 12598894.
- Reactive oxygen species and extracellular signal-regulated kinase 1/2 mitogen-activated protein kinase mediate hyperoxia-induced cell death in lung epithelium.Zhang X, Shan P, Sasidhar M, Chupp GL, Flavell RA, Choi AM, Lee PJ. Am J Respir Cell Mol Biol. 2003 Mar. PMID: 12594056.
- The voltage-gated potassium channel Kv1.3 regulates energy homeostasis and body weight.Xu J, Koni PA, Wang P, Li G, Kaczmarek L, Wu Y, Li Y, Flavell RA, Desir GV. Hum Mol Genet. 2003 Mar 1. PMID: 12588802.
- The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases.Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Söll D, Steitz TA. Proc Natl Acad Sci U S A. 2003 Feb 18; 2003 Feb 10. PMID: 12578991.
- STAT3 deletion during hematopoiesis causes Crohn's disease-like pathogenesis and lethality: a critical role of STAT3 in innate immunity.Welte T, Zhang SS, Wang T, Zhang Z, Hesslein DG, Yin Z, Kano A, Iwamoto Y, Li E, Craft JE, Bothwell AL, Fikrig E, Koni PA, Flavell RA, Fu XY. Proc Natl Acad Sci U S A. 2003 Feb 18; 2003 Feb 5. PMID: 12571365.
- The transcriptional activity of human Chromosome 22.Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. Genes Dev. 2003 Feb 15. PMID: 12600945.
- Searching for the advantages of virus sex.Turner PE. Orig Life Evol Biosph. 2003 Feb. PMID: 12967275.
- Identification of pseudogenes in the Drosophila melanogaster genome.Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M. Nucleic Acids Res. 2003 Feb 1. PMID: 12560500.
- Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA.McConnell TS, Lokken RP, Steitz JA. RNA. 2003 Feb. PMID: 12554862.
- After the ribosome structures: how does peptidyl transferase work?Moore PB, Steitz TA. RNA. 2003 Feb. PMID: 12554855.
- Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.Lan N, Montelione GT, Gerstein M. Curr Opin Chem Biol. 2003 Feb. PMID: 12547426.
- Transcription dependence of chromosomal gene targeting by triplex-forming oligonucleotides.Macris MA, Glazer PM. J Biol Chem. 2003 Jan 31; 2002 Nov 12. PMID: 12431993.
- Src kinase mediates phosphatidylinositol 3-kinase/Akt-dependent rapid endothelial nitric-oxide synthase activation by estrogen.Haynes MP, Li L, Sinha D, Russell KS, Hisamoto K, Baron R, Collinge M, Sessa WC, Bender JR. J Biol Chem. 2003 Jan 24; 2002 Nov 12. PMID: 12431978.
- Vaginal submucosal dendritic cells, but not Langerhans cells, induce protective Th1 responses to herpes simplex virus-2.Zhao X, Deak E, Soderberg K, Linehan M, Spezzano D, Zhu J, Knipe DM, Iwasaki A. J Exp Med. 2003 Jan 20. PMID: 12538655.
- Carbon monoxide inhibition of apoptosis during ischemia-reperfusion lung injury is dependent on the p38 mitogen-activated protein kinase pathway and involves caspase 3.Zhang X, Shan P, Otterbein LE, Alam J, Flavell RA, Davis RJ, Choi AM, Lee PJ. J Biol Chem. 2003 Jan 10; 2002 Oct 23. PMID: 12399465.
- Flower development: initiation, differentiation, and diversification.Zik M, Irish VF. Annu Rev Cell Dev Biol. 2003. PMID: 14570566.
- The structural basis of large ribosomal subunit function.Moore PB, Steitz TA. Annu Rev Biochem. 2003. PMID: 14527328.
- Probing the yeast proteome for RNA-processing factors.Granneman S, Baserga SJ. Genome Biol. 2003; 2003 Sep 22. PMID: 14519190.
- Biochemical detection of adenosine and cytidine ionization within RNA by interference analysis.Strobel SA, Jones FD, Oyelere AK, Ryder SP. Nucleic Acids Res Suppl. 2003. PMID: 14510464.
- Comparing protein abundance and mRNA expression levels on a genomic scale.Greenbaum D, Colangelo C, Williams K, Gerstein M. Genome Biol. 2003; 2003 Aug 29. PMID: 12952525.
- Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.Zhang Z, Gerstein M. J Biol. 2003; 2003 Jun 6. PMID: 12814519.
- A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.Harrison PM, Gerstein M. Genome Biol. 2003; 2003 May 30. PMID: 12801414.
- Cost-reducing protein production and delivery for sexually transmitted disease prevention.Saltzman WM. IEEE Eng Med Biol Mag. 2003 Jan-Feb. PMID: 12683061.
- MolMovDB: analysis and visualization of conformational change and structural flexibility.Echols N, Milburn D, Gerstein M. Nucleic Acids Res. 2003 Jan 1. PMID: 12520056.
- Global identification of target genes regulated by APETALA3 and PISTILLATA floral homeotic gene action.Zik M, Irish VF. Plant Cell. 2003 Jan. PMID: 12509532.
- Endogenous human papillomavirus E6 and E7 proteins differentially regulate proliferation, senescence, and apoptosis in HeLa cervical carcinoma cells.DeFilippis RA, Goodwin EC, Wu L, DiMaio D. J Virol. 2003 Jan. PMID: 12502868.
2002
- Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast.Rosas-Sandoval G, Ambrogelly A, Rinehart J, Wei D, Cruz-Vera LR, Graham DE, Stetter KO, Guarneros G, Söll D. Proc Natl Acad Sci U S A. 2002 Dec 24; 2002 Dec 10. PMID: 12475929.
- Site-directed recombination via bifunctional PNA-DNA conjugates.Rogers FA, Vasquez KM, Egholm M, Glazer PM. Proc Natl Acad Sci U S A. 2002 Dec 24; 2002 Dec 2. PMID: 12461167.
- Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP.Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA. Cell. 2002 Dec 13. PMID: 12526808.
- An mRNA structure that controls gene expression by binding FMN.Winkler WC, Cohen-Chalamish S, Breaker RR. Proc Natl Acad Sci U S A. 2002 Dec 10; 2002 Nov 27. PMID: 12456892.
- Thermostability of membrane protein helix-helix interaction elucidated by statistical analysis.Schneider D, Liu Y, Gerstein M, Engelman DM. FEBS Lett. 2002 Dec 4. PMID: 12459496.
- Functional exploration of the C. elegans genome using DNA microarrays.Reinke V. Nat Genet. 2002 Dec. PMID: 12454651.
- Marrow-derived cells as vehicles for delivery of gene therapy to pulmonary epithelium.Grove JE, Lutzko C, Priller J, Henegariu O, Theise ND, Kohn DB, Krause DS. Am J Respir Cell Mol Biol. 2002 Dec. PMID: 12444022.
- The adaptor molecule TIRAP provides signalling specificity for Toll-like receptors.Horng T, Barton GM, Flavell RA, Medzhitov R. Nature. 2002 Nov 21. PMID: 12447442.
- Assembly, purification and crystallization of an active HIV-1 reverse transcriptase initiation complex.Pata JD, King BR, Steitz TA. Nucleic Acids Res. 2002 Nov 15. PMID: 12433988.
- Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase.Yin YW, Steitz TA. Science. 2002 Nov 15; 2002 Sep 19. PMID: 12242451.
- Digging deep for ancient relics: a survey of protein motifs in the intergenic sequences of four eukaryotic genomes.Zhang ZL, Harrison PM, Gerstein M. J Mol Biol. 2002 Nov 8. PMID: 12417195.
- Interleukin-13 mediates a fundamental pathway for airway epithelial mucus induced by CD4 T cells and interleukin-9.Whittaker L, Niu N, Temann UA, Stoddard A, Flavell RA, Ray A, Homer RJ, Cohn L. Am J Respir Cell Mol Biol. 2002 Nov. PMID: 12397019.
- Genomic and proteomic analysis of the myeloid differentiation program: global analysis of gene expression during induced differentiation in the MPRO cell line.Lian Z, Kluger Y, Greenbaum DS, Tuck D, Gerstein M, Berliner N, Weissman SM, Newburger PE. Blood. 2002 Nov 1. PMID: 12384419.
- Mice with targeted deletion of eNOS develop hyperdynamic circulation associated with portal hypertension.Iwakiri Y, Cadelina G, Sessa WC, Groszmann RJ. Am J Physiol Gastrointest Liver Physiol. 2002 Nov. PMID: 12381520.
- Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.Winkler W, Nahvi A, Breaker RR. Nature. 2002 Oct 31; 2002 Oct 16. PMID: 12410317.
- A one-step method for in vitro production of tRNA transcripts.Korencić D, Söll D, Ambrogelly A. Nucleic Acids Res. 2002 Oct 15. PMID: 12384607.
- Subunits of IgM reconstitute defective contact sensitivity in B-1 cell-deficient xid mice: kappa light chains recruit T cells independent of complement.Paliwal V, Tsuji RF, Szczepanik M, Kawikova I, Campos RA, Kneilling M, Röcken M, Schuurman J, Redegeld FA, Nijkamp FP, Askenase PW. J Immunol. 2002 Oct 15. PMID: 12370339.
- Definition of an inhibitory juxtamembrane WW-like domain in the platelet-derived growth factor beta receptor.Irusta PM, Luo Y, Bakht O, Lai CC, Smith SO, DiMaio D. J Biol Chem. 2002 Oct 11; 2002 Aug 13. PMID: 12181311.
- Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms.Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Söll D. J Biol Chem. 2002 Oct 4; 2002 Jul 30. PMID: 12149259.
- Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.Zhang Z, Harrison P, Gerstein M. Genome Res. 2002 Oct. PMID: 12368239.
- Components of an interdependent unit within the SSU processome regulate and mediate its activity.Wehner KA, Gallagher JE, Baserga SJ. Mol Cell Biol. 2002 Oct. PMID: 12242301.
- Methanocaldococcus jannaschii prolyl-tRNA synthetase charges tRNA(Pro) with cysteine.Ambrogelly A, Ahel I, Polycarpo C, Bunjun-Srihari S, Krett B, Jacquin-Becker C, Ruan B, Köhrer C, Stathopoulos C, RajBhandary UL, Söll D. J Biol Chem. 2002 Sep 20; 2002 Jul 18. PMID: 12130658.
- Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases.Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Söll D. J Biol Chem. 2002 Sep 20; 2002 Jul 18. PMID: 12130657.
- Genomic analysis of membrane protein families: abundance and conserved motifs.Liu Y, Engelman DM, Gerstein M. Genome Biol. 2002 Sep 19; 2002 Sep 19. PMID: 12372142.
- Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center.Parnell KM, Seila AC, Strobel SA. Proc Natl Acad Sci U S A. 2002 Sep 3; 2002 Aug 16. PMID: 12185248.
- Structural insights into peptide bond formation.Hansen JL, Schmeing TM, Moore PB, Steitz TA. Proc Natl Acad Sci U S A. 2002 Sep 3; 2002 Aug 16. PMID: 12185246.
- Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M. Proteins. 2002 Sep 1. PMID: 12211036.
- Immunofluorescence analysis of poliovirus receptor expression in Peyer's patches of humans, primates, and CD155 transgenic mice: implications for poliovirus infection.Iwasaki A, Welker R, Mueller S, Linehan M, Nomoto A, Wimmer E. J Infect Dis. 2002 Sep 1; 2002 Aug 9. PMID: 12195344.
- Inhibitor of apoptosis protein survivin regulates vascular injury.Blanc-Brude OP, Yu J, Simosa H, Conte MS, Sessa WC, Altieri DC. Nat Med. 2002 Sep; 2002 Aug 12. PMID: 12172543.
