Graduate Group in Genomics and Computational Biology

Hongzhe Li (Lee), Ph.D.

faculty photo
Professor of Biostatistics in Biostatistics and Epidemiology
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
B.S. (Mathematics/Information)
Peking University, 1989.
Ph.D. (Statistics)
University of Washington, 1995.
Permanent link

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 H: Microbiome, metagenomics and high dimensional compositional data analysis. Annual Review of Statistics and Its Application 2: 73-94, Apr 2015.

Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H: Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics March 2015 Notes: pii: btv183 [Epub ahead of print]

Zsiros E, Duttagupta P, Dangaj D, Li H, Frank R, Garrabrant T, Hagemann IS, Levine BL, June CH, Zhang L, Wang E, Marincola FM, Bedognetti D, Powell DJ Jr, Tanyi J, Feldman MD, Kandalaft LE, Coukos G: The Ovarian Cancer Chemokine Landscape is Conducive to Homing of Vaccine-primed and CD3/CD28 Costimulated T cells Prepared for Adoptive Therapy. Clinical Cancer Research Feb 2015 Notes: Epub ahead of print.

Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, Penubarthi S, Sun H, Baldwin DA, Fraser NW: Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection. PLoS One 10(2): e0117471, Feb 2015.

Wu Q, Won KJ, Li H: Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data. Cancer Informatics 14(Suppl. 1): 11-22, Jan 2015.

Zhao, S.D., Cai, T.T., Li, H.: More powerful genetic association testing via a new statistical framework for integrative genomics. Biometrics 70(4): 881-890, Dec 2014.

Lin W, Shi P, Feng R, Li H: Variable selection in regression with compositional covariates. Biometrika 101(4): 785-797, Dec 2014.

Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD: Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147(5): 1055-1063.e8, Nov 2014.

Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albernberg LG, Nessel L, Gilroy E, Star J, Weijie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD : Comparative Metabolomics in Vegans and Omnivores Reveal Constraints on Diet-Dependent Gut Microbiota Metabolite Production. Gut Nov 2014 Notes: pii: gutjnl-2014-308209. doi: 10.1136/gutjnl-2014-308209. [Epub ahead of print]

Hu X, Feng Y, Zhang D, Zhao SD, Hu Z, Greshock J, Zhang Y, Yang L, Zhong X, Wang LP, Jean S, Li C, Huang Q, Katsaros D, Montone KT, Tanyi JL, Lu Y, Boyd J, Nathanson KL, Li H, Mills GB, Zhang L: A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell 26(3): 344-357, Sep 2014.

back to top
Last updated: 05/15/2015
The Trustees of the University of Pennsylvania