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Lin Chen

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentPublic Health Sciences
AddressChicago IL 60637
Email
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    Collapse Overview 
    Collapse overview
    Dr. Chen's overall research interests focus on developing statistical methods for analyzing 'big' integrative genomics data. Her lab has developed statistical methods for ‘omics’ studies that involve multiple types of large-scale high-dimensional data sets, for example, genetic data, gene transcriptional expression data, proteomic data and complex phenotypes. Besides methodology development, her lab has also developed many R packages.


    Collapse Biography 
    Collapse education and training
    Fred Hutchinson Cancer Research Center, SeattlePostdoctoral Training08/2010Statistical genomics
    University of Washington, SeattlePhD01/2008Biostatistics
    Peking University , BeijingBS06/2002Economics
    Collapse awards and honors
    2017 - 2018The Departmental Best Dissertation Award (for Dr. Chen's PhD student), Department of Public Health Sciences
    2020Reviewer for BMRD study section, NIH
    2020 - 2021Program Chair-Elect for the Section on Statistics in Genomics and Genetics, American Statistical Association
    2018Associate Editor for Biometrics

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Research 
    Collapse research activities and funding
    R03CA174984     (CHEN, LIN)Mar 7, 2013 - Feb 28, 2015
    NIH
    Multivariate functional analysis of the genetic basis of cancer
    Role: Principal Investigator

    R01GM108711     (CHEN, LIN)Feb 15, 2014 - May 31, 2023
    NIH
    Integrative multivariate association and genomic analyses
    Role: Principal Investigator

    U24CA210993     (WANG, PEI)Sep 19, 2016 - Aug 31, 2021
    NIH
    Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision Medicine
    Role: Co-Investigator

    R35ES028379     (PIERCE, BRANDON LEE)Sep 15, 2017 - Jul 31, 2025
    NIH
    Arsenic and the Human Genome: susceptibility and response to exposure
    Role: Co-Investigator

    R01CA229618     (STRANGER, BARBARA E)Jun 1, 2019 - May 31, 2024
    NIH
    Genetic mechanisms underlying sexual dimorphism in cancer and response to therapy
    Role: Co-Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüs ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 2020 Jan 09; 180(1):207. PMID: 31923397.
      View in: PubMed
    2. Wang J, Wang P, Hedeker D, Chen LS. Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness. Biostatistics. 2019 10 01; 20(4):648-665. PMID: 29939200.
      View in: PubMed
    3. Song X, Ji J, Gleason KJ, Yang F, Martignetti JA, Chen LS, Wang P. Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis. Mol Cell Proteomics. 2019 08 09; 18(8 suppl 1):S52-S65. PMID: 31227599.
      View in: PubMed
    4. Pierce BL, Tong L, Argos M, Demanelis K, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Chen LS, Ahsan H. Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms. Nat Commun. 2018 02 23; 9(1):804. PMID: 29476079.
      View in: PubMed
    5. Wang J, Liu Q, Pierce BL, Huo D, Olopade OI, Ahsan H, Chen LS. A meta-analysis approach with filtering for identifying gene-level gene-environment interactions. Genet Epidemiol. 2018 07; 42(5):434-446. PMID: 29430690.
      View in: PubMed
    6. Yang F, Wang J. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 11; 27(11):1859-1871. PMID: 29021290.
      View in: PubMed
    7. Chen LS, Wang J, Wang X, Wang P. A MIXED-EFFECTS MODEL FOR INCOMPLETE DATA FROM LABELING-BASED QUANTITATIVE PROTEOMICS EXPERIMENTS. Ann Appl Stat. 2017 Mar; 11(1):114-138. PMID: 29743963.
      View in: PubMed
    8. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Am J Hum Genet. 2016 Apr 07; 98(4):697-708. PMID: 27040689.
      View in: PubMed
    9. Liu Q, Chen LS, Nicolae DL, Pierce BL. A unified set-based test with adaptive filtering for gene-environment interaction analyses. Biometrics. 2016 06; 72(2):629-38. PMID: 26496228.
      View in: PubMed
    10. Pierce BL, Tong L, Chen LS, Rahaman R, Argos M, Jasmine F, Roy S, Paul-Brutus R, Westra HJ, Franke L, Esko T, Zaman R, Islam T, Rahman M, Baron JA, Kibriya MG, Ahsan H. Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians. PLoS Genet. 2014 Dec; 10(12):e1004818. PMID: 25474530.
      View in: PubMed
    11. Chen LS, Prentice RL, Wang P. A penalized EM algorithm incorporating missing data mechanism for Gaussian parameter estimation. Biometrics. 2014 Jun; 70(2):312-22. PMID: 24471933.
      View in: PubMed
    12. Liu Q, Nicolae DL, Chen LS. Marbled inflation from population structure in gene-based association studies with rare variants. Genet Epidemiol. 2013 Apr; 37(3):286-92. PMID: 23468125.
      View in: PubMed
    13. Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DL. An exponential combination procedure for set-based association tests in sequencing studies. Am J Hum Genet. 2012 Dec 07; 91(6):977-86. PMID: 23159251.
      View in: PubMed
    14. Chen LS, Paul D, Prentice RL, Wang P. A regularized Hotelling's T2 test for pathway analysis in proteomic studies. J Am Stat Assoc. 2011 Dec; 106(496):1345-1360. PMID: 23997374.
      View in: PubMed
    15. Chen LS, Hutter CM, Potter JD, Liu Y, Prentice RL, Peters U, Hsu L. Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data. Am J Hum Genet. 2010 Jun 11; 86(6):860-71. PMID: 20560206.
      View in: PubMed
    16. Chen LS, Emmert-Streib F, Storey JD. Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol. 2007; 8(10):R219. PMID: 17931418.
      View in: PubMed
    17. Chen L, Storey JD. Relaxed significance criteria for linkage analysis. Genetics. 2006 Aug; 173(4):2371-81. PMID: 16783025.
      View in: PubMed
    18. Gleason KJ, Yang F, Pierce BL, He X, Chen LS. Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traits.
    19. Yang F, Gleason KJ, Wang J, The GTEx consortium, Duan J, He X, Pierce BP, Chen LS. CCmed: Cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits.
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