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Recent Publications

2023

  • Unified views on variant impact across many diseases.Kumar S, Gerstein M. Trends Genet. 2023 Jun; 2023 Feb 28. PMID: 36858880.
  • Genetic determination of regional connectivity in modelling the spread of COVID-19 outbreak for more efficient mitigation strategies.Salichos L, Warrell J, Cevasco H, Chung A, Gerstein M. Sci Rep. 2023 May 25; 2023 May 25. PMID: 37231011.
  • Calculating the futureQuantum Supremacy: How the Quantum Computer Revolution Will Change Everything Michio Kaku Doubleday, 2023. 352 pp.Greenbaum D, Gerstein M. Science. 2023 May 12; 2023 May 11. PMID: 37167370.
  • The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties.Jiang R, Roy B, Wu Q, Mohanty S, Nowak RJ, Shaw AC, Kleinstein SH, O'Connor KC. Immunohorizons. 2023 May 1. PMID: 37171806.
  • Age-associated B cells are heterogeneous and dynamic drivers of autoimmunity in mice.Nickerson KM, Smita S, Hoehn KB, Marinov AD, Thomas KB, Kos JT, Yang Y, Bastacky SI, Watson CT, Kleinstein SH, Shlomchik MJ. J Exp Med. 2023 May 1; 2023 Feb 24. PMID: 36828389.
  • Author Correction: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.Zeng Y, Li J, Wei C, Zhao H, Wang T. Genome Biol. 2023 Apr 21; 2023 Apr 21. PMID: 37085916.
  • Early breast cancer risk detection: a novel framework leveraging polygenic risk scores and machine learning.Tao LR, Ye Y, Zhao H. J Med Genet. 2023 Apr 13; 2023 Apr 13. PMID: 37055164.
  • The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. Cell. 2023 Mar 30. PMID: 37001506.
  • Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson's disease.Vidyadhara DJ, Somayaji M, Wade N, Yücel B, Zhao H, Shashaank N, Ribaudo J, Gupta J, Lam TT, Sames D, Greene LE, Sulzer DL, Chandra SS. Cell Rep. 2023 Mar 28; 2023 Mar 14. PMID: 36920906.
  • Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH, Campbell PJ, Tubio JMC. Nat Genet. 2023 Mar 21; 2023 Mar 21. PMID: 36944736.
  • HBV-infected hepatocellular carcinoma can be robustly classified into three clinically relevant subgroups by a novel analytical protocol.Cheng Z, Li L, Zhang Y, Ren Y, Gu J, Wang X, Zhao H, Lu H. Brief Bioinform. 2023 Mar 19. PMID: 36736372.
  • A genome-wide association study of frailty identifies significant genetic correlation with neuropsychiatric, cardiovascular, and inflammation pathways.Ye Y, Noche RB, Szejko N, Both CP, Acosta JN, Leasure AC, Brown SC, Sheth KN, Gill TM, Zhao H, Falcone GJ. Geroscience. 2023 Mar 16; 2023 Mar 16. PMID: 36928559.
  • OTTERS: a powerful TWAS framework leveraging summary-level reference data.Dai Q, Zhou G, Zhao H, Võsa U, Franke L, Battle A, Teumer A, Lehtimäki T, Raitakari OT, Esko T, Epstein MP, Yang J. Nat Commun. 2023 Mar 7; 2023 Mar 7. PMID: 36882394.
  • Whole-Exome Sequencing Analyses Support a Role of Vitamin D Metabolism in Ischemic Stroke.Xie Y, Acosta JN, Ye Y, Demarais ZS, Conlon CJ, Chen M, Zhao H, Falcone GJ. Stroke. 2023 Mar; 2023 Feb 10. PMID: 36762557.
  • NLRP6 deficiency expands a novel CD103(+) B cell population that confers immune tolerance in NOD mice.Pearson JA, Peng J, Huang J, Yu X, Tai N, Hu Y, Sha S, Flavell RA, Zhao H, Wong FS, Wen L. Front Immunol. 2023; 2023 Feb 23. PMID: 36911699.
  • Binding peptide generation for MHC Class I proteins with deep reinforcement learning.Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C, Min MR. Bioinformatics. 2023 Feb 3. PMID: 36692135.
  • Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Nature. 2023 Feb. PMID: 36697832.
  • Platelet response to influenza vaccination reflects effects of aging.Konstorum A, Mohanty S, Zhao Y, Melillo A, Vander Wyk B, Nelson A, Tsang S, Blevins TP, Belshe RB, Chawla DG, Rondina MT, Gill TM, Montgomery RR, Allore HG, Kleinstein SH, Shaw AC. Aging Cell. 2023 Feb; 2023 Jan 19. PMID: 36656789.
  • PD-1(high)CXCR5(-)CD4(+) peripheral helper T cells promote CXCR3(+) plasmablasts in human acute viral infection.Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. Cell Rep. 2023 Jan 31; 2023 Jan 2. PMID: 36596303.
  • Privacy-preserving cancer type prediction with homomorphic encryption.Sarkar E, Chielle E, Gursoy G, Chen L, Gerstein M, Maniatakos M. Sci Rep. 2023 Jan 30; 2023 Jan 30. PMID: 36717667.
  • 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.
  • 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.
  • TP53-mediated clonal hematopoiesis confers increased risk for incident atherosclerotic disease.Zekavat SM, Viana-Huete V, Matesanz N, Jorshery SD, Zuriaga MA, Uddin MM, Trinder M, Paruchuri K, Zorita V, Ferrer-Pérez A, Amorós-Pérez M, Kunderfranco P, Carriero R, Greco CM, Aroca-Crevillen A, Hidalgo A, Damrauer SM, Ballantyne CM, Niroula A, Gibson CJ, Pirruccello J, Griffin G, Ebert BL, Libby P, Fuster V, Zhao H, Ghassemi M, Natarajan P, Bick AG, Fuster JJ, Klarin D. Nat Cardiovasc Res. 2023 Jan 16. PMID: 36949957.
  • 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.
  • SDPRX: A statistical method for cross-population prediction of complex traits.Zhou G, Chen T, Zhao H. Am J Hum Genet. 2023 Jan 5; 2022 Dec 1. PMID: 36460009.
  • Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children.Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Oguz C, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Kitakule MM, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, McGuire PJ, Pittaluga S, Germain RN, Apps R, Schwartz DM, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Nat Immunol. 2023 Jan; 2022 Dec 19. PMID: 36536106.
  • 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.

2022

  • Association of Gulf War Illness with Characteristics in Deployed vs. Non-Deployed Gulf War Era Veterans in the Cooperative Studies Program 2006/Million Veteran Program 029 Cohort: A Cross-Sectional Analysis.Duong LM, Nono Djotsa ABS, Vahey J, Steele L, Quaden R, Harrington KM, Ahmed ST, Polimanti R, Streja E, Gaziano JM, Concato J, Zhao H, Radhakrishnan K, Hauser ER, Helmer DA, Aslan M, Gifford EJ. Int J Environ Res Public Health. 2022 Dec 24; 2022 Dec 24. PMID: 36612580.
  • Molecular Markers in Maternal Blood Exosomes Allow Early Detection of Fetal Alcohol Spectrum Disorders.Darbinian N, Darbinyan A, Sinard J, Tatevosian G, Merabova N, D'Amico F, Khader T, Bajwa A, Martirosyan D, Gawlinski AK, Pursnani R, Zhao H, Amini S, Morrison M, Goetzl L, Selzer ME. Int J Mol Sci. 2022 Dec 21; 2022 Dec 21. PMID: 36613580.
  • Multi-objective optimization identifies a specific and interpretable COVID-19 host response signature.Cappuccio A, Chawla DG, Chen X, Rubenstein AB, Cheng WS, Mao W, Burke TW, Tsalik EL, Petzold E, Henao R, McClain MT, Woods CW, Chikina M, Troyanskaya OG, Sealfon SC, Kleinstein SH, Zaslavsky E. Cell Syst. 2022 Dec 21. PMID: 36549275.
  • Benchmarking transcriptional host response signatures for infection diagnosis.Chawla DG, Cappuccio A, Tamminga A, Sealfon SC, Zaslavsky E, Kleinstein SH. Cell Syst. 2022 Dec 21. PMID: 36549274.
  • 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.
  • Benchmarking automated cell type annotation tools for single-cell ATAC-seq data.Wang Y, Sun X, Zhao H. Front Genet. 2022; 2022 Dec 13. PMID: 36583014.
  • An unbiased kinship estimation method for genetic data analysis.Jiang W, Zhang X, Li S, Song S, Zhao H. BMC Bioinformatics. 2022 Dec 6; 2022 Dec 6. PMID: 36474154.
  • 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.
  • GATTACA is still pertinent 25 years later.Greenbaum D, Gerstein M. Nat Genet. 2022 Dec. PMID: 36424501.
  • Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination.Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH, Sékaly RP. Nat Immunol. 2022 Dec; 2022 Oct 31. PMID: 36316476.
  • Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses.Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH, Pulendran B. Nat Immunol. 2022 Dec; 2022 Oct 31. PMID: 36316475.
  • 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.
  • A curated collection of human vaccination response signatures.Smith KC, Chawla DG, Dhillon BK, Ji Z, Vita R, van der Leest EC, Weng JYJ, Tang E, Abid A, Peters B, Hancock REW, Floratos A, Kleinstein SH. Sci Data. 2022 Nov 8; 2022 Nov 8. PMID: 36347894.
  • 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.
  • Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy.Fichtner ML, Hoehn KB, Ford EE, Mane-Damas M, Oh S, Waters P, Payne AS, Smith ML, Watson CT, Losen M, Martinez-Martinez P, Nowak RJ, Kleinstein SH, O'Connor KC. Acta Neuropathol Commun. 2022 Oct 28; 2022 Oct 28. PMID: 36307868.
  • 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.
  • The Immune Signatures data resource, a compendium of systems vaccinology datasets.Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S, Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn P, Campbell J, Sarwal M, Tsang JS, Levy O, Pulendran B, Sekaly R, Floratos A, Gottardo R, Kleinstein SH, Suárez-Fariñas M. Sci Data. 2022 Oct 20; 2022 Oct 20. PMID: 36266291.
  • Prioritized candidate causal haplotype blocks in plant genome-wide association studies.Wu X, Jiang W, Fragoso C, Huang J, Zhou G, Zhao H, Dellaporta S. PLoS Genet. 2022 Oct; 2022 Oct 17. PMID: 36251695.
  • 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.
  • A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data.Zhu B, Li H, Zhang L, Chandra SS, Zhao H. Brief Bioinform. 2022 Sep 20. PMID: 35514182.
  • FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines.Ren Y, Kong Y, Zhou X, Genchev GZ, Zhou C, Zhao H, Lu H. Commun Biol. 2022 Sep 16; 2022 Sep 16. PMID: 36114280.
  • Pangenomic analysis of Chinese gastric cancer.Yu Y, Zhang Z, Dong X, Yang R, Duan Z, Xiang Z, Li J, Li G, Yan F, Xue H, Jiao D, Lu J, Lu H, Zhang W, Wei Y, Fan S, Li J, Jia J, Zhang J, Ji J, Liu P, Lu H, Zhao H, Chen S, Wei C, Chen H, Zhu Z. Nat Commun. 2022 Sep 15; 2022 Sep 15. PMID: 36109518.
  • The immunology of Parkinson's disease.Zhu B, Yin D, Zhao H, Zhang L. Semin Immunopathol. 2022 Sep; 2022 Jun 8. PMID: 35674826.
  • Sex-specific genetic association between psychiatric disorders and cognition, behavior and brain imaging in children and adults.Gui Y, Zhou X, Wang Z, Zhang Y, Wang Z, Zhou G, Zhao Y, Liu M, Lu H, Zhao H. Transl Psychiatry. 2022 Aug 26; 2022 Aug 26. PMID: 36028495.
  • Genomic research data and the justice system.Greenbaum D, Gerstein M. Science. 2022 Aug 19; 2022 Aug 18. PMID: 35981024.
  • ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks.Wang Y, Liu T, Zhao H. Bioinformatics. 2022 Aug 10. PMID: 35771600.
