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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.
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    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 Research 
    Collapse research activities and funding
    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
    R35ES028379     (PIERCE, BRANDON LEE)Sep 15, 2017 - Jul 31, 2025
    NIH
    Arsenic and the Human Genome: susceptibility and response to exposure
    Role: Co-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
    R01GM108711     (CHEN, LIN)Feb 15, 2014 - May 31, 2024
    NIH
    Integrative multivariate association and genomic analyses
    Role: Principal Investigator
    R03CA174984     (CHEN, LIN)Mar 7, 2013 - Feb 28, 2015
    NIH
    Multivariate functional analysis of the genetic basis of cancer
    Role: Principal 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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    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, 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, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H, Clinical Proteomic Tumor Analysis Consortium, Gümüs ZH, Fenyö D. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 2020 Jan 09; 180(1):207. PMID: 31923397.
      Citations: 30     Fields:    
    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; PMCID: PMC6797056.
      Citations: 2     Fields:    Translation:Humans
    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; PMCID: PMC6692782.
      Citations: 16     Fields:    Translation:HumansCells
    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; PMCID: PMC5824840.
      Citations: 32     Fields:    Translation:HumansCells
    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; PMCID: PMC6013347.
      Citations: 3     Fields:    Translation:Humans
    6. Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 11; 27(11):1859-1871. PMID: 29021290; PMCID: PMC5668943.
      Citations: 34     Fields:    Translation:Humans
    7. Lee CI, Chen LE, Elmore JG. Risk-based Breast Cancer Screening: Implications of Breast Density. Med Clin North Am. 2017 Jul; 101(4):725-741. PMID: 28577623; PMCID: PMC5458625.
      Citations: 37     Fields:    Translation:Humans
    8. 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; PMCID: PMC5937554.
      Citations: 8     
    9. 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; PMCID: PMC4833292.
      Citations: 21     Fields:    Translation:HumansCells
    10. 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; PMCID: PMC4842175.
      Citations: 8     Fields:    
    11. 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; PMCID: PMC4256471.
      Citations: 47     Fields:    Translation:Humans
    12. 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; PMCID: PMC4061266.
      Citations: 9     Fields:    Translation:Humans
    13. 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; PMCID: PMC3716585.
      Citations: 21     Fields:    Translation:Humans
    14. 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; PMCID: PMC3516612.
      Citations: 21     Fields:    Translation:Humans
    15. 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; PMCID: PMC3755504.
      Citations: 9     
    16. 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; PMCID: PMC3032068.
      Citations: 89     Fields:    Translation:Humans
    17. 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; PMCID: PMC2246293.
      Citations: 58     Fields:    Translation:Animals
    18. Chen L, Storey JD. Relaxed significance criteria for linkage analysis. Genetics. 2006 Aug; 173(4):2371-81. PMID: 16783025; PMCID: PMC1569719.
      Citations: 51     Fields:    
    19. 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. View Publication.
    20. 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. View Publication.
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