- Divergent regulation of the HEMA gene family encoding glutamyl-tRNA reductase in Arabidopsis thaliana: expression of HEMA2 is regulated by sugars, but is independent of light and plastid signalling.Ujwal ML, McCormac AC, Goulding A, Kumar AM, Söll D, Terry MJ. Plant Mol Biol. 2002 Sep. PMID: 12139011.
- Identification of A-minor tertiary interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping.Soukup JK, Minakawa N, Matsuda A, Strobel SA. Biochemistry. 2002 Aug 20. PMID: 12173929.
- Survival motor neuron protein in the nucleolus of mammalian neurons.Wehner KA, Ayala L, Kim Y, Young PJ, Hosler BA, Lorson CL, Baserga SJ, Francis JW. Brain Res. 2002 Aug 2. PMID: 12126878.
- Differential involvement of p38 mitogen-activated protein kinase kinases MKK3 and MKK6 in T-cell apoptosis.Tanaka N, Kamanaka M, Enslen H, Dong C, Wysk M, Davis RJ, Flavell RA. EMBO Rep. 2002 Aug; 2002 Jul 15. PMID: 12151339.
- Development of a murine hematopoietic progenitor complementary DNA microarray using a subtracted complementary DNA library.Ma X, Husain T, Peng H, Lin S, Mironenko O, Maun N, Johnson S, Tuck D, Berliner N, Krause DS, Perkins AS. Blood. 2002 Aug 1. PMID: 12130493.
- IGF1 receptor expression protects against microenvironmental stress found in the solid tumor.Peretz S, Kim C, Rockwell S, Baserga R, Glazer PM. Radiat Res. 2002 Aug. PMID: 12105987.
- Hyporesponsiveness to vaccination with Borrelia burgdorferi OspA in humans and in TLR1- and TLR2-deficient mice.Alexopoulou L, Thomas V, Schnare M, Lobet Y, Anguita J, Schoen RT, Medzhitov R, Fikrig E, Flavell RA. Nat Med. 2002 Aug; 2002 Jul 1. PMID: 12091878.
- IRAK-M is a negative regulator of Toll-like receptor signaling.Kobayashi K, Hernandez LD, Galán JE, Janeway CA Jr, Medzhitov R, Flavell RA. Cell. 2002 Jul 26. PMID: 12150927.
- The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.Luscombe NM, Qian J, Zhang Z, Johnson T, Gerstein M. Genome Biol. 2002 Jul 25; 2002 Jul 25. PMID: 12186647.
- Site-specific cross-linking analyses reveal an asymmetric protein distribution for a box C/D snoRNP.Cahill NM, Friend K, Speckmann W, Li ZH, Terns RM, Terns MP, Steitz JA. EMBO J. 2002 Jul 15. PMID: 12110593.
- The splicing of U12-type introns can be a rate-limiting step in gene expression.Patel AA, McCarthy M, Steitz JA. EMBO J. 2002 Jul 15. PMID: 12110592.
- Cutting edge: changes in histone acetylation at the IL-4 and IFN-gamma loci accompany Th1/Th2 differentiation.Fields PE, Kim ST, Flavell RA. J Immunol. 2002 Jul 15. PMID: 12097365.
- The involvement of RNA in ribosome function.Moore PB, Steitz TA. Nature. 2002 Jul 11. PMID: 12110899.
- Nitric oxide-releasing aspirin decreases vascular injury by reducing inflammation and promoting apoptosis.Yu J, Rudic RD, Sessa WC. Lab Invest. 2002 Jul. PMID: 12118084.
- A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis.Dragon F, Gallagher JE, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ. Nature. 2002 Jun 27; 2002 Jun 9. PMID: 12068309.
- Mechanism of transforming growth factor beta-induced inhibition of T helper type 1 differentiation.Gorelik L, Constant S, Flavell RA. J Exp Med. 2002 Jun 3. PMID: 12045248.
- Salp15, an ixodes scapularis salivary protein, inhibits CD4(+) T cell activation.Anguita J, Ramamoorthi N, Hovius JW, Das S, Thomas V, Persinski R, Conze D, Askenase PW, Rincón M, Kantor FS, Fikrig E. Immunity. 2002 Jun. PMID: 12121666.