  • Observation of WWW Production in pp Collisions at sqrt[s]=13  TeV with the ATLAS Detector.Aad G, Abbott B, Abbott DC, Abed Abud A, Abeling K, Abhayasinghe DK, Abidi SH, Aboulhorma A, Abramowicz H, Abreu H, Abulaiti Y, Abusleme Hoffman AC, Acharya BS, Achkar B, Adam L, Adam Bourdarios C, Adamczyk L, Adamek L, Addepalli SV, Adelman J, Adiguzel A, Adorni S, Adye T, Affolder AA, Afik Y, Agapopoulou C, Agaras MN, Agarwala J, Aggarwal A, Agheorghiesei C, Aguilar-Saavedra JA, Ahmad A, Ahmadov F, Ahmed WS, Ai X, Aielli G, Aizenberg I, Akbiyik M, Åkesson TPA, Akimov AV, Al Khoury K, Alberghi GL, Albert J, Albicocco P, Alconada Verzini MJ, Alderweireldt S, Aleksa M, Aleksandrov IN, Alexa C, Alexopoulos T, Alfonsi A, Alfonsi F, Alhroob M, Ali B, Ali S, Aliev M, Alimonti G, Allaire C, Allbrooke BMM, Allport PP, Aloisio A, Alonso F, Alpigiani C, Alunno Camelia E, Alvarez Estevez M, Alviggi MG, Amaral Coutinho Y, Ambler A, Ambroz L, Amelung C, Amidei D, Amor Dos Santos SP, Amoroso S, Amos KR, Amrouche CS, Ananiev V, Anastopoulos C, Andari N, Andeen T, Anders JK, Andrean SY, Andreazza A, Angelidakis S, Angerami A, Anisenkov AV, Annovi A, Antel C, Anthony MT, Antipov E, Antonelli M, Antrim DJA, Anulli F, Aoki M, Aparisi Pozo JA, Aparo MA, Aperio Bella L, Aranzabal N, Araujo Ferraz V, Arcangeletti C, Arce ATH, Arena E, Arguin JF, Argyropoulos S, Arling JH, Armbruster AJ, Arnaez O, Arnold H, Arrubarrena Tame ZP, Artoni G, Asada H, Asai K, Asai S, Asbah NA, Asimakopoulou EM, Assahsah J, Assamagan K, Astalos R, Atkin RJ, Atkinson M, Atlay NB, Atmani H, Atmasiddha PA, Augsten K, Auricchio S, Austrup VA, Avner G, Avolio G, Ayoub MK, Azuelos G, Babal D, Bachacou H, Bachas K, Bachiu A, Backman F, Badea A, Bagnaia P, Bahmani M, Bailey AJ, Bailey VR, Baines JT, Bakalis C, Baker OK, Bakker PJ, Bakos E, Bakshi Gupta D, Balaji S, Balasubramanian R, Baldin EM, Balek P, Ballabene E, Balli F, Baltes LM, Balunas WK, Balz J, Banas E, Bandieramonte M, Bandyopadhyay A, Bansal S, Barak L, Barberio EL, Barberis D, Barbero M, Barbour G, Barends KN, Barillari T, Barisits MS, Barkeloo J, Barklow T, Barnett RM, Baron P, Baroncelli A, Barone G, Barr AJ, Barranco Navarro L, Barreiro F, Barreiro Guimarães da Costa J, Barron U, Barsov S, Bartels F, Bartoldus R, Bartolini G, Barton AE, Bartos P, Basalaev A, Basan A, Baselga M, Bashta I, Bassalat A, Basso MJ, Basson CR, Bates RL, Batlamous S, Batley JR, Batool B, Battaglia M, Bauce M, Bauer F, Bauer P, Bayirli A, Beacham JB, Beau T, Beauchemin PH, Becherer F, Bechtle P, Beck HP, Becker K, Becot C, Beddall AJ, Bednyakov VA, Bee CP, Beemster LJ, Beermann TA, Begalli M, Begel M, Behera A, Behr JK, Beirao Da Cruz E Silva C, Beirer JF, Beisiegel F, Belfkir M, Bella G, Bellagamba L, Bellerive A, Bellos P, Beloborodov K, Belotskiy K, Belyaev NL, Benchekroun D, Benhammou Y, Benjamin DP, Benoit M, Bensinger JR, Bentvelsen S, Beresford L, Beretta M, Berge D, Bergeaas Kuutmann E, Berger N, Bergmann B, Bergsten LJ, Beringer J, Berlendis S, Bernardi G, Bernius C, Bernlochner FU, Berry T, Berta P, Bertram IA, Bessidskaia Bylund O, Bethke S, Betti A, Bevan AJ, Bhatta S, Bhattacharya DS, Bhattarai P, Bhopatkar VS, Bi R, Bi R, Bianchi RM, Biebel O, Bielski R, Biesuz NV, Biglietti M, Billoud TRV, Bindi M, Bingul A, Bini C, Biondi S, Biondini A, Birch-Sykes CJ, Bird GA, Birman M, Bisanz T, Biswal JP, Biswas D, Bitadze A, Bjørke K, Bloch I, Blocker C, Blue A, Blumenschein U, Blumenthal J, Bobbink GJ, Bobrovnikov VS, Boehler M, Bogavac D, Bogdanchikov AG, Bohm C, Boisvert V, Bokan P, Bold T, Bomben M, Bona M, Boonekamp M, Booth CD, Borbély AG, Borecka-Bielska HM, Borgna LS, Borissov G, Bortoletto D, Boscherini D, Bosman M, Bossio Sola JD, Bouaouda K, Boudreau J, Bouhova-Thacker EV, Boumediene D, Bouquet R, Boveia A, Boyd J, Boye D, Boyko IR, Bracinik J, Brahimi N, Brandt G, Brandt O, Braren F, Brau B, Brau JE, Breaden Madden WD, Brendlinger K, Brener R, Brenner L, Brenner R, Bressler S, Brickwedde B, Britton D, Britzger D, Brock 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  • 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.
