CM69CliffordMeyerClifford Meyer, Ph.D.42.33789600000000-71.1072493000000056879Meyer, Clifford617/632-5337Senior Research Scientistcatalyst:eCommonsLogineCommons Loginprns:coAuthorOfcoauthor ofFaculty Rankprns:fullNamefull nameprns:hasAuthorListauthor listprns:hasFacultyRankhas faculty rankprns: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:positionInDepartmentposition in departmentprns:positionInDivisionposition in divisionprns:predicateNodepredicate nodeprns:publicationDatepublication dateprns:similