Faculty Publications

2023

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.
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.
Discovering riboswitches: the past and the future.Kavita K, Breaker RR. Trends Biochem Sci. 2023 Feb; 2022 Sep 20. PMID: 36150954.
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 Jan 26; 2023 Jan 26. PMID: 36702900.
Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen A, Lakdawala S, Alwine J, Casadevall A, Imperiale M, 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 Jan 26; 2023 Jan 26. PMID: 36700653.
Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen A, Lakdawala S, Alwine J, Casadevall A, Imperiale M, 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 Jan 26; 2023 Jan 26. PMID: 36700642.
Virology under the Microscope-a Call for Rational Discourse.Goodrum F, Lowen A, Lakdawala S, Alwine J, Casadevall A, Imperiale M, 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 Jan 26; 2023 Jan 26. PMID: 36700640.
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 Jan 25; 2023 Jan 25. PMID: 36697832.
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 Jan 25; 2023 Jan 25. PMID: 36697369.
Exploiting natural riboswitches for aptamer engineering and validation.Mohsen MG, Midy MK, Balaji A, Breaker RR. Nucleic Acids Res. 2023 Jan 25. PMID: 36617976.
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 Jan 24; 2023 Jan 24. PMID: 36692135.
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.
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 Jan 19; 2023 Jan 19. PMID: 36682579.
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.
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.
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, Cosme 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, Fernandez-Hernando C, Kaminski N. JCI Insight. 2023 Jan 10; 2023 Jan 10. PMID: 36626225.
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.
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.
Is it the time to integrate novel sequencing technologies into clinical practice?VanOudenhove J, Halene S, Mendez L. Curr Opin Hematol. 2023 Jan 2; 2023 Jan 2. PMID: 36602939.
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.
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.
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

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. 2022 Dec 24; 2022 Dec 24. PMID: 36596303.
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.
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. 2022 Dec 17; 2022 Dec 17. PMID: 36528755.
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.
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade.Vathiotis IA, Salichos L, Martinez-Morilla S, Gavrielatou N, Aung TN, Shafi S, Wong PF, Jessel S, Kluger HM, Syrigos KN, Warren S, Gerstein M, Rimm DL. NPJ Precis Oncol. 2022 Dec 15; 2022 Dec 15. PMID: 36522538.
Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in Preclinical Models of Pulmonary Fibrosis.Ahangari F, Becker C, Foster DG, Chioccioli M, Nelson M, Beke K, Wang X, Justet A, Adams T, Readhead B, Meador C, Correll K, Lili LN, Roybal HM, Rose KA, Ding S, Barnthaler T, Briones N, DeIuliis G, Schupp JC, Li Q, Omote N, Aschner Y, Sharma L, Kopf KW, Magnusson B, Hicks R, Backmark A, Dela Cruz CS, Rosas I, Cousens LP, Dudley JT, Kaminski N, Downey GP. Am J Respir Crit Care Med. 2022 Dec 15. PMID: 35998281.
Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure.Qu R, Kluger Y, Yang J, Zhao J, Hafler DA, Krause DS, Bersenev A, Bosenberg M, Hurwitz M, Lucca L, Kluger HM. Mol Cancer. 2022 Dec 14; 2022 Dec 14. PMID: 36514045.
Recruited monocytes/macrophages drive pulmonary neutrophilic inflammation and irreversible lung tissue remodeling in cystic fibrosis.Öz HH, Cheng EC, Di Pietro C, Tebaldi T, Biancon G, Zeiss C, Zhang PX, Huang PH, Esquibies SS, Britto CJ, Schupp JC, Murray TS, Halene S, Krause DS, Egan ME, Bruscia EM. Cell Rep. 2022 Dec 13. PMID: 36516754.
Differential IL18 signaling via IL18 receptor and Na-Cl co-transporter discriminating thermogenesis and glucose metabolism regulation.Zhang X, Luo S, Wang M, Cao Q, Zhang Z, Huang Q, Li J, Deng Z, Liu T, Liu CL, Meppen M, Vromman A, Flavell RA, Hotamışlıgil GS, Liu J, Libby P, Liu Z, Shi GP. Nat Commun. 2022 Dec 8; 2022 Dec 8. PMID: 36482059.
Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation.Hong Z, Adlakha J, Wan N, Guinn E, Giska F, Gupta K, Melia TJ, Reinisch KM. J Cell Biol. 2022 Dec 5; 2022 Oct 25. PMID: 36282247.
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.
Double knockout CRISPR screen for cancer resistance to T cell cytotoxicity.Park JJ, Codina A, Ye L, Lam S, Guo J, Clark P, Zhou X, Peng L, Chen S. J Hematol Oncol. 2022 Dec 1; 2022 Dec 1. PMID: 36456981.
