Research Overview

I am interested in developing statistical methods for high-dimensional genomics data and exploring the theory behind them. I also implement those methods into software so that these ideas can be broadly used. Always motivated by real data problems, I appreciate collaborations with epidemiologists, genetics and other scientists, and wish to contribute to the statistical methodology development that facilitates the understanding of complex disease etiology and molecular biology.

Education & Background

  • B. S., 09/98 - 06/02
    School of Economics, Peking University, Beijing, China
  • Ph.D., Biostatistics, 06/03 - 01/08
    Department of Biostatistics, University of Washington
    Advisor: John D. Storey
    Thesis Title: Causal Modeling in Quantitative Genomics
  • Postdoctoral Research Associate, 02/08 - 07/08
    Lewis-Sigler Institute for Integrative Genomics, Princeton University
    Advisor: John D. Storey
  • Postdoctoral Research Associate, 07/08 - 07/10
    Fred Hutchinson Cancer Research Center
    Advisor: Ross L. Prentice and Li Hsu
  • Assistant Professor , 08/10 - present
    Department of Health Studies, the University of Chicago


  • Chen L and Storey JD. (2006) Relaxed significance criteria for linkage analysis. Genetics, 173: 2371-2381. [Web Site]
  • Dembo G, Chen L, Vater Y, Breslow N and Martay K. (2006) Double blind randomized controlled trial on the effects of mannitol on the postreperfusion syndrome during orthotopic liver transplantations. International Journal of Anaesthesia, 6: 1-13.
  • Chen LS, Emmert-Streib F, and Storey JD. (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8: R219. [Web Site]
  • Chen LS and Storey JD. (2008) Eigen-R2 for dissecting the variation of high-dimensional studies, Bioinformatics, 24 (19): 2260-2262. [Web Site]
  • Pitteri SJ, Hanash SM, Agragaki A, Amon L, Chen L, Buson TB, Paczesny S, Katayama H, Wang H, Johnson MM, Zhang Q, McIntosh M, Wang P, Kooperberg C, Rossouw JE, Jackson R, Manson JE, Hsia J, Liu S, Martin L and Prentice RL. (2009) Postmenopausal estrogen and progestin effects on the serum proteome. Genome Medicine, 1(12) 1.
  • Chen LS, Hutter CM, Potter JD, Liu Y, Prentice RL, Peters U and Hsu L. (2010) Insights into colon cancer etiology using a regularized approach to gene set analysis of GWAS data. The American Journal of Human Genetics, 86(6): 860-871. [Source Code]
  • Prentice RL, Paczesny S, Aragaki A, Amon L, Chen LS, Pitteri S, McIntosh M, Wang P, Busald TB, Hsia J, Jackson R, Rossouw JE, Manson JE, Johnson K, Eaton C, Hanash SM. (2010)Novel proteins associated with risk for coronary heart disease or stroke among postmenopausal women identified by in-depth plasma proteome profiling. Genome Medicine , 2(7):48.
  • Chen LS, Paul D, Prentice RL and Wang P. (2011) A regularized Hotelling's T-square test for pathway analysis in proteomics studies. Journal of the American Statistical Association, accepted.
  • Software

    • EigenR2: Chen LS and Storey JD. (2008), an R software package for dissecting variation in high-dimensional data. [Web Site]
    • Iga: Chen LS and Storey JD. (2010), an R software package for analyzing integrative genomic data, available upon request.
    • SNPath: Chen LS (2010), an R software package for pathway analysis in SNP association study. [Source Code]

    Professional Activities and Affiliations

    • Referee for Annals of Applied Statistics, Bioinformatics, Biometrics, BMC Bioinformatics, BMC Genetics, BMC System Biology, Journal of Biopharmaceutical Statistics, Nature Biotechnology, PLoS Genetics, PLoS ONE, Statistics and Its Interface, Statistical Applications in Genetics and Molecular Biology..
    • Student Representative for American Statistical Association Puget Sound Chapter, 2007 - 2008
    • Member of American Statistical Association, American Society of Human Genetics, ENAR International Biometric Society