LinChen22FhDq81EenYnW5sLkT99yvv/MO06rRZfzd/cvg=Lin Chen41.78927490000000-87.601250000000002636Chen, Linbig data, integrative genomics, statistical methods, software developmentDr. 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.Associate Professorplugins:TwitterTwitterprns:awardConferredByaward conferred byprns:coAuthorOfcoauthor ofprns:emailEncryptedemail addressprns:endDateend dateprns:fullNamefull nameprns:grantAwardedBygrant awarded byprns:hasAuthorListauthor listprns:hasNetworkhas networkprns:hasPublicationVenuepublished inprns:informationResourceReferenceinformation resource referenceprns:isPrimaryPositionis primary positionprns:latitudelatitudeprns:longitudelongitudeprns:mainImagephotoprns:maxWeightmaximum weightprns:medlineTAjournal title abbreviationprns:meshDescriptorUIMeSH DescriptorUIprns:meshSemanticGroupNameMeSH semantic group nameprns:minWeightminimum weightprns:numberOfAuthorsnumber of authorsprns:numberOfConnectionsnumber of connectionsprns:numberOfPublicationsnumber of publicationsprns:personIdPerson IDprns:personInPrimaryPositionperson in primary positionprns:physicalNeighborOfphysical neighborprns:pluginSearchableDataProfilesRNS Plugin Searchable Dataprns:positionInDepartmentposition in departmentprns:predicateNodepredicate nodeprns:principalInvestigatorNameprincipal investigator nameprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:startDatestart dateprns:trainingAtOrganizationeducational organizationprns:trainingLocationtraining locationprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provinceAgreementvivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipvivo:awardOrHonorawards and honorsAward or Honor Receiptvivo:degreeEarneddegree earnedDepartmentvivo:educationalTrainingeducation and trainingEducational Trainingvivo:freetextKeywordkeywordsGrantvivo:hasResearchArearesearch areasvivo:hasResearcherRoleresearch activitiesvivo:hrJobTitleHR job titleInformation Resourcevivo:linkAnchorTextlink anchor textvivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:majorFieldmajor field of degreevivo:overviewoverviewvivo:personInPositionpositionsPositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titleResearcher Rolevivo:researcherRoleOfresearcher role ofRolevivo:roleContributesTocontributes tovivo:sponsorAwardIdsponsor award idURLLinkvivo:webpagewebpagerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPersonD000465Concepts & Ideas53018280.544707Algorithms29476079Pierce 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 HNature communicationsCo-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms. Nat Commun. 2018 02 23; 9(1):804.Nat Commun2018-02-23T00:00:002018Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms.29939200Wang J, Wang P, Hedeker D, Chen LSBiostatistics (Oxford, England)Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness. Biostatistics. 2019 10 01; 20(4):648-665.Biostatistics2019-10-01T00:00:002019Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness.29430690Wang J, Liu Q, Pierce BL, Huo D, Olopade OI, Ahsan H, Chen LSGenetic epidemiologyA meta-analysis approach with filtering for identifying gene-level gene-environment interactions. Genet Epidemiol. 2018 07; 42(5):434-446.Genet Epidemiol2018-02-11T00:00:002018A meta-analysis approach with filtering for identifying gene-level gene-environment interactions.29021290Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LSGenome researchIdentifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017 11; 27(11):1859-1871.Genome Res2017-10-11T00:00:002017Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.Authorship 13026814Authorship 1302704Authorship 1302715Authorship 1302721Authorship 1302739Authorship 1302742Authorship 1302751Authorship 1302763Authorship 1302771Authorship 1302781Authorship 1302791Authorship 1302811Authorship 1302823Authorship 130283724471933Chen LS, Prentice RL, Wang PBiometricsA penalized EM algorithm incorporating missing data mechanism for Gaussian parameter estimation. Biometrics. 2014 Jun; 70(2):312-22.Biometrics2014-01-28T00:00:002014A penalized EM algorithm incorporating missing data mechanism for Gaussian parameter estimation.23997374Chen LS, Paul D, Prentice RL, Wang PJournal of the American Statistical AssociationA regularized Hotelling's T2 test for pathway analysis in proteomic studies. J Am Stat Assoc. 