  • Comparative Proteome and Cis-Regulatory Element Analysis Reveals Specific Molecular Pathways Conserved in Dog and Human Brains.Hong H, Zhao Z, Huang X, Guo C, Zhao H, Wang GD, Zhang YP, Zhao JP, Shi J, Wu QF, Jiang YH, Wang Y, Li LM, Du Z, Zhang YQ, Xiong Y. Mol Cell Proteomics. 2022 Aug; 2022 Jun 20. PMID: 35738554.
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  • Comparison of Methods Utilizing Sex-Specific PRSs Derived From GWAS Summary Statistics.Zhang C, Ye Y, Zhao H. Front Genet. 2022; 2022 Jul 8. PMID: 35873490.
  • 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.
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  • 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.
  • Hemodynamic differences between women and men with elevated blood pressure in China: A non-invasive assessment of 45,082 adults using impedance cardiography.Caraballo C, Mahajan S, Gu J, Lu Y, Spatz ES, Dreyer RP, Zhang M, Sun N, Ren Y, Zheng X, Zhao H, Lu H, Ma ZJ, Krumholz HM. PLoS One. 2022; 2022 Jun 14. PMID: 35700163.
  • Network assisted analysis of de novo variants using protein-protein interaction information identified 46 candidate genes for congenital heart disease.Xie Y, Jiang W, Dong W, Li H, Jin SC, Brueckner M, Zhao H. PLoS Genet. 2022 Jun; 2022 Jun 7. PMID: 35671298.
  • phyloMDA: an R package for phylogeny-aware microbiome data analysis.Liu T, Zhou C, Wang H, Zhao H, Wang T. BMC Bioinformatics. 2022 Jun 6; 2022 Jun 6. PMID: 35668363.
  • Quantifying concordant genetic effects of de novo mutations on multiple disorders.Guo H, Hou L, Shi Y, Jin SC, Zeng X, Li B, Lifton RP, Brueckner M, Zhao H, Lu Q. Elife. 2022 Jun 6; 2022 Jun 6. PMID: 35666111.
  • A multi-population phenome-wide association study of genetically-predicted height in the Million Veteran Program.Raghavan S, Huang J, Tcheandjieu C, Huffman JE, Litkowski E, Liu C, Ho YA, Hunter-Zinck H, Zhao H, Marouli E, North KE, Lange E, Lange LA, Voight BF, Gaziano JM, Pyarajan S, Hauser ER, Tsao PS, Wilson PWF, Chang KM, Cho K, O'Donnell CJ, Sun YV, Assimes TL. PLoS Genet. 2022 Jun; 2022 Jun 2. PMID: 35653334.
  • Photoreceptor Layer Thinning Is an Early Biomarker for Age-Related Macular Degeneration: Epidemiologic and Genetic Evidence from UK Biobank OCT Data.Zekavat SM, Sekimitsu S, Ye Y, Raghu V, Zhao H, Elze T, Segrè AV, Wiggs JL, Natarajan P, Del Priore L, Zebardast N, Wang JC. Ophthalmology. 2022 Jun; 2022 Feb 8. PMID: 35149155.