- Rational design of 'water-soluble' bacteriorhodopsin variants.Mitra K, Steitz TA, Engelman DM. Protein Eng. 2002 Jun. PMID: 12082167.
- Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M. Nucleic Acids Res. 2002 Jun 1. PMID: 12034841.
- Plasticity of marrow-derived stem cells.Krause DS. Gene Ther. 2002 Jun. PMID: 12032704.
- Phosphorylation of eNOS initiates excessive NO production in early phases of portal hypertension.Iwakiri Y, Tsai MH, McCabe TJ, Gratton JP, Fulton D, Groszmann RJ, Sessa WC. Am J Physiol Heart Circ Physiol. 2002 Jun. PMID: 12003815.
- Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.Harrison PM, Gerstein M. J Mol Biol. 2002 May 17. PMID: 12083509.
- Regulation of hematopoietic stem cell fate.Krause DS. Oncogene. 2002 May 13. PMID: 12032767.
- Functional reconstitution of endothelial nitric oxide synthase reveals the importance of serine 1179 in endothelium-dependent vasomotion.Scotland RS, Morales-Ruiz M, Chen Y, Yu J, Rudic RD, Fulton D, Gratton JP, Sessa WC. Circ Res. 2002 May 3. PMID: 11988492.
- Domain mapping studies reveal that the M domain of hsp90 serves as a molecular scaffold to regulate Akt-dependent phosphorylation of endothelial nitric oxide synthase and NO release.Fontana J, Fulton D, Chen Y, Fairchild TA, McCabe TJ, Fujita N, Tsuruo T, Sessa WC. Circ Res. 2002 May 3. PMID: 11988487.
- SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M. Pharmacogenomics. 2002 May. PMID: 12052146.
- Branchpoint selection in the splicing of U12-dependent introns in vitro.McConnell TS, Cho SJ, Frilander MJ, Steitz JA. RNA. 2002 May. PMID: 12022225.
- Regulation of APETALA3 floral homeotic gene expression by meristem identity genes.Lamb RS, Hill TA, Tan QK, Irish VF. Development. 2002 May. PMID: 11959818.
- Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds.Hegyi H, Lin J, Greenbaum D, Gerstein M. Proteins. 2002 May 1. PMID: 11933060.
- Efficient transposition of preformed synaptic Tn5 complexes in Trypanosoma brucei.Shi H, Wormsley S, Tschudi C, Ullu E. Mol Biochem Parasitol. 2002 Apr 30. PMID: 11985870.
- Outcome of conservatively managed early-onset breast cancer by BRCA1/2 status.Haffty BG, Harrold E, Khan AJ, Pathare P, Smith TE, Turner BC, Glazer PM, Ward B, Carter D, Matloff E, Bale AE, Alvarez-Franco M. Lancet. 2002 Apr 27. PMID: 11988246.
- Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts.Greenbaum D, Jansen R, Gerstein M. Bioinformatics. 2002 Apr. PMID: 12016056.
- Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus.Feng L, Stathopoulos C, Ahel I, Mitra A, Tumbula-Hansen D, Hartsch T, Söll D. Extremophiles. 2002 Apr. PMID: 12013438.
- pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping.Oyelere AK, Kardon JR, Strobel SA. Biochemistry. 2002 Mar 19. PMID: 11888283.
- Subcellular localization of the yeast proteome.Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M. Genes Dev. 2002 Mar 15. PMID: 11914276.
- Comparative analysis of hairpin ribozyme structures and interference data.Ryder SP, Strobel SA. Nucleic Acids Res. 2002 Mar 15. PMID: 11884625.
- RICK/Rip2/CARDIAK mediates signalling for receptors of the innate and adaptive immune systems.Kobayashi K, Inohara N, Hernandez LD, Galán JE, Núñez G, Janeway CA, Medzhitov R, Flavell RA. Nature. 2002 Mar 14. PMID: 11894098.
