Hongzhe Li, Ph.D.

Link to Professor's Lab of Statistical Genetics and Genomics

Hongzhe Li joined the biostatistics faculty at the University of Pennsylvania in May 2005 as Professor of
Biostatistics to lead the statistical genetics and genomics group in the Division of Biostatistics. He spent
three years at the Mayo Clinic as a Research Associate Biostatistician and six years at UC Davis as an
Assistant and Associate Professor. His statistical research interests include statistical methods for analysis
of genetic and genomic data, survival analysis, analysis of high-dimensional data, computational biology and
functional genomics. Since 1998, his research has been supported by an NIH R01 grant on developing
survival analysis methods for mapping genes for complex diseases. Dr. Li is the PI of another NIH R01 grant
to develop statistical methods for analysis of genomic data with graphical structures. Dr. Li is also involved in
funded collaborative research on genetic and genomic studies of autoimmune diseases and cancers and metagenomics. He
serves as an Associate Editor of Journal of the American Statistical Association, Biometrics, and Statistics in
Biosciences. He was elected as a fellow of the American Statistical Association in 2008 and was a permenent
member of the Biostatistics Methods and Research Design (BMRD) Study Section of NIH.
Professor Hongzhe Li has published papers in JASA, Annals of Applied Statistics, Annals of Statistics,
Biometrika, Biometrics, JRSS-B, Science, Nature, Developmental Cells, and Nature Genetics.


Selected Statistical Methods Publications

  1. *Jeng XJ, Cai TT and Li H (2013): Simultaneous Discovery of Rare and Common Segment Variants.
    Biometrika, accepted.
  2. Deng W, Geng Z, Li H (2013): Learning Local Directed Acyclic Graphs Based On Multivariate Time Series Data. Annals of Applied Statistics, accepted.
  3. Cai TT, Li H, Liu W and *Xie J (2013): Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics. Biometrika, accepted.
  4. *Chen J and Li H (2013):Variable Selection for Sparse Dirichlet-Multinomial Regression with An Application to Microbiome Data Analysis. Annals of Applied Statistics, in press.
  5. Cai T, Jeng J and Li H (2012): Robust Detection and Identification of Sparse Segments in Ultra-High Dimensional Data Analysis. Journal of Royal Statistical Society, Series B., 74 (5): 773-797.
  6. Daye J, Xie J, Li H (2012): A Sparse Structured Shrinkage Estimator for Nonparametric Varying-Coefficient Model with an Application in Genomics. Journal of Computational and Graphical Statistics, 21 (1): 110-133.
  7. Huang J, Ma S, Li H and Zhang CH (2011): The Sparse Laplacian Shrinkage Estimator for High-Dimensional Regression. Annals of Statistics, 39(4), 2021-2046.
  8. *Yin J and Li H (2011): A Sparse Conditional Gaussian Graphical Model for Analysis of Genetical Genomics Data. Annals of Applied Statistics, 5(4): 2630-2650.
  9. Lu T, Liang H, Li H , Wu H (2011): High Dimensional ODEs Coupled with Mixed-Effects Modeling Techniques for Dynamic Gene Regulatory Network Identification. Journal of American Statistical Association, 106: 1242-1258.
  10. Xie J, Cai TT, Li H (2011): Sample Size and Power Analysis for Sparse Signal Recovery in Genome-Wide Association Studies. Biometrika, 98(2), 273-290.
  11. Jeng J, Cai TT and Li H (2010): Optimal sparse segment identification with application in copy number variation analysis. Journal of American Statistical Association,105 (491): 1156-1166.
  12. *Li C and Li H (2010): Variable Selection and Regression Analysis for Graph-Structured Covariates with an Application to Genomics. Annals of Applied Statistics, 4(3): 1498-1516.
  13. *Wang L, Li H and Huang J (2008): Variable selection in nonparametric varying-coefficient models for analysis of repeated measurements. Journal of the American Statistical Association, 103: 1556-1569.
  14. *Monni S and Li H (2008): Vertex clustering of graphs using reversible jump MCMC. Journal of Computational and Graphical Statistics, 17(2): 388-409.
  15. *Wei Z and Li H (2008): A Hidden Spatial-temporal Markov Random Field Model for Network-based Analysis of Time Course Gene Expression Data. Annals of Applied Statistics, 2(1), 408-429.


