Publications
Recent Publications
2022
- 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.
- 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 Jun 20; 2022 Jun 20. PMID: 35738554.
- 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.
- The immunology of Parkinson's disease.Zhu B, Yin D, Zhao H, Zhang L. Semin Immunopathol. 2022 Jun 8; 2022 Jun 8. PMID: 35674826.
- 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 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 May 5; 2022 May 5. PMID: 35514182.
- 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, Tao W. Genome Biol. 2022 Apr 14; 2022 Apr 14. PMID: 35422001.
- Cancer Relevance of Human Genes.Qing T, Mohsen H, Cannataro V, Marczyk M, Rozenblit M, Foldi J, Murray M, Townsend J, Kluger Y, Gerstein M, Pusztai L. J Natl Cancer Inst. 2022 Apr 13; 2022 Apr 13. PMID: 35417011.
- 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.
- 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.
- 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.
- 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.
- Clustering high-dimensional data via feature selection.Liu T, Lu Y, Zhu B, Zhao H. Biometrics. 2022 Mar 25; 2022 Mar 25. PMID: 35338489.
- 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.
- fastANCOM: a fast method for analysis of compositions of microbiomes.Zhou C, Wang H, Zhao H, Wang T. Bioinformatics. 2022 Feb 3; 2022 Feb 3. PMID: 35134120.
- 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
- 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.
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- 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.
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Zoladek T, Zong WX, Zorov DB, Zorzano A, Zou W, Zou Z, Zou Z, Zuryn S, Zwerschke W, Brand-Saberi B, Dong XC, Kenchappa CS, Li Z, Lin Y, Oshima S, Rong Y, Sluimer JC, Stallings CL, Tong CK. Autophagy. 2021 Jan; 2021 Feb 8. PMID: 33634751.
- Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption.Sarkar E, Chielle E, Gürsoy G, Mazonka O, Gerstein M, Maniatakos M. IEEE Access. 2021; 2021 Jun 28. PMID: 34476144.
- Sex-Biased Aging Effects on Ig Somatic Hypermutation Targeting.Cui A, Chawla DG, Kleinstein SH. J Immunol. 2021 Jan 1; 2020 Dec 7. PMID: 33288546.
- Transcriptomic organization of the human brain in post-traumatic stress disorder.Girgenti MJ, Wang J, Ji D, Cruz DA, Stein MB, Gelernter J, Young KA, Huber BR, Williamson DE, Friedman MJ, Krystal JH, Zhao H, Duman RS. Nat Neurosci. 2021 Jan; 2020 Dec 21. PMID: 33349712.
2020
- Position-Dependent Differential Targeting of Somatic Hypermutation.Zhou JQ, Kleinstein SH. J Immunol. 2020 Dec 15; 2020 Nov 13. PMID: 33188076.
- Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF. bioRxiv. 2020 Dec 9; 2020 Dec 9. PMID: 32935102.
- STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.Lee D, Shi M, Moran J, Wall M, Zhang J, Liu J, Fitzgerald D, Kyono Y, Ma L, White KP, Gerstein M. Genome Biol. 2020 Dec 8; 2020 Dec 8. PMID: 33292397.
- Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men.Samuel RM, Majd H, Richter MN, Ghazizadeh Z, Zekavat SM, Navickas A, Ramirez JT, Asgharian H, Simoneau CR, Bonser LR, Koh KD, Garcia-Knight M, Tassetto M, Sunshine S, Farahvashi S, Kalantari A, Liu W, Andino R, Zhao H, Natarajan P, Erle DJ, Ott M, Goodarzi H, Fattahi F. Cell Stem Cell. 2020 Dec 3; 2020 Nov 17. PMID: 33232663.
- Thymus-derived B cell clones persist in the circulation after thymectomy in myasthenia gravis.Jiang R, Hoehn KB, Lee CS, Pham MC, Homer RJ, Detterbeck FC, Aban I, Jacobson L, Vincent A, Nowak RJ, Kaminski HJ, Kleinstein SH, O'Connor KC. Proc Natl Acad Sci U S A. 2020 Dec 1; 2020 Nov 16. PMID: 33199596.
- Data Sanitization to Reduce Private Information Leakage from Functional Genomics.Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Cell. 2020 Nov 12. PMID: 33186529.
Select Publications
2017
- 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.
- Blockchain Technology: Applications in Health Care.Angraal S, Krumholz HM, Schulz WL. Circ Cardiovasc Qual Outcomes. 2017 Sep. PMID: 28912202.
- 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.
- 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.
- 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.
- 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.
- 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.