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
Education:
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

Cai T, Li H, Liu W, Xie J: Joint Estimation of Multiple High-dimensional Precision Matrices. Statistica Sinica 26(2): 445-464, Apr 2016.

Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison H, Sogin M, Li H, Moore JH, Karagas MR: Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatrics 170(3): 212-219, Mar 2016.

Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger 5, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie 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 65(1): 63-72, Jan 2016.

Chen EZ, Bushman FD, Li H: A Model-based Approach for Species Abundance Quantification Based on Shotgun Metagenomic Data. Statistics in Biosciences in press 2016 Notes: 16 May. doi:10.1007/s12561-016-9148-x. [Epub ahead of print]

Schoch H, Kreibich AS, Ferri SL, White RS, D Bohorquez, A Banerjee, RG Port, Dow HC, Cordero L, Pallathra AA, Kim H, Li H, Bilker W, Hirano S, Schultz RT, Borgmann-Winter K, Hahn C-G, Feldmeyer D, Carlson GC, Abel T, Brodkin ES : Sociability Deficits and Altered Amygdala Circuits in Mice Lacking Pcdh10, an Autism Associated Gene. Biological Psychiatry in press 2016 Notes: 2016 June 16. http://dx.doi.org/10.1016/j.biopsych.2016.06.008 [Epub ahead of print]

Chen EZ, Li H: A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics in press 2016 Notes: 2016 May 14. pii: btw308. [Epub ahead of print]

Shi P, Zhang A, Li H: Regression Analysis for Microbiome Compositional Data. Annals of Applied Statistics in press 2016.

Ferri SL, Kreibich AS, Torre M, Picccoli CT, Dow H, Pallathra AA, Li H, Bilker WB, Gur R, Abel T, and Brodkin ES : Activation of Basolateral Amygdala in Juvenil C57BL/6J Mice During Social Approach Behavior. Neuroscience in press 2016.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD: Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Cell Host Microbe 18(4): 489-500, Oct 2015.

Li YR, Zhao SD, Li J, Bradfield JP, Mohebnasab M, Steel L, Kobie J, Abrams DJ, Mentch FD, Glessner JT, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Li D, Maggadottir SM, Thomas KA, Qui H, Chiavacci RM, Kim CE, Wang F1, Snyder J, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Strisciuglio C, Staiano A, Miele E, Silverberg MS, Lie BA, Punaro M, Russell RK, Wilson DC, Dubinsky MC, Monos DS, Annese V, Munro JE, Wise C, Chapel H, Cunningham-Rundles C, Orange JS, Behrens EM, Sullivan KE, Kugathasan S, Griffiths AM, Satsangi J, Grant SF, Sleiman PM, Finkel TH, Polychronakos C, Baldassano RN, Luning Prak ET, Ellis JA, Li H, Keating BJ, Hakonarson H: Genetic sharing and heritability of paediatric age of onset autoimmune diseases. Nature Communications 6: 8442, Oct 2015.

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Last updated: 07/21/2016
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