- Cysteinyl-tRNA formation and prolyl-tRNA synthetase.Jacquin-Becker C, Ahel I, Ambrogelly A, Ruan B, Söll D, Stathopoulos C. FEBS Lett. 2002 Mar 6. PMID: 11904177.
- Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation.Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Söll D. Proc Natl Acad Sci U S A. 2002 Mar 5. PMID: 11880622.
- GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. Proc Natl Acad Sci U S A. 2002 Mar 5; 2002 Feb 26. PMID: 11867748.
- A question of size: the eukaryotic proteome and the problems in defining it.Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. Nucleic Acids Res. 2002 Mar 1. PMID: 11861898.
- A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits.Schmeing TM, Seila AC, Hansen JL, Freeborn B, Soukup JK, Scaringe SA, Strobel SA, Moore PB, Steitz TA. Nat Struct Biol. 2002 Mar. PMID: 11828326.
- Decreased synaptic vesicle recycling efficiency and cognitive deficits in amphiphysin 1 knockout mice.Di Paolo G, Sankaranarayanan S, Wenk MR, Daniell L, Perucco E, Caldarone BJ, Flavell R, Picciotto MR, Ryan TA, Cremona O, De Camilli P. Neuron. 2002 Feb 28. PMID: 11879655.
- Identification of an active site ligand for a group I ribozyme catalytic metal ion.Szewczak AA, Kosek AB, Piccirilli JA, Strobel SA. Biochemistry. 2002 Feb 26. PMID: 11851398.
- A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M. J Mol Biol. 2002 Feb 22. PMID: 11866506.
- Localization of endothelial nitric-oxide synthase phosphorylated on serine 1179 and nitric oxide in Golgi and plasma membrane defines the existence of two pools of active enzyme.Fulton D, Fontana J, Sowa G, Gratton JP, Lin M, Li KX, Michell B, Kemp BE, Rodman D, Sessa WC. J Biol Chem. 2002 Feb 8; 2001 Nov 29. PMID: 11729179.
- Rapid vascular cell responses to estrogen and membrane receptors.Haynes MP, Li L, Russell KS, Bender JR. Vascul Pharmacol. 2002 Feb. PMID: 12379956.
- Pancreatic lymph node-derived CD4(+)CD25(+) Treg cells: highly potent regulators of diabetes that require TRANCE-RANK signals.Green EA, Choi Y, Flavell RA. Immunity. 2002 Feb. PMID: 11869680.
- The divergent U12-type spliceosome is required for pre-mRNA splicing and is essential for development in Drosophila.Otake LR, Scamborova P, Hashimoto C, Steitz JA. Mol Cell. 2002 Feb. PMID: 11864616.
- The sigma(70)-like motif: a eukaryotic RNA binding domain unique to a superfamily of proteins required for ribosome biogenesis.Wehner KA, Baserga SJ. Mol Cell. 2002 Feb. PMID: 11864606.
- Engineered allosteric ribozymes as biosensor components.Breaker RR. Curr Opin Biotechnol. 2002 Feb. PMID: 11849955.
- Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M. Genome Res. 2002 Feb. PMID: 11827946.
- Endothelial cell seeding influences lesion development following arterial injury in the cholesterol-fed rabbit.Conte MS, VanMeter GA, Akst LM, Clemons T, Kashgarian M, Bender JR. Cardiovasc Res. 2002 Feb 1. PMID: 11827702.
- Expression of DC-SIGN by dendritic cells of intestinal and genital mucosae in humans and rhesus macaques.Jameson B, Baribaud F, Pöhlmann S, Ghavimi D, Mortari F, Doms RW, Iwasaki A. J Virol. 2002 Feb. PMID: 11799181.
- RNA interference: advances and questions.Ullu E, Djikeng A, Shi H, Tschudi C. Philos Trans R Soc Lond B Biol Sci. 2002 Jan 29. PMID: 11839183.
- Proteomics. Integrating interactomes.Gerstein M, Lan N, Jansen R. Science. 2002 Jan 11. PMID: 11786630.