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.
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. 2022 Nov 30; 2022 Nov 30. PMID: 36450109.
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.
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. 2022 Nov 27; 2022 Nov 27. PMID: 36437356.
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.
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. 2022 Nov 23; 2022 Nov 23. PMID: 36416142.
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.
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. 2022 Nov 17; 2022 Nov 17. PMID: 36394352.
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.
Single-cell RNAseq uncovers cellular heterogeneity and provides a signature for pediatric sleep apnea.Cortese R, Adams TS, Cataldo KH, Hummel J, Kaminski N, Kheirandish-Gozal L, Gozal D. Eur Respir J. 2022 Nov 10; 2022 Nov 10. PMID: 36356973.
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.
Lung Cell Atlases in Health and Disease.Adams TS, Marlier A, Kaminski N. Annu Rev Physiol. 2022 Nov 9; 2022 Nov 9. PMID: 36351366.
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.
Paul E. Turner.Turner PE. Curr Biol. 2022 Nov 7. PMID: 36347223.
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.
Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma.Chow RD, Michaels T, Bellone S, Hartwich TM, Bonazzoli E, Iwasaki A, Song E, Santin AD. Cancer Discov. 2022 Oct 27; 2022 Oct 27. PMID: 36301137.
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.
An agenda to advance research in MDS: A TOP 10 Priority List from the first international workshop in MDS (iwMDS).Stahl M, Abdel-Wahab O, Wei AH, Savona MR, Xu ML, Xie Z, Taylor J, Starczynowski DT, Sanz GF, Sallman DA, Santini V, Roboz GJ, Patnaik MM, Padron E, Odenike O, Nazha A, Nimer SD, Majeti R, Little RF, Gore SD, List AF, Kuchroo V, Komrokji RS, Kim TK, Kim N, Hourigan CS, Hasserjian RP, Halene S, Griffiths EA, Greenberg PL, Figueroa ME, 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. 2022 Oct 19; 2022 Oct 19. PMID: 36260702.
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.
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. 2022 Oct 18; 2022 Oct 18. PMID: 36256912.
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.
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.
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. 2022 Oct 10; 2022 Oct 10. PMID: 36216496.
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.
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. 2022 Sep 12; 2022 Sep 12. PMID: 36097331.
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.
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. 2022 Sep 6; 2022 Sep 6. PMID: 36066606.
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.
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. 2022 Aug 18; 2022 Aug 18. PMID: 35979721.
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.
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.
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. 2022 Aug 10; 2022 Aug 10. PMID: 35947128.
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.
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.
Genome Engineering for Next-Generation Cellular Immunotherapies.Park JJ, Lee KAV, Lam SZ, Tang K, Chen S. Biochemistry. 2022 Aug 5; 2022 Aug 5. PMID: 35930700.
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.
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. 2022 Jul 28; 2022 Jul 28. PMID: 35901838.
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.
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 Jul 11; 2022 Jul 11. PMID: 35849999.
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.
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 (N Y). 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.
AMIGOS III: Pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids.Shine M, Zhang C, Pyle AM. Bioinformatics. 2022 Apr 6; 2022 Apr 6. PMID: 35385068.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria.Brewer KI, Gaffield GJ, Puri M, Breaker RR. Bioinformatics. 2021 Sep 15; 2021 Sep 15. PMID: 34524415.
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.
Enoxacin Up-Regulates MicroRNA Biogenesis and Down-Regulates Cytotoxic CD8 T-Cell Function in Autoimmune Cholangitis.Itoh A, Adams D, Huang W, Wu Y, Kachapati K, Bednar KJ, Leung PSC, Zhang W, Flavell RA, Gershwin ME, Ridgway WM. Hepatology. 2021 Aug; 2021 Aug 10. PMID: 33462854.
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.
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 (N Y). 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.
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 Apr 1; 2021 Apr 1. PMID: 33792640.
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.
Skin-resident innate lymphoid cells converge on a pathogenic effector state.Bielecki P, Riesenfeld SJ, Hütter JC, Torlai Triglia E, Kowalczyk MS, Ricardo-Gonzalez RR, Lian M, Amezcua Vesely MC, Kroehling L, Xu H, Slyper M, Muus C, Ludwig LS, Christian E, Tao L, Kedaigle AJ, Steach HR, York AG, Skadow MH, Yaghoubi P, Dionne D, Jarret A, McGee HM, Porter CBM, Licona-Limón P, Bailis W, Jackson R, Gagliani N, Gasteiger G, Locksley RM, Regev A, Flavell RA. Nature. 2021 Apr; 2021 Feb 3. PMID: 33536623.
