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 - present
    Fred Hutchinson Cancer Research Center
    Advisor: Ross L. Prentice and Li Hsu

Publications

  • 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. In press Genome Medicine.
  • Chen LS, Hutter CM, Potter JD, Liu Y, Prentice RL, Peters U and Hsu L. (2009) Insights into colon cancer etiology using a regularized approach to gene set analysis of GWAS data. In revision by American Journal of Human Genetics. [Source Code]
  • Chen LS, Prentice RL and Wang P. (2009) A regularized Hotelling's T-square test for pathway analysis in proteomics studies. Under review by Journal of the American Statistical Association. [PDF]
  • Prentice RL, Paczesny S, Aragaki A, Amon L, Chen LS, Pitteri S, McIntosh M, Wang P, Hsia J, Jackson R, Rossouw JE, Manson JE, Johnson K, Eaton C, Hanash SM. (2009) Plasma protein concentrations and the risk of coronary heart disease and stroke among postmenopausal women. Submitted to Nature Medicine .

Manuscripts in Preparation

  • Hutter CM*, Chen LS*, Liu Y, Slattery M, Carlson C, Vijayaraghavan R, Taverna D, Duggan D, Curtin K, Berndt S, Schoen R, Caan B, Jackson B, Kooperberg C, LaCroix A, Ulrich C, Chanock S, Prentice RL, Hayes RB, Potter JD, Hsu L, Peters U. (2010) Gene-set enrichment analysis of colon cancer genome-wide association data: Identification of the TGF-beta pathway.
    In preparation to submit to Nature Genetics. Abstract has been submitted to the American Association for Cancer Research annual meeting. (*     Both authors contributed equally.    )
  • Chen LS, others, Schadt EE and Storey JD. (2010) Expression genetic mapping shows BACE1 expression affects total cholesterol.

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. (2009), an R software package for analyzing integrative genomic data, available upon request.
  • GRASS: Chen LS (2009), an R software package for gene set enrichment analysis in association study using group penalized regression. [Source Code]

Professional Activities and Affiliations

  • Referee for Nature Biotechnology, PLoS Genetics, Bioinformatics, BMC genetics, Statistical Applications in Genetics and Molecular Biology, PLoS ONE, the Journal of Biopharmaceutical Statistics.
  • 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