  • Pan-Cancer Single-Cell Analysis Reveals the Core Factors and Pathway in Specific Cancer Stem Cells of Upper Gastrointestinal Cancer.Li L, Zhang Y, Ren Y, Cheng Z, Zhang Y, Wang X, Zhao H, Lu H. Front Bioeng Biotechnol. 2022; 2022 May 13. PMID: 35646860.
  • Comprehensive analysis of ubiquitously expressed genes in human, from a data-driven perspective.Gu J, Dai J, Lu H, Zhao H. Genomics Proteomics Bioinformatics. 2022 May 12; 2022 May 12. PMID: 35569803.
  • Leveraging LD eigenvalue regression to improve the estimation of SNP heritability and confounding inflation.Song S, Jiang W, Zhang Y, Hou L, Zhao H. Am J Hum Genet. 2022 May 5; 2022 Apr 13. PMID: 35421325.
  • 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 NL, Thomann LO, Ho YL, Iyengar SK, Luoh SW, Carr R, Crawford DC, Efird JT, Huffman JE, Hung A, Ivey KL, Levin MG, Lynch J, Natarajan P, Pyarajan S, Bick AG, Costa L, Genovese G, Hauger R, Madduri R, Pathak GA, Polimanti R, Voight B, Vujkovic M, Zekavat SM, Zhao H, Ritchie MD, Chang KM, Cho K, Casas JP, Tsao PS, Gaziano JM, O'Donnell C, Damrauer SM, Liao KP. PLoS Genet. 2022 Apr; 2022 Apr 28. PMID: 35482673.
  • Phylogenetic analysis of migration, differentiation, and class switching in B cells.Hoehn KB, Pybus OG, Kleinstein SH. PLoS Comput Biol. 2022 Apr; 2022 Apr 25. PMID: 35468128.
  • mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis.Zeng Y, Li J, Wei C, Zhao H, Wang T. Genome Biol. 2022 Apr 14; 2022 Apr 14. PMID: 35422001.
  • Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders.Wang Y, Zhao H. PLoS Comput Biol. 2022 Apr; 2022 Apr 1. PMID: 35363784.
  • Fibrillar Collagen Variants in Spontaneous Coronary Artery Dissection.Zekavat SM, Chou EL, Zekavat M, Pampana A, Paruchuri K, Lino Cardenas CL, Koyama S, Ghazzawi Y, Kii E, Uddin MM, Pirruccello J, Zhao H, Wood M, Natarajan P, Lindsay ME. JAMA Cardiol. 2022 Apr 1. PMID: 35234813.
  • 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.
  • Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information.Maihofer AX, Choi KW, Coleman JRI, Daskalakis NP, Denckla CA, Ketema E, Morey RA, Polimanti R, Ratanatharathorn A, Torres K, Wingo AP, Zai CC, Aiello AE, Almli LM, Amstadter AB, Andersen SB, Andreassen OA, Arbisi PA, Ashley-Koch AE, Austin SB, Avdibegović E, Borglum AD, Babić D, Bækvad-Hansen M, Baker DG, Beckham JC, Bierut LJ, Bisson JI, Boks MP, Bolger EA, Bradley B, Brashear M, Breen G, Bryant RA, Bustamante AC, Bybjerg-Grauholm J, Calabrese JR, Caldas-de-Almeida JM, Chen CY, Dale AM, Dalvie S, Deckert J, Delahanty DL, Dennis MF, Disner SG, Domschke K, Duncan LE, Džubur Kulenović A, Erbes CR, Evans A, Farrer LA, Feeny NC, Flory JD, Forbes D, Franz CE, Galea S, Garrett ME, Gautam A, Gelaye B, Gelernter J, Geuze E, Gillespie CF, Goçi A, Gordon SD, Guffanti G, Hammamieh R, Hauser MA, Heath AC, Hemmings SMJ, Hougaard DM, Jakovljević M, Jett M, Johnson EO, Jones I, Jovanovic T, Qin XJ, Karstoft KI, Kaufman ML, Kessler RC, Khan A, Kimbrel NA, King AP, Koen N, Kranzler HR, Kremen WS, Lawford BR, Lebois LAM, Lewis C, Liberzon I, Linnstaedt SD, Logue MW, Lori A, Lugonja B, Luykx JJ, Lyons MJ, Maples-Keller JL, Marmar C, Martin NG, Maurer D, Mavissakalian MR, McFarlane A, McGlinchey RE, McLaughlin KA, McLean SA, Mehta D, Mellor R, Michopoulos V, Milberg