Faculty

Hongzhe Li (Lee), Ph.D.

Perelman Professor in Biostatistics, Epidemiology, and Informatics

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

Office: 215-573-5038
Fax: 215-573 1050

Email:
hongzhe@upenn.edu

Education
B.S. (Mathematics/Information)
Peking University, 1989.
Ph.D. (Statistics)
University of Washington, 1995.

Links
Dr. Li's Statistical Genetics and Genomics Laboratory

Permanent link

> Perelman School of Medicine > Faculty > Details

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

Li C, Richards SM, Quinn G, Abedini A, Zhu M, Verma T, Mohandes S, Pitts R, Barros V, Qiu X, Shin T, Loureiro JJ, Finkel N, Surapaneni A, Coresh J, Grams ME, Karihaloo A, Li H, Verma A, Ritchie M, Rader DJ; Penn Medicine BioBank; Dietrich WF, Jennings LL, Susztak K: Proteomic risk score for early prediction of kidney disease progression in individuals with APOL1 high-risk genotypes. Nature Medicine 32(5): 1701-1707, May 2026.

Ostner J, Li H, Müller CL: Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data. Statistics in Medicine 45(8-9): e70534, Apr 2026.

Damani R, Vasisht S, Luks V, Vargas G, Compher C, Titchenell PM, Tasian G, Li H, Wu GD, Witschey WR, Gershuni VM : Sex-based differences in imaging-derived body composition and their association with clinical malnutrition in abdominal surgery patients. Nutrients 18(5): 839, Mar 2026.

Mayer LS, Arnold J, Roettele F, Reuter N, Pattekar A, Ohtani T, Ribeiro MM, Siwicki R, Bruder K, Obwegs D, Stahl E, Buechel S, Roehlen N, Kolter J, Mansoori Moghadam Z, Alaswad A, Zhumalidova Z, Li G, Liu X, Li Y, Singh A, Villacorta Hidalgo J, Paraskevopoulou MD, Yajnik V, Juarez J, Ren Y, Li H, Wherry EJ, Lewis JD, Wu GD, Bewtra M, Tomov VT, Thimme R, Bengsch B, Hasselblatt P, Picelli S, Hofmann M, Sagar: Single-cell Profiling Reveals Diverse γδ T Cell Subsets in Ulcerative Colitis. Science Immunology 11(116): eadx8474, Feb 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, Feb 2026.

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.

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.