The case of the missing allosteric ribozymes.Panchapakesan SSS, Breaker RR. Nat Chem Biol. 2021 Apr; 2021 Jan 25. PMID: 33495645.
Elevated plasma level of Pentraxin 3 is associated with emphysema and mortality in smokers.Zhang Y, Tedrow J, Nouraie M, Li X, Chandra D, Bon J, Kass DJ, Fuhrman CR, Leader JK, Duncan SR, Kaminski N, Sciurba FC. Thorax. 2021 Apr; 2021 Jan 21. PMID: 33479043.
Nuclear mechanisms of gene expression control: pre-mRNA splicing as a life or death decision.Gordon JM, Phizicky DV, Neugebauer KM. Curr Opin Genet Dev. 2021 Apr; 2020 Dec 5. PMID: 33291060.
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 TJS, Gong G, Desai N, Haimovich A, Taylor RA, Gunel M, Dela Cruz CS, 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. PLoS One. 2021; 2021 Mar 31. PMID: 33788846.
Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance.Evans RM, Krahn N, Murphy BJ, Lee H, Armstrong FA, Söll D. Proc Natl Acad Sci U S A. 2021 Mar 30. PMID: 33753519.
Ribosomal RNA Transcription Regulation in Breast Cancer.Harold CM, Buhagiar AF, Cheng Y, Baserga SJ. Genes (Basel). 2021 Mar 29; 2021 Mar 29. PMID: 33805424.
Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.Zhang CH, Stone EA, Deshmukh M, Ippolito JA, Ghahremanpour MM, Tirado-Rives J, Spasov KA, Zhang S, Takeo Y, Kudalkar SN, Liang Z, Isaacs F, Lindenbach B, Miller SJ, Anderson KS, Jorgensen WL. ACS Cent Sci. 2021 Mar 24; 2021 Feb 22. PMID: 33786375.
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.
The fluoride transporter FLUORIDE EXPORTER (FEX) is the major mechanism of tolerance to fluoride toxicity in plants1.Tausta SL, Berbasova T, Peverelli M, Strobel SA. Plant Physiol. 2021 Mar 21; 2021 Mar 21. PMID: 33787927.
The fluoride transporter FLUORIDE EXPORTER (FEX) is the major mechanism of tolerance to fluoride toxicity in plants.Tausta SL, Berbasova T, Peverelli M, Strobel SA. Plant Physiol. 2021 Mar 21; 2021 Mar 21. PMID: 33744970.
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.
Intrahost speciations and host switches played an important role in the evolution of herpesviruses.Brito AF, Baele G, Nahata KD, Grubaugh ND, Pinney JW. Virus Evol. 2021 Jan; 2021 Mar 18. PMID: 33927887.
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.
Presynaptic Kv3 channels are required for fast and slow endocytosis of synaptic vesicles.Wu XS, Subramanian S, Zhang Y, Shi B, Xia J, Li T, Guo X, El-Hassar L, Szigeti-Buck K, Henao-Mejia J, Flavell RA, Horvath TL, Jonas EA, Kaczmarek LK, Wu LG. Neuron. 2021 Mar 17; 2021 Jan 27. PMID: 33508244.
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.
Nanoparticles for delivery of agents to fetal lungs.Ullrich SJ, Freedman-Weiss M, Ahle S, Mandl HK, Piotrowski-Daspit AS, Roberts K, Yung N, Maassel N, Bauer-Pisani T, Ricciardi AS, Egan ME, Glazer PM, Saltzman WM, Stitelman DH. Acta Biomater. 2021 Mar 15; 2021 Jan 21. PMID: 33484911.
PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern.Vogels CBF, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, 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. medRxiv. 2021 Mar 12; 2021 Mar 12. PMID: 33758901.
SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity.Vogels CBF, Watkins AE, Harden CA, Brackney DE, Shafer J, Wang J, Caraballo C, Kalinich CC, Ott IM, Fauver JR, Kudo E, Lu P, Venkataraman A, Tokuyama M, Moore AJ, Muenker MC, Casanovas-Massana A, Fournier J, Bermejo S, Campbell M, Datta R, Nelson A, Dela Cruz CS, Ko AI, Iwasaki A, Krumholz HM, Matheus JD, Hui P, Liu C, Farhadian SF, Sikka R, Wyllie AL, Grubaugh ND. Med (N Y). 2021 Mar 12; 2020 Dec 26. PMID: 33521748.
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.
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.
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.
Saliva for Detection of SARS-CoV-2. Reply.Wyllie AL, Vogels CBF, Grubaugh ND. N Engl J Med. 2021 Mar 4; 2021 Feb 3. PMID: 33534974.
