Graduate Group in Genomics and Computational Biology

Hongzhe Li (Lee), Ph.D.

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Professor of Biostatistics in Biostatistics and Epidemiology
Department: Biostatistics and Epidemiology

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.
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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

Hu Y, Liu Y, Mao X, Jia C, Ferguson J, Xue C, Reilly M, Li H, Li M: PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Research Page: Feb;42(3):e20. doi: 10.1093/nar/gkt1304, 2014.

Wang W, Li H and Wei Z : A change-point model for identifying 3'UTR switching by next-generation RNA sequencing. \{A change-point model for identifying 3'UTR switching by next-generation RNA sequencing} Page: Apr 11. [Epub ahead of print] 2014.

Koeth, R.A., Wang, Z., Levison, B.S., Buffa, J.A., Org, E., Sheehy, B., Britt, E.B., Fu, X., Wu, Y., Li, L., Smith, J.D., DiDonato, J.A., Chen, J., Li, H., Wu, G.D., Lewis, J.D., Warrier, M., Brown, J.M., Krauss, R.M., Tang, W.H., Bushman, F.D., Lusis, A.J., and Hazen, S.L.: Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis Nature Medicine 19(5): 576-585, May 2013.

Chen, J., Bushman, F.D., Lewis, J., Wu, G.D. and Li, H. : Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Biostatistics 14(2): 244-258, Apr 2013.

Yin, J. and Li, H. : Adjusting for high-dimensional covariates in sparse precision matrix estimation by ℓ1-Penalization. Journal of Multivariate Analysis 116: 365-381, Apr 2013.

Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu,, G.D., Lew, J.D., Bushman, F.D.: Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One Page: Jun 17;8(6):e66019. doi: 10.1371/journal.pone.0066019, 2013.

Jen, X.J., Cai, T.T. and Li, H. : Simultaneous discovery of rare and common segment variants. Biometrika 100(1): 157-172, 2013.

Vardhanabhuti, S., Li, M. and Li, H. : A hierarchical Bayesian model for estimating and inferring differential isoform expression for multi-sample RNA-Seq data. Statistics in Biosciences 5(1): 119-137, 2013.

Deng, W., Geng, Z. and Li, H. : Learning local directed acyclic graphs based on multivariate time series data. Annals of Applied Statistics 7(3): 1663-1683, 2013.

Chen, J. and Li, H. : Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis. Annals of Applied Statistics 7(1): 418-442, 2013.

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Last updated: 12/05/2014
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