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Publications

Recent Publications

2022

2021

  • 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.
  • Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses.Cui C, Wang J, Fagerberg E, Chen PM, Connolly KA, Damo M, Cheung JF, Mao T, Askari AS, Chen S, Fitzgerald B, Foster GG, Eisenbarth SC, Zhao H, Craft J, Joshi NS. Cell. 2021 Dec 9; 2021 Nov 30. PMID: 34852236.
  • Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats.Moreno Santillán DD, Lama TM, Gutierrez Guerrero YT, Brown AM, Donat P, Zhao H, Rossiter SJ, Yohe LR, Potter JH, Teeling EC, Vernes SC, Davies KTJ, Myers E, Hughes GM, Huang Z, Hoffmann F, Corthals AP, Ray DA, Dávalos LM. Mol Ecol. 2021 Dec; 2021 Jul 4. PMID: 34146369.
  • Human B cell lineages associated with germinal centers following influenza vaccination are measurably evolving.Hoehn KB, Turner JS, Miller FI, Jiang R, Pybus OG, Ellebedy AH, Kleinstein SH. Elife. 2021 Nov 17; 2021 Nov 17. PMID: 34787567.
  • 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.
  • M-DATA: A statistical approach to jointly analyzing de novo mutations for multiple traits.Xie Y, Li M, Dong W, Jiang W, Zhao H. PLoS Genet. 2021 Nov; 2021 Nov 4. PMID: 34735430.
  • The impact of removing former drinkers from genome-wide association studies of AUDIT-C.Dao C, Zhou H, Small A, Gordon KS, Li B, Kember RL, Ye Y, Gelernter J, Xu K, Kranzler HR, Zhao H, Justice AC. Addiction. 2021 Nov; 2021 May 6. PMID: 33861876.
  • 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.
  • Elevated N-Linked Glycosylation of IgG V Regions in Myasthenia Gravis Disease Subtypes.Mandel-Brehm C, Fichtner ML, Jiang R, Winton VJ, Vazquez SE, Pham MC, Hoehn KB, Kelleher NL, Nowak RJ, Kleinstein SH, Wilson MR, DeRisi JL, O'Connor KC. J Immunol. 2021 Oct 15; 2021 Sep 20. PMID: 34544801.
  • A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program.Verma A, Tsao N, Thomann L, Ho YL, Iyengar S, Luoh SW, Carr R, Crawford D, Efird JT, Huffman J, Hung A, Ivey K, Levin M, Lynch J, Natarajan P, Pyarajan S, Bick A, Costa L, Genovese G, Hauger R, Madduri R, Pathak G, Polimanti R, Voight B, Vujkovic M, Zekavat M, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O'Donnell C, Damrauer S, Liao K. medRxiv. 2021 Oct 15; 2021 Oct 15. PMID: 34642702.
  • B Cell Mobilization, Dissemination, Fine Tuning of Local Antigen Specificity and Isotype Selection in Asthma.Ohm-Laursen L, Meng H, Hoehn KB, Nouri N, Jiang Y, Clouser C, Johnstone TG, Hause R, Sandhar BS, Upton NEG, Chevretton EB, Lakhani R, Corrigan CJ, Kleinstein SH, Gould HJ. Front Immunol. 2021; 2021 Oct 14. PMID: 34721376.
  • Circadian Rhythm Analysis Using Wearable Device Data: Novel Penalized Machine Learning Approach.Li X, Kane M, Zhang Y, Sun W, Song Y, Dong S, Lin Q, Zhu Q, Jiang F, Zhao H. J Med Internet Res. 2021 Oct 14; 2021 Oct 14. PMID: 34647895.
  • Calculating Orthologous Protein-Coding Sequence Set Probability Using the Poisson Process.Liu J, Wang Y, Zhao H. J Comput Biol. 2021 Oct; 2021 Sep 1. PMID: 34491118.
  • 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.
  • 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.
  • SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits.Zhang Y, Lu Q, Ye Y, Huang K, Liu W, Wu Y, Zhong X, Li B, Yu Z, Travers BG, Werling DM, Li JJ, Zhao H. Genome Biol. 2021 Sep 7; 2021 Sep 7. PMID: 34493297.
  • Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics.Zhang Y, Cheng Y, Jiang W, Ye Y, Lu Q, Zhao H. Brief Bioinform. 2021 Sep 2. PMID: 33497438.
  • 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.
  • Mind the gap from research laboratory to clinic: Challenges and opportunities for next-generation assays in human diseases.D'Souza MP, Palin AC, Calder T, Golding H, Kleinstein SH, Milliken EL, O'Connor D, Tomaras G, Warren J, Boggiano C. Vaccine. 2021 Aug 31; 2021 Aug 6. PMID: 34366145.
  • LinkedImm: a linked data graph database for integrating immunological data.Bukhari SAC, Pawar S, Mandell J, Kleinstein SH, Cheung KH. BMC Bioinformatics. 2021 Aug 25; 2021 Aug 25. PMID: 34433410.
  • 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.
  • RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators.Wang X, Zhang Z, Qin W, Liu S, Liu C, Genchev GZ, Hui L, Zhao H, Lu H. Genomics Proteomics Bioinformatics. 2021 Aug; 2021 Mar 10. PMID: 33713851.
  • DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease.Kundishora AJ, Peters ST, Pinard A, Duran D, Panchagnula S, Barak T, Miyagishima DF, Dong W, Smith H, Ocken J, Dunbar A, Nelson-Williams C, Haider S, Walker RL, Li B, Zhao H, Thumkeo D, Marlier A, Duy PQ, Diab NS, Reeves BC, Robert SM, Sujijantarat N, Stratman AN, Chen YH, Zhao S, Roszko I, Lu Q, Zhang B, Mane S, Castaldi C, López-Giráldez F, Knight JR, Bamshad MJ, Nickerson DA, Geschwind DH, Chen SL, Storm PB, Diluna ML, Matouk CC, Orbach DB, Alper SL, Smith ER, Lifton RP, Gunel M, Milewicz DM, Jin SC, Kahle KT. JAMA Neurol. 2021 Aug 1. PMID: 34125151.
  • A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics.Zhou G, Zhao H. PLoS Genet. 2021 Jul; 2021 Jul 26. PMID: 34310601.
  • Transformation and differential abundance analysis of microbiome data incorporating phylogeny.Zhou C, Zhao H, Wang T. Bioinformatics. 2021 Jul 24; 2021 Jul 24. PMID: 34302462.
  • Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders.Brioschi S, Wang WL, Peng V, Wang M, Shchukina I, Greenberg ZJ, Bando JK, Jaeger N, Czepielewski RS, Swain A, Mogilenko DA, Beatty WL, Bayguinov P, Fitzpatrick JAJ, Schuettpelz LG, Fronick CC, Smirnov I, Kipnis J, Shapiro VS, Wu GF, Gilfillan S, Cella M, Artyomov MN, Kleinstein SH, Colonna M. Science. 2021 Jul 23; 2021 Jun 3. PMID: 34083450.
  • Comparing Host Module Activation Patterns and Temporal Dynamics in Infection by Influenza H1N1 Viruses.Nudelman I, Kudrin D, Nudelman G, Deshpande R, Hartmann BM, Kleinstein SH, Myers CL, Sealfon SC, Zaslavsky E. Front Immunol. 2021; 2021 Jul 14. PMID: 34335598.
  • 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.
  • 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.
  • Genomics of Gulf War Illness in U.S. Veterans Who Served during the 1990-1991 Persian Gulf War: Methods and Rationale for Veterans Affairs Cooperative Study #2006.Radhakrishnan K, Hauser ER, Polimanti R, Helmer DA, Provenzale D, McNeil RB, Maffucci A, Quaden R, Zhao H, Whitbourne SB, Harrington KM, Vahey J, Gelernter J, Levey DF, Huang GD, Gaziano JM, Concato J, Aslan M. Brain Sci. 2021 Jun 25; 2021 Jun 25. PMID: 34202057.
  • Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells.Jiang R, Meng H, Raddassi K, Fleming I, Hoehn KB, Dardick KR, Belperron AA, Montgomery RR, Shalek AK, Hafler DA, Kleinstein SH, Bockenstedt LK. JCI Insight. 2021 Jun 22; 2021 Jun 22. PMID: 34061047.
  • 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.
  • Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection.Zekavat SM, Lin SH, Bick AG, Liu A, Paruchuri K, Wang C, Uddin MM, Ye Y, Yu Z, Liu X, Kamatani Y, Bhattacharya R, Pirruccello JP, Pampana A, Loh PR, Kohli P, McCarroll SA, Kiryluk K, Neale B, Ionita-Laza I, Engels EA, Brown DW, Smoller JW, Green R, Karlson EW, Lebo M, Ellinor PT, Weiss ST, Daly MJ, Terao C, Zhao H, Ebert BL, Reilly MP, Ganna A, Machiela MJ, Genovese G, Natarajan P. Nat Med. 2021 Jun; 2021 Jun 7. PMID: 34099924.
  • Integrative modeling of transmitted and de novo variants identifies novel risk genes for congenital heart disease.Li M, Zeng X, Jin C, Jin SC, Dong W, Brueckner M, Lifton R, Lu Q, Zhao H. Quant Biol. 2021 Jun. PMID: 35414959.
  • 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.
  • Transcriptome-wide association analysis of brain structures yields insights into pleiotropy with complex neuropsychiatric traits.Zhao B, Shan Y, Yang Y, Yu Z, Li T, Wang X, Luo T, Zhu Z, Sullivan P, Zhao H, Li Y, Zhu H. Nat Commun. 2021 May 17; 2021 May 17. PMID: 34001886.
  • 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.
  • 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.
  • A unified framework for cross-population trait prediction by leveraging the genetic correlation of polygenic traits.Cai M, Xiao J, Zhang S, Wan X, Zhao H, Chen G, Yang C. Am J Hum Genet. 2021 Apr 1; 2021 Mar 25. PMID: 33770506.
  • 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.
  • Genome-Wide Association Studies of Schizophrenia and Bipolar Disorder in a Diverse Cohort of US Veterans.Bigdeli TB, Fanous AH, Li Y, Rajeevan N, Sayward F, Genovese G, Gupta R, Radhakrishnan K, Malhotra AK, Sun N, Lu Q, Hu Y, Li B, Chen Q, Mane S, Miller P, Cheung KH, Gur RE, Greenwood TA, Braff DL, Achtyes ED, Buckley PF, Escamilla MA, Lehrer D, Malaspina DP, McCarroll SA, Rapaport MH, Vawter MP, Pato MT, Pato CN, Zhao H, Kosten TR, Brophy M, Pyarajan S, Shi Y, O'Leary TJ, Gleason T, Przygodzki R, Muralidhar S, Gaziano JM, Huang GD, Concato J, Siever LJ, Aslan M, Harvey PD. Schizophr Bull. 2021 Mar 16. PMID: 33169155.
  • Overview of PAX gene family: analysis of human tissue-specific variant expression and involvement in human disease.Thompson B, Davidson EA, Liu W, Nebert DW, Bruford EA, Zhao H, Dermitzakis ET, Thompson DC, Vasiliou V. Hum Genet. 2021 Mar; 2020 Jul 29. PMID: 32728807.
  • CD4+ follicular regulatory T cells optimize the influenza virus-specific B cell response.Lu Y, Jiang R, Freyn AW, Wang J, Strohmeier S, Lederer K, Locci M, Zhao H, Angeletti D, O'Connor KC, Kleinstein SH, Nachbagauer R, Craft J. J Exp Med. 2021 Mar 1. PMID: 33326020.
  • Identifying modules of cooperating cancer drivers.Klein MI, Cannataro VL, Townsend JP, Newman S, Stern DF, Zhao H. Mol Syst Biol. 2021 Mar. PMID: 33769711.
  • Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsy.Jin SC, Lewis SA, Bakhtiari S, Zeng X, Sierant MC, Shetty S, Nordlie SM, Elie A, Corbett MA, Norton BY, van Eyk CL, Haider S, Guida BS, Magee H, Liu J, Pastore S, Vincent JB, Brunstrom-Hernandez J, Papavasileiou A, Fahey MC, Berry JG, Harper K, Zhou C, Zhang J, Li B, Zhao H, Heim J, Webber DL, Frank MSB, Xia L, Xu Y, Zhu D, Zhang B, Sheth AH, Knight JR, Castaldi C, Tikhonova IR, López-Giráldez F, Keren B, Whalen S, Buratti J, Doummar D, Cho M, Retterer K, Millan F, Wang Y, Waugh JL, Rodan L, Cohen JS, Fatemi A, Lin AE, Phillips JP, Feyma T, MacLennan SC, Vaughan S, Crompton KE, Reid SM, Reddihough DS, Shang Q, Gao C, Novak I, Badawi N, Wilson YA, McIntyre SJ, Mane SM, Wang X, Amor DJ, Zarnescu DC, Lu Q, Xing Q, Zhu C, Bilguvar K, Padilla-Lopez S, Lifton RP, Gecz J, MacLennan AH, Kruer MC. Nat Genet. 2021 Mar. PMID: 33432185.
  • Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes.Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Niroula A, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IY, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P. Nature. 2021 Mar. PMID: 33707633.
  • Alignment free identification of clones in B cell receptor repertoires.Lindenbaum O, Nouri N, Kluger Y, Kleinstein SH. Nucleic Acids Res. 2021 Feb 26. PMID: 33330933.
  • 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.
  • Cortical Transcriptomic Alterations in Association With Appetitive Neuropeptides and Body Mass Index in Posttraumatic Stress Disorder.Stone LA, Girgenti MJ, Wang J, Ji D, Zhao H, Krystal JH, Duman RS. Int J Neuropsychopharmacol. 2021 Feb 15. PMID: 32951025.
  • Elevated Blood Pressure Increases Pneumonia Risk: Epidemiological Association and Mendelian Randomization in the UK Biobank.Zekavat SM, Honigberg M, Pirruccello JP, Kohli P, Karlson EW, Newton-Cheh C, Zhao H, Natarajan P. Med (N Y). 2021 Feb 12; 2020 Nov 30. PMID: 33283203.
  • Toll-like receptor 7 deficiency suppresses type 1 diabetes development by modulating B-cell differentiation and function.Huang J, Peng J, Pearson JA, Efthimiou G, Hu Y, Tai N, Xing Y, Zhang L, Gu J, Jiang J, Zhao H, Zhou Z, Wong FS, Wen L. Cell Mol Immunol. 2021 Feb; 2021 Jan 11. PMID: 33432061.
  • Interactions Between Enhanced Polygenic Risk Scores and Lifestyle for Cardiovascular Disease, Diabetes, and Lipid Levels.Ye Y, Chen X, Han J, Jiang W, Natarajan P, Zhao H. Circ Genom Precis Med. 2021 Feb; 2021 Jan 12. PMID: 33433237.
  • A comprehensive genetic and epidemiological association analysis of vitamin D with common diseases/traits in the UK Biobank.Ye Y, Yang H, Wang Y, Zhao H. Genet Epidemiol. 2021 Feb; 2020 Sep 12. PMID: 32918767.
  • A pooled genome-wide association study identifies pancreatic cancer susceptibility loci on chromosome 19p12 and 19p13.3 in the full-Jewish population.Streicher SA, Klein AP, Olson SH, Kurtz RC, Amundadottir LT, DeWan AT, Zhao H, Risch HA. Hum Genet. 2021 Feb; 2020 Jul 15. PMID: 32671597.
  • FANCY: fast estimation of privacy risk in functional genomics data.Gürsoy G, Brannon CM, Navarro FCP, Gerstein M. Bioinformatics. 2021 Jan 29. PMID: 32726397.
  • 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.
  • 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.
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2012

  • Architecture of the human regulatory network derived from ENCODE data.Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Nature. 2012 Sep 6. PMID: 22955619.
  • Quantifying selection in high-throughput Immunoglobulin sequencing data sets.Yaari G, Uduman M, Kleinstein SH. Nucleic Acids Res. 2012 Sep 1; 2012 May 27. PMID: 22641856.

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