Publications
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 I, Brooijmans G, Brooks WK, Brost E, Bruckman de Renstrom PA, Brüers B, Bruncko D, Bruni A, Bruni G, Bruschi M, Bruscino N, Bryngemark L, Buanes T, Buat Q, Buchholz P, Buckley AG, Budagov IA, Bugge MK, Bulekov O, Bullard BA, Burdin S, Burgard CD, Burger AM, Burghgrave B, Burr JTP, Burton CD, Burzynski JC, Busch EL, Büscher V, Bussey PJ, Butler JM, Buttar CM, Butterworth JM, Buttinger W, Buxo Vazquez CJ, Buzykaev AR, Cabras G, Cabrera Urbán S, Caforio D, Cai H, Cairo VMM, Cakir O, Calace N, Calafiura P, Calderini G, Calfayan P, Callea G, Caloba LP, Calvet D, Calvet S, Calvet TP, Calvetti M, Camacho Toro R, Camarda S, Camarero Munoz D, Camarri P, Camerlingo MT, Cameron D, Camincher C, Campanelli M, Camplani A, Canale V, Canesse A, Cano Bret M, Cantero J, Cao Y, Capocasa F, Capua M, Carbone A, Cardarelli R, Cardenas JCJ, Cardillo F, Carducci G, Carli T, Carlino G, Carlson BT, Carlson EM, Carminati L, Carnesale M, Caron S, Carquin E, Carrá S, Carratta G, Carter JWS, Carter TM, Casadei D, 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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.
- Mendelian randomization for causal inference accounting for pleiotropy and sample structure using genome-wide summary statistics.Hu X, Zhao J, Lin Z, Wang Y, Peng H, Zhao H, Wan X, Yang C. Proc Natl Acad Sci U S A. 2022 Jul 12; 2022 Jul 5. PMID: 35787050.
- 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.
- 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.
- 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.
- 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
- Transformation and differential abundance analysis of microbiome data incorporating phylogeny.Zhou C, Zhao H, Wang T. Bioinformatics. 2021 Dec 11. PMID: 34302462.
- 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.
Select Publications
2017
- Blockchain Technology: Applications in Health Care.Angraal S, Krumholz HM, Schulz WL. Circ Cardiovasc Qual Outcomes. 2017 Sep. PMID: 28912202.
- A Dirichlet-tree multinomial regression model for associating dietary nutrients with gut microorganisms.Wang T, Zhao H. Biometrics. 2017 Sep; 2017 Jan 23. PMID: 28112797.
- On joint estimation of Gaussian graphical models for spatial and temporal data.Lin Z, Wang T, Yang C, Zhao H. Biometrics. 2017 Sep; 2017 Jan 18. PMID: 28099997.
- Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses.Sci Immunol. 2017 Aug 25. PMID: 28842433.
- Can machine learning complement traditional medical device surveillance? A case study of dual-chamber implantable cardioverter-defibrillators.Ross JS, Bates J, Parzynski CS, Akar JG, Curtis JP, Desai NR, Freeman JV, Gamble GM, Kuntz R, Li SX, Marinac-Dabic D, Masoudi FA, Normand ST, Ranasinghe I, Shaw RE, Krumholz HM. Med Devices (Auckl). 2017; 2017 Aug 16. PMID: 28860874.
- Systematic tissue-specific functional annotation of the human genome highlights immune-related DNA elements for late-onset Alzheimer's disease.Lu Q, Powles RL, Abdallah S, Ou D, Wang Q, Hu Y, Lu Y, Liu W, Li B, Mukherjee S, Crane PK, Zhao H. PLoS Genet. 2017 Jul; 2017 Jul 24. PMID: 28742084.
- Multiple network-constrained regressions expand insights into influenza vaccination responses.Avey S, Mohanty S, Wilson J, Zapata H, Joshi SR, Siconolfi B, Tsang S, Shaw AC, Kleinstein SH. Bioinformatics. 2017 Jul 15. PMID: 28881994.
- Describing the performance of U.S. hospitals by applying big data analytics.Downing NS, Cloninger A, Venkatesh AK, Hsieh A, Drye EE, Coifman RR, Krumholz HM. PLoS One. 2017; 2017 Jun 29. PMID: 28662045.
- Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction.Hu Y, Lu Q, Liu W, Zhang Y, Li M, Zhao H. PLoS Genet. 2017 Jun; 2017 Jun 9. PMID: 28598966.
- Reevaluating the Efficacy and Predictability of Antidepressant Treatments: A Symptom Clustering Approach.Chekroud AM, Gueorguieva R, Krumholz HM, Trivedi MH, Krystal JH, McCarthy G. JAMA Psychiatry. 2017 Apr 1. PMID: 28241180.
- Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.Gupta NT, Adams KD, Briggs AW, Timberlake SC, Vigneault F, Kleinstein SH. J Immunol. 2017 Mar 15; 2017 Feb 8. PMID: 28179494.