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.
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.
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.
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.
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 Jan 20; 2021 Jan 20. PMID: 33471102.
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.
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 Jan 13; 2021 Jan 13. PMID: 33441348.
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.
Mentorship in Science: Response to AlShebli et al., Nature Communications 2020.Mummery C, Little M, Lin H, Clark A, Zaret K, Srivastava D, Fuchs E, Watt F, Temple S. Stem Cell Reports. 2021 Jan 12. PMID: 33440177.
Massively parallel discovery of human-specific substitutions that alter enhancer activity.Uebbing S, Gockley J, Reilly SK, Kocher AA, Geller E, Gandotra N, Scharfe C, Cotney J, Noonan JP. Proc Natl Acad Sci U S A. 2021 Jan 12. PMID: 33372131.
Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic.Petrone ME, Earnest R, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND, Tapia L. Nat Commun. 2021 Jan 8; 2021 Jan 8. PMID: 33420058.
Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs.Wang C, Lin H. Genome Biol. 2021 Jan 8; 2021 Jan 8. PMID: 33419460.
GENCODE 2021.Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P. Nucleic Acids Res. 2021 Jan 8. PMID: 33270111.
Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection.Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Cell. 2021 Jan 7; 2020 Oct 20. PMID: 33147444.
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Zoladek T, Zong WX, Zorov DB, Zorzano A, Zou W, Zou Z, Zou Z, Zuryn S, Zwerschke W, Brand-Saberi B, Dong XC, Kenchappa CS, Li Z, Lin Y, Oshima S, Rong Y, Sluimer JC, Stallings CL, Tong CK. Autophagy. 2021 Jan; 2021 Feb 8. PMID: 33634751.
Ultradeep sequencing differentiates patterns of skin clonal mutations associated with sun-exposure status and skin cancer burden.Wei L, Christensen SR, Fitzgerald ME, Graham J, Hutson ND, Zhang C, Huang Z, Hu Q, Zhan F, Xie J, Zhang J, Liu S, Remenyik E, Gellen E, Colegio OR, Bax M, Xu J, Lin H, Huss WJ, Foster BA, Paragh G. Sci Adv. 2021 Jan; 2021 Jan 1. PMID: 33523857.
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

Ythdf m(6)A Readers Function Redundantly during Zebrafish Development.Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Cell Rep. 2020 Dec 29. PMID: 33378672.
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.
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 (N Y). 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 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. 2020 Dec 2; 2020 Dec 2. PMID: 33268519.
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.
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.
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. 2020 Nov 25; 2020 Nov 25. PMID: 33239456.
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.
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.
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.
Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.Zuo Y, De S, Feng Y, Steitz TA. iScience. 2020 Aug 11; 2020 Aug 11. PMID: 32829286.
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.
Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood.Li S, Crawford FW, Gerstein MB. Nat Commun. 2020 Jul 17; 2020 Jul 17. PMID: 32681003.
Inflammasomes and Pyroptosis as Therapeutic Targets for COVID-19.Yap JKY, Moriyama M, Iwasaki A. J Immunol. 2020 Jul 15; 2020 Jun 3. PMID: 32493814.
Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium.Ravindra NG, Alfajaro MM, Gasque V, Habet V, Wei J, Filler RB, Huston NC, Wan H, Szigeti-Buck K, Wang B, Wang G, Montgomery RR, Eisenbarth SC, Williams A, Pyle AM, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, van Dijk D, Wilen CB. bioRxiv. 2020 Jul 13; 2020 Jul 13. PMID: 32511382.
Phage steering of antibiotic-resistance evolution in the bacterial pathogen, Pseudomonas aeruginosa.Gurney J, Pradier L, Griffin JS, Gougat-Barbera C, Chan BK, Turner PE, Kaltz O, Hochberg ME. Evol Med Public Health. 2020; 2020 Jul 11. PMID: 34254028.
Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.Huston NC, Wan H, de Cesaris Araujo Tavares R, Wilen C, Pyle AM. bioRxiv. 2020 Jul 10; 2020 Jul 10. PMID: 32676598.
Bacillus halodurans OapB forms a high-affinity complex with the P13 region of the noncoding RNA OLE.Widner DL, Harris KA, Corey L, Breaker RR. J Biol Chem. 2020 Jul 10; 2020 May 6. PMID: 32376692.
Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis.Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Sci Adv. 2020 Jul; 2020 Jul 8. PMID: 32832599.
Vitamin B12 and folic acid alleviate symptoms of nutritional deficiency by antagonizing aryl hydrocarbon receptor.Kim DJ, Venkataraman A, Jain PC, Wiesler EP, De