Selected Collaborative Publications

  1. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy B, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WHW, Bushman FD, Lusis AJ, and Hazen SL (2013): Gut microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine, minor revision.
  2. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA,
    Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (2011): Linking long-term dietary patterns with gut microbial enterotypes. Science, 334:105-108.
  3. Winter C, Austin RS, Blanvillain-Baufumi B, Reback MA, Monniaux M, Wu MF, Sang Y, Yamaguchi A,
    Yamaguchi N, Parker JE, Parcy F, Jensen ST, Li H and Wagner D (2011): LEAFY Target Genes Reveal a Direct Link Between Biotic Stimulus Response and Flower. Developmental Cell, 20: 430-443.
  4. Wang K, SJ. Diskin, H Zhang, EF Attiyeh, C Winter, C Hou, RW Schnepp, M Diamond, K Bosse, PA. Mayes, J Glessner, C Kim, E Frackelton, M Garris, Q Wang, W Glaberson, R Chiavacci, L Nguyen, J Jagannathan, N Saeki, H Sasaki, SFA Grant, A Iolascon, YP Mosse, KA Cole, Li H, M Devoto, PW McGrady, WB London, M Capasson, N Rahman, H Hakonarson & JM Maris (2011): Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Nature, 469: 216-220.
  5. *Nguyen LB, Diskin SJ, Cappasso M, Wang K, Diamond MA, Glessner J, Kim C, Attiyeh EF, Mosse YP, Cole K, Lolascon A, Devoto M, Hakonarson H, Li H, Maris JM (2011): Phenotype Restricted Genome-Wide Association Study Using a Gene-Centric Approach Identifies Three Low-Risk Neuroblastoma Susceptibility Loci. PLoS Genetics, 7(3): e1002026. doi:10.1371/journal.pgen.1002026.
  6. Sleiman P, Marcin Imielinski, Jonathan P. Bradfield, Kiran Annaiah, Saffron A.G. Willis-Owen, Nicholas M. Rafaels, Sven Michel, Klaus Bxnnelykke, Cecilia E. Kim, Edward C. Frackelton, Joseph T. Glessne, Cuiping Hou, James Flory, F. George Otieno, Erin Santa, Kelly Thomas, Ryan M. Smith,Wendy R. Glaberson, Maria Garris, Rosetta M. Chiavacci, Terri H Beaty, Ingo Ruczinski, Julian Allen, Jonathan M. Spergel, Robert Grundmeier, Rasika A. Mathias, Jason D. Christie, Erika von Mutius, William O.C. Cookson, Michael Kabesch, Miriam F. Moffatt, Michael M. Grunstein, Li H, Kathleen C. Barnes, Marcella Devoto, Mark Magnusson, Struan F.A. Grant,Hans Bisgaard and Hakon Hakonarson (2010): A locus on 1q31 harboring /DENND1B/ is associated with asthma susceptibility in both Caucasian and African American children. New England Journal of Medicine, 362: 36-44.
  7. Diskin, SJ, Cuiping Hou, Joseph T. Glessner, Edward F. Attiyeh, Marci Laudenslager, Kristopher Bosse, Kristina Cole, Yael P. Mosse, Andrew Wood, Jill E. Lynch, Katlyn Pecor, Maura Diamond, Cynthia Winter, Kai Wang, Cecilia Kim, Elizabeth A. Geiger, Patrick W. McGrady, Alexandra I. F. Blakemore, Wendy B. London, Tamim H. Shaikh, Jonathan Bradfield, Struan F. A. Grant, Li H, Marcella Devoto, Eric R. Rappaport, Hakon Hakonarson, John M. Maris (2009): Copy number variation at 1q21.1 associated with neuroblastoma. Nature, 459: 987-991.
  8. Capasso M, Hou C, Asgharzadeh S, Attiyeh EF, Mosse YP, Diskin SJ, Cole K, Bosse K, Diamond M, Laudenslager M, Winter C, Bradfield JP, Scott RH, Jagannathan J, Glessner JT, Kim C, London, WB, Seeger RC, Li H, Rahman N, Rappaport E, Hakonarson H, Devoto M, Maris J (2009): Common variations in the BARD1 tumor
    suppressor gene influence susceptibility to high-risk neuroblastoma. Nature Genetics, 41(6): 718-723.
  9. Kamoun M, Holmes JH, Israni AK, Kearns JD, Teal V, Yang W, Rosasa SE, Joffe MM, Li H , Feldman HI (2008): HLA-A amino acid polymorphism and delayed kidney allograft function. Proceedings of National Academy of Sciences, 105(48): 18883-18888.
  10. Maris JM, Yael PM, Bradfield JP, Hou C, Monni S, Scott RH, Asgharzadeh S, Attiveh EF, Diskin SJ, Laudenslager M, Winter C, Cole K, Glessner JT, Kim C, Frackelton EC, Casalunovo T, Eckert AW, Capasso M, Rappaport EF, McConville C, London WB, Seeger RC, Rahman N, Devoto M, Grant SFA, Li H and Hakonarson H (2008): A genome-wide association study identifies a susceptibility locus to clinically aggressive neuroblastoma at 6p22. New England Journal of Medicine, 358: 2585-2593.