2011 Dec; 106(496):1345-1360.J Am Stat Assoc2011-12-01T00:00:002011A regularized Hotelling's T2 test for pathway analysis in proteomic studies.29743963Chen LS, Wang J, Wang X, Wang PThe annals of applied statisticsA MIXED-EFFECTS MODEL FOR INCOMPLETE DATA FROM LABELING-BASED QUANTITATIVE PROTEOMICS EXPERIMENTS. Ann Appl Stat. 2017 Mar; 11(1):114-138.Ann Appl Stat2017-04-08T00:00:002017A MIXED-EFFECTS MODEL FOR INCOMPLETE DATA FROM LABELING-BASED QUANTITATIVE PROTEOMICS EXPERIMENTS.20560206Chen LS, Hutter CM, Potter JD, Liu Y, Prentice RL, Peters U, Hsu LAmerican journal of human geneticsInsights 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.Am J Hum Genet2010-06-11T00:00:002010Insights into colon cancer etiology via a regularized approach to gene set analysis of GWAS data.17931418Chen LS, Emmert-Streib F, Storey JDGenome biologyHarnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biol. 2007; 8(10):R219.Genome Biol2007-01-01T00:00:002007Harnessing naturally randomized transcription to infer regulatory relationships among genes.16783025Chen L, Storey JDGeneticsRelaxed significance criteria for linkage analysis. Genetics. 2006 Aug; 173(4):2371-81.Genetics2006-06-18T00:00:002006Relaxed significance criteria for linkage analysis.01/2008University of WashingtonSeattleUniversity of Washington, BiostatisticsPhDBiostatistics06/2002Peking University BeijingPeking University , EconomicsBSEconomicsPrincipal InvestigatorAuthorship 1358436Authorship 135844Authorship 135845Authorship 13584619Department of Public Health Sciences20182017The Departmental Best Dissertation Award (for Dr. Chen's PhD student)NIH2020Reviewer for BMRD study sectionAmerican Statistical Association20212020Program Chair-Elect for the Section on Statistics in Genomics and Genetics2018Associate Editor for Biometrics08/2010Fred Hutchinson Cancer Research CenterSeattleFred Hutchinson Cancer Research Center, Statistical genomicsPostdoctoral TrainingStatistical genomicsCo-InvestigatorCo-InvestigatorCo-InvestigatorPrincipal Investigator2025-07-31NIHPIERCE, BRANDON LEE2017-09-15Arsenic and the Human Genome: susceptibility and response to exposureR35ES0283792021-08-31NIHWANG, PEI2016-09-19Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision MedicineU24CA2109932015-02-28NIHCHEN, LIN2013-03-07Multivariate functional analysis of the genetic basis of cancerR03CA1749842024-05-31NIHSTRANGER, BARBARA E2019-06-01Genetic mechanisms underlying sexual dimorphism in cancer and response to therapyR01CA2296182024-05-31NIHCHEN, LIN2014-02-15Integrative multivariate association and genomic analysesR01GM10871131923397Clark 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, Clinical Proteomic Tumor Analysis ConsortiumCellIntegrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 2020 Jan 09; 180(1):207.Cell2020-01-09T00:00:002020Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.31227599Song X, Ji J, Gleason KJ, Yang F, Martignetti JA, Chen LS, Wang PMolecular & cellular proteomics : MCPInsights 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.Mol Cell Proteomics2019-06-21T00:00:002019Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis.Gleason KJ, Yang F, Pierce BL, He X, Chen LSPrimo: 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. 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. 1900-01-01T00:00:001900Primo: integration of multiple GWAS and omics QTL summary statistics for elucidation of molecular mechanisms of trait-associated SNPs and detection of pleiotropy in complex traitsYang F, Gleason KJ, Wang J, The GTEx consortium, Duan J, He X, Pierce BP, Chen LSCCmed: Cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits. CCmed: Cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits. 1900-01-01T00:00:001900CCmed: Cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traitsAuthorship 146262228577623Lee CI, Chen LE, Elmore JGThe Medical clinics of North AmericaRisk-based Breast Cancer Screening: Implications of Breast Density. Med Clin North Am. 2017 Jul; 101(4):725-741.Med Clin North Am2017-07-01T00:00:002017Risk-based Breast Cancer Screening: Implications of Breast Density.D040901Occupations1322110.862162ProteomicsPublic Health SciencesD015233Concepts & Ideas2395740.745819Models, StatisticalD055106Procedures21716110.566048Genome-Wide Association Studyhttp://www.urb-bd.org/UChicago Research Bangladeshhttp://home.uchicago.edu/lchen11/My Lab Sitehttp://stephenslab.uchicago.edu/lab websitehttps://github.com/stephenslabgithub pagehttps://ipph.uchicago.edu/Institute for Population and Precision Healthhttps://allofus.uchicago.edu/Illinois Precision Medicine Consortium – All of Us Research Programhttps://www.chicago-cachet.org/ChicAgo Center for Health and EnvironmenT (CACHET)https://voices.uchicago.edu/piercelab/Pierce Labhttps://compass.uchicago.edu/Chicago Multiethnic Population and Surveillance Study (COMPASS)mstephens999@BrandonL_Pierce25474530Pierce 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 HPLoS geneticsMediation 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.PLoS Genet2014-12-04T00:00:002014Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians.MatthewStephensMatthew Stephens0.000000000000000.000000000000003155Stephens, MatthewProfessorD040641Genes & Molecular Sequences1215760.73605Quantitative Trait LociHuman GeneticsMedicineUniversity of ChicagoRonaldThistedxWN9GIF1GuTQkntjbwjr93A=Ronald Thisted41.78927490000000-87.601250000000001004Thisted, RonaldEmeritus/Emerita, ProfessorNancy JeanCox2WFmE4EXCuiXhHlsaUXv9Gq0+s+oNancy Jean Cox41.78927490000000-87.601250000000001011Cox, Nancy JeanEmeritus/EmeritaSusannahSpiessxHF5AqQGOeLWg25sc07h4WC08Nm6Susannah Spiess41.78927490000000-87.601250000000001012Spiess, SusannahJonathanPritchardJonathan K. Pritchard41.78927490000000-87.601250000000001284Pritchard, JonathanPROFESSORHabibulAhsan32NrAqM1DO/RmHllZ0mg9mHvHabibul Ahsan41.78927490000000-87.601250000000001510Ahsan, HabibulProfessorNingqiHouNingqi Hou41.78927490000000-87.601250000000002021Hou, NingqiPostdoctoral Scholar1.325110.0082609181research areas0.9012890.032771414coauthor of31.71044.1503460similar to1120selected publicationsDan LiviuNicolaeDan Liviu Nicolae41.78927490000000-87.60125000000000578Nicolae, Dan LiviuProfessorYusukeNakamuraYusuke Nakamura41.78927490000000-87.60125000000000582Nakamura, YusukeEmeritus/Emerita, ProfessorDianeLauderdale025oHqUQC+j5hHlsaUXv9Gq0+s+oDiane Lauderdale41.78927490000000-87.60125000000000605Lauderdale, DianeProfessorYoavGiladYoav Gilad41.78927490000000-87.60125000000000747Gilad, YoavProfessorBenjaminLaheyBenjamin Lahey41.78927490000000-87.60125000000000757Lahey, BenjaminProfessorBrandon L.PierceBrandon L. Pierce41.78927490000000-87.60125000000000809Pierce, Brandon L.Professortrue1true1PROFESSORPROFESSORtrue1Emeritus/Emerita, ProfessorEmeritus/Emerita, Professortrue1Emeritus/EmeritaEmeritus/Emeritatrue1ProfessorProfessortrue1Associate ProfessorAssociate Professortrue1Postdoctoral ScholarPostdoctoral Scholartrue1ProfessorProfessortrue1Emeritus/Emerita, ProfessorEmeritus/Emerita, Professortrue1ProfessorProfessortrue1ProfessorProfessortrue1ProfessorProfessortrue1ProfessorProfessortrue1ProfessorProfessorChicago60637IL27040689Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LSAmerican journal of human geneticsImputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Am J Hum Genet. 2016 Apr 07; 98(4):697-708.Am J Hum Genet2016-03-31T00:00:002016Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx.26496228Liu Q, Chen LS, Nicolae DL, Pierce BLBiometricsA unified set-based test with adaptive filtering for gene-environment interaction analyses. Biometrics. 2016 06; 72(2):629-38.Biometrics2015-10-23T00:00:002015A unified set-based test with adaptive filtering for gene-environment interaction analyses.Statistics Authorship 60610123159251Chen LS, Hsu L, Gamazon ER, Cox NJ, Nicolae DLAmerican journal of human geneticsAn exponential combination procedure for set-based association tests in sequencing studies. Am J Hum Genet. 2012 Dec 07; 91(6):977-86.Am J Hum Genet2012-11-15T00:00:002012An exponential combination procedure for set-based association tests in sequencing studies.23468125Liu Q, Nicolae DL, Chen LSGenetic epidemiologyMarbled inflation from population structure in gene-based association studies with rare variants. Genet Epidemiol. 2013 Apr; 37(3):286-92.Genet Epidemiol2013-03-06T00:00:002013Marbled inflation from population structure in gene-based association studies with rare variants.