Hongzhe Li (Lee), Ph.D.
Perelman Professor in Biostatistics, Epidemiology, and Informatics
Member, Biomedical Graduate Studies (BGS), University of Pennsylvania Perelman School of Medicine
Senior Scholar, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine
Director, Program in Statistical Evaluation of the Human Microbiome, University of Pennsylvania Perelman School of Medicine
Director, Center for Statistical Methods for Big Data, Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine
Member, Penn Center for Precision Medicine, University of Pennsylvania Perelman School of Medicine
Vice Chair of Integrative Research, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine
Member, Executive Committee, University of Pennsylvania Perelman School of Medicine, Applied Mathematics and Computational Sciences (AMCS)
Member, University of Pennsylvania Perelman School of Medicine,Faculty Advisory Committee for Research Computing
Department: Biostatistics and Epidemiology
Graduate Group Affiliations
Contact information
Department of Biostatistics and Epidemiology
University of Pennsylvania Perelman School of Medicine
215 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021
University of Pennsylvania Perelman School of Medicine
215 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021
Office: 215-573-5038
Fax: 215-573 1050
Fax: 215-573 1050
Email:
hongzhe@upenn.edu
hongzhe@upenn.edu
Education:
B.S. (Mathematics/Information)
Peking University, 1989.
Ph.D. (Statistics)
University of Washington, 1995.
Permanent linkB.S. (Mathematics/Information)
Peking University, 1989.
Ph.D. (Statistics)
University of Washington, 1995.
Description of Research Expertise
My methods reserach was mostly motivated by problems in genetics and genoimics. I have worked on a variety problems in statistical genetics and genomics, including methods for family-based genetic linkage and association analysis, methods for admixture mapping, methods for genome-wide association analysis, methods for analysis of microarray time course gene expression data, high dimensional regression analysis for genomic data, methods for copy number variation analysis and methods for analysis of next generation sequence data. I have published both statistical methodological research in top statistics/biostatistics journals (JASA, AOS, AOAS, Biometrika, Biometrics, Biostatistics etc ) and in top genetics journals (AJHG, Plos Genetics, etc) and collaborative research in top scientific journals (Science, NEJM, Nature, Nature Genetics, PNAS, Developmental Cell etc).Selected Publications
Fengling Hu 1, Jiayi Tong 2 3, Margaret Gardner 4; Lifespan Brain Chart Consortium; Andrew A Chen 5, Richard A I Bethlehem 6, Jakob Seidlitz 4 7 8 9, Hongzhe Li 10, Aaron Alexander-Bloch 4 7 8 9, Yong Chen 2, Russell T Shinohara : dGAMLSS: an exact, distributed algorithm to fit Generalized Additive Models for Location, Scale, and Shape for privacy-preserving population reference charts. Bioinformatics 42(1): btaf625, Jan 2026.Whiteside SA, McGinniss JE, Deek RA, Merenstein C, Britton N, Simon-Soro A, Oyster M, Kalman L, Brown MC, Graham-Wooten J, McDyer JF, Shah P, D'Alessio F, Cantu E, Clausen ES, Li H, Diamond JM, Bushman FD, Christie JD, Collman RG: Lung transplant for CF: Low lung bacterial burden and immune mediators in year one associate with CLAD development. Journal of Cystic Fibrosis 25(1): 52-62, Jan 2026.
Hu X, Huang J, Yuan J, Sun Y, Wang Y, Hu Z, Jiang J, Wang Z, Wang B, Long M, Maxwell KN, Fan Y, Tanyi JL, Montone KT, Li H, Kim SH, Nathanson KL, Rebbeck TR, Domchek SM, Vonderheide RH, Zhang L: Immune gene diversity and STING1 variants in shaping cancer immunity across different genetic ancestry populations. Cell reports 45(2): 116882, Jan 2026.
White BE, Ren Y, Li H, DeMarshall M, Yang Z, Falk GW : Indefinite for dysplasia in Barrett's esophagus carries substantial risk for prevalent and incident neoplasia: updated outcomes and long-term follow-up. Gastrointestinal Endoscopy 103(1): 73-83, Jan 2026.
Tanes C, Li Y, Falk GW, Ginsberg GG, Wang KK, Iyer PG, Lightdale CJ, Del Portillo A, Lagana SM, Wang TC, Rustgi AK, Quante M, Jin Z, Wu GD, Friedman ES, Bittinger K, Li H, Abrams JA: Increased reflux secondary bile acids are associated with changes to the microbiome and transcriptome in Barrett's esophagus. Gut Microbes 17(1): 2545420, Dec 2025.
Ren Y, Segal MR, Shafi T, Pico AR, Shin MG, Traglia M, Li H, Rosas SE, Choles HR, Rao PS, Bhat Z, Anderson AH, Chen J, He J, Sozio S, Jaar B, Estrella MM, Chen W, Chertow GM, Parekh RS, Ganz P, Dubin RF; CRIC Study Investigators: Risk factors for mortality in patients with kidney failure on hemodialysis identified by proteomic analysis of CRIC and PACE studies. Nature communications 16(1): 11689, Nov 2025.
Kang H, Goudra B, Devaro D, Schanzer N, Bogardus C, Ren Y, Li H, Lewis JD, Panganamamula K: Relationship Between Timing of Hemodialysis and Procedure-Related Complications Following Endoscopy in Patients with End-Stage Renal Disease. Digestive diseases and sciences 70(11): 3863-3872, Nov 2025.
Communications biology: RCANE: a deep learning algorithm for whole-genome pan-cancer somatic copy number aberration prediction using RNA-seq data. Ge C, Hu X, Zhang L, Li H 8(1): 1354, Sep 2025.
Litichevskiy L, Maya Considine, Jasleen Gill, Vasuprada Shandar, Timothy O. Cox, Hélène C. Descamps, Kevin M. Wright, Kevin R. Amses, Lenka Dohnalová, Megan J. Liou, Monika Tetlak, Mario R. Galindo-Fiallos, Andrea C. Wong, Patrick Lundgren, Junwon Kim, Giulia T. Uhr, Ryan J. Rahman, Sydney Mason, Carter Merenstein, Frederic D. Bushma, Anil Raj, Fiona Harding, Zhenghao Chen, G.V. Prateek, Martin Mullis, Andrew G. Deighan, Laura Robinson, Ceylan Tanes, Kyle Bittinger, Meenakshi Chakraborty, Ami S. Bhatt, Li H, Ian Barnett, Emily R. Davenport, Karl W. Broman, Maayan Levy, Robert L. Cohen, David Botstein, Adam Freund, Andrea Di Francesco, Gary A. Churchill, Mingyao Li, Christoph A. Thaiss : Gut metagenomes reveal interactions between dietary restriction, aging, and the microbiome in genetically diverse mice. Nature Microbiology 10(5): 1240-1257, May 2025.
Bustamante MS, Pierson SK, Ren Y, Bagg A, Brandstadter JD, Srkalovic G, Mango N, Alapat D, Lechowicz MJ, Li H, Rhee FV, Lim MS, Fajgenbaum DC: Erratum to: Longitudinal, natural history study reveals the disease burden of idiopathic multicentric Castleman disease. Haematologica 110(5): 1238-1241, May 2025.