- Integration of genomic datasets to predict protein complexes in yeast.Jansen R, Lan N, Qian J, Gerstein M. J Struct Funct Genomics. 2002. PMID: 12836664.
- BM-derived stem cells for the treatment of nonhematopoietic diseases.Krause DS. Cytotherapy. 2002. PMID: 12568982.
- YMD: a microarray database for large-scale gene expression analysis.Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K. Proc AMIA Symp. 2002. PMID: 12463803.
- Developmental genomic approaches in model organisms.Reinke V, White KP. Annu Rev Genomics Hum Genet. 2002; 2002 Apr 15. PMID: 12142361.
- Unconventional rules of small nuclear RNA transcription and cap modification in trypanosomatids.Tschudi C, Ullut E. Gene Expr. 2002. PMID: 11868986.
- Structural genomics: a new era for pharmaceutical research.Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, Gerstein M. Genome Biol. 2002; 2002 Jan 14. PMID: 11864367.
- Pulmonary overexpression of IL-9 induces Th2 cytokine expression, leading to immune pathology.Temann UA, Ray P, Flavell RA. J Clin Invest. 2002 Jan. PMID: 11781348.
- Relating whole-genome expression data with protein-protein interactions.Jansen R, Greenbaum D, Gerstein M. Genome Res. 2002 Jan. PMID: 11779829.
- An integrated approach for finding overlooked genes in yeast.Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. Nat Biotechnol. 2002 Jan. PMID: 11753363.
2001
- Multi-organ, multi-lineage engraftment by a single bone marrow-derived stem cell.Krause DS, Theise ND, Collector MI, Henegariu O, Hwang S, Gardner R, Neutzel S, Sharkis SJ. Cell. 2001 May 4. PMID: 11348593.
- Xenotransplantation of immunodeficient mice with mobilized human blood CD34+ cells provides an in vivo model for human megakaryocytopoiesis and platelet production.Perez LE, Rinder HM, Wang C, Tracey JB, Maun N, Krause DS. Blood. 2001 Mar 15. PMID: 11238102.
2000
- Isolation and flow cytometric analysis of T-cell-depleted CD34+ PBPCs.Debelak J, Shlomchik MJ, Snyder EL, Cooper D, Seropian S, McGuirk J, Smith B, Krause DS. Transfusion. 2000 Dec. PMID: 11134567.
- Regulation of CD34 transcription by Sp1 requires sites upstream and downstream of the transcription start site.Taranenko N, Krause DS. Exp Hematol. 2000 Aug. PMID: 10989198.
1999
- Functional activity of murine CD34+ and CD34- hematopoietic stem cell populations.Donnelly DS, Zelterman D, Sharkis S, Krause DS. Exp Hematol. 1999 May. PMID: 10340393.
1998
- Normal neutrophil differentiation and secondary granule gene expression in the EML and MPRO cell lines.Lawson ND, Krause DS, Berliner N. Exp Hematol. 1998 Nov. PMID: 9808058.
- Cytosine deaminase adenoviral vector and 5-fluorocytosine selectively reduce breast cancer cells 1 million-fold when they contaminate hematopoietic cells: a potential purging method for autologous transplantation.Garcia-Sanchez F, Pizzorno G, Fu SQ, Nanakorn T, Krause DS, Liang J, Adams E, Leffert JJ, Yin LH, Cooperberg MR, Hanania E, Wang WL, Won JH, Peng XY, Cote R, Brown R, Burtness B, Giles R, Crystal R, Deisseroth AB. Blood. 1998 Jul 15. PMID: 9657770.
1997
- In Vitro Selection of Catalytic Polynucleotides.Breaker RR. Chem Rev. 1997 Apr 1. PMID: 11848875.
1995
- Safety and immunogenicity of an outer surface protein A vaccine in subjects with previous Lyme disease.Schoen RT, Meurice F, Brunet CM, Cretella S, Krause DS, Craft JE, Fikrig E. J Infect Dis. 1995 Nov. PMID: 7594671.