- Statistical Models for the Analysis of Zero-Inflated Pain Intensity Numeric Rating Scale Data.Goulet JL, Buta E, Bathulapalli H, Gueorguieva R, Brandt CA. J Pain. 2017 Mar; 2016 Dec 2. PMID: 27919777.
- graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.Chung D, Kim HJ, Zhao H. PLoS Comput Biol. 2017 Feb; 2017 Feb 17. PMID: 28212402.
2016
- Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes.Liu Y, Zhao H. Bioinformatics. 2016 Dec 15; 2016 Aug 18. PMID: 27540269.
- CCor: A whole genome network-based similarity measure between two genes.Hu Y, Zhao H. Biometrics. 2016 Dec; 2016 Mar 8. PMID: 26953524.
- Analysis of Machine Learning Techniques for Heart Failure Readmissions.Mortazavi BJ, Downing NS, Bucholz EM, Dharmarajan K, Manhapra A, Li SX, Negahban SN, Krumholz HM. Circ Cardiovasc Qual Outcomes. 2016 Nov; 2016 Nov 8. PMID: 28263938.
- The Promise of Big Data: Opportunities and Challenges.Krumholz HM. Circ Cardiovasc Qual Outcomes. 2016 Nov; 2016 Nov 8. PMID: 28263935.
- Estimating healthcare mobility in the Veterans Affairs Healthcare System.Wang KH, Goulet JL, Carroll CM, Skanderson M, Fodeh S, Erdos J, Womack JA, Abel EA, Bathulapalli H, Justice AC, Nunez-Smith M, Brandt CA. BMC Health Serv Res. 2016 Oct 21; 2016 Oct 21. PMID: 27769221.
- Evolution of Gene Regulation in Humans.Reilly SK, Noonan JP. Annu Rev Genomics Hum Genet. 2016 Aug 31; 2016 Apr 21. PMID: 27147089.
- Origin and evolution of developmental enhancers in the mammalian neocortex.Emera D, Yin J, Reilly SK, Gockley J, Noonan JP. Proc Natl Acad Sci U S A. 2016 May 10; 2016 Apr 25. PMID: 27114548.
2015
- The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment.Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. Nat Commun. 2015 Mar 10; 2015 Mar 10. PMID: 25752243.
- Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.Reilly SK, Yin J, Ayoub AE, Emera D, Leng J, Cotney J, Sarro R, Rakic P, Noonan JP. Science. 2015 Mar 6. PMID: 25745175.
- Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.Gadala-Maria D, Yaari G, Uduman M, Kleinstein SH. Proc Natl Acad Sci U S A. 2015 Feb 24; 2015 Feb 9. PMID: 25675496.
2014
- On an Additive Semigraphoid Model for Statistical Networks With Application to Pathway Analysis.Li B, Chun H, Zhao H. J Am Stat Assoc. 2014 Sep. PMID: 26401064.
- B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.Stern JN, Yaari G, Vander Heiden JA, Church G, Donahue WF, Hintzen RQ, Huttner AJ, Laman JD, Nagra RM, Nylander A, Pitt D, Ramanan S, Siddiqui BA, Vigneault F, Kleinstein SH, Hafler DA, O'Connor KC. Sci Transl Med. 2014 Aug 6. PMID: 25100741.
- Big data and new knowledge in medicine: the thinking, training, and tools needed for a learning health system.Krumholz HM. Health Aff (Millwood). 2014 Jul. PMID: 25006142.
2013
- Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data.Yaari G, Vander Heiden JA, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O'Connor KC, Hafler DA, Laserson U, Vigneault F, Kleinstein SH. Front Immunol. 2013; 2013 Nov 15. PMID: 24298272.
- Integrative annotation of variants from 1092 humans: application to cancer genomics.Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Science. 2013 Oct 4. PMID: 24092746.
- Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.Yaari G, Bolen CR, Thakar J, Kleinstein SH. Nucleic Acids Res. 2013 Oct; 2013 Aug 5. PMID: 23921631.
- Semi-supervised clinical text classification with Laplacian SVMs: an application to cancer case management.Garla V, Taylor C, Brandt C. J Biomed Inform. 2013 Oct; 2013 Jul 8. PMID: 23845911.
- The evolution of lineage-specific regulatory activities in the human embryonic limb.Cotney J, Leng J, Yin J, Reilly SK, DeMare LE, Emera D, Ayoub AE, Rakic P, Noonan JP. Cell. 2013 Jul 3. PMID: 23827682.
- Complementary ensemble clustering of biomedical data.Fodeh SJ, Brandt C, Luong TB, Haddad A, Schultz M, Murphy T, Krauthammer M. J Biomed Inform. 2013 Jun; 2013 Feb 27. PMID: 23454721.
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.
2010
- Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18; 2010 May 3. PMID: 20439753.
2006
- Relating three-dimensional structures to protein networks provides evolutionary insights.Kim PM, Lu LJ, Xia Y, Gerstein MB. Science. 2006 Dec 22. PMID: 17185604.
2003
- A Bayesian networks approach for predicting protein-protein interactions from genomic data.Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. Science. 2003 Oct 17. PMID: 14564010.