W, Miller MW, Morris CP, Mors O, Mortensen PB, Nelson EC, Nordentoft M, Norman SB, O'Donnell M, Orcutt HK, Panizzon MS, Peters ES, Peterson AL, Peverill M, Pietrzak RH, Polusny MA, Rice JP, Risbrough VB, Roberts AL, Rothbaum AO, Rothbaum BO, Roy-Byrne P, Ruggiero KJ, Rung A, Rutten BPF, Saccone NL, Sanchez SE, Schijven D, Seedat S, Seligowski AV, Seng JS, Sheerin CM, Silove D, Smith AK, Smoller JW, Sponheim SR, Stein DJ, Stevens JS, Teicher MH, Thompson WK, Trapido E, Uddin M, Ursano RJ, van den Heuvel LL, Van Hooff M, Vermetten E, Vinkers CH, Voisey J, Wang Y, Wang Z, Werge T, Williams MA, Williamson DE, Winternitz S, Wolf C, Wolf EJ, Yehuda R, Young KA, Young RM, Zhao H, Zoellner LA, Haas M, Lasseter H, Provost AC, Salem RM, Sebat J, Shaffer RA, Wu T, Ripke S, Daly MJ, Ressler KJ, Koenen KC, Stein MB, Nievergelt CM. Biol Psychiatry. 2022 Apr 1; 2021 Sep 28. PMID: 34865855.
  • fastANCOM: a fast method for analysis of compositions of microbiomes.Zhou C, Wang H, Zhao H, Wang T. Bioinformatics. 2022 Mar 28. PMID: 35134120.
  • Clustering high-dimensional data via feature selection.Liu T, Lu Y, Zhu B, Zhao H. Biometrics. 2022 Mar 25; 2022 Mar 25. PMID: 35338489.
  • Robust, persistent adaptive immune responses to SARS-CoV-2 in the oropharyngeal lymphoid tissue of children.Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, Pittaluga S, Germain RN, Apps R, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Res Sq. 2022 Mar 23; 2022 Mar 23. PMID: 35350206.
  • Inferring Time-Lagged Causality Using the Derivative of Single-Cell Expression.Wei H, Lu H, Zhao H. Int J Mol Sci. 2022 Mar 20; 2022 Mar 20. PMID: 35328768.
  • Association of China's two-child policy with changes in number of births and birth defects rate, 2008-2017.Chen H, Wei T, Wang H, Zhou Y, Chen H, Sun L, Xiao S, Ma W, Zhao H, Chen G, Liang X, Zhang D, Zheng W, Zhou Y, Yu Z. BMC Public Health. 2022 Mar 4; 2022 Mar 4. PMID: 35246096.
  • 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.
  • 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.
  • Low depression frequency is associated with decreased risk of cardiometabolic disease.Honigberg MC, Ye Y, Dattilo L, Sarma AA, Scott NS, Smoller JW, Zhao H, Wood MJ, Natarajan P. Nat Cardiovasc Res. 2022 Feb; 2022 Feb 14. PMID: 35991864.
  • 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.
  • MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys.Liu T, Xu P, Du Y, Lu H, Zhao H, Wang T. Brief Bioinform. 2022 Jan 17. PMID: 34718406.
  • Deep Learning of the Retina Enables Phenome- and Genome-Wide Analyses of the Microvasculature.Zekavat SM, Raghu VK, Trinder M, Ye Y, Koyama S, Honigberg MC, Yu Z, Pampana A, Urbut S, Haidermota S, O'Regan DP, Zhao H, Ellinor PT, Segrè AV, Elze T, Wiggs JL, Martone J, Adelman RA, Zebardast N, Del Priore L, Wang JC, Natarajan P. Circulation. 2022 Jan 11; 2021 Nov 8. PMID: 34743558.
  • Posttraumatic Stress Disorder Brain Transcriptomics: Convergent Genomic Signatures Across Biological Sex.Wang J, Zhao H, Girgenti MJ. Biol Psychiatry. 2022 Jan 1; 2021 Feb 22. PMID: 33840456.

2021

Select Publications

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2016

2015

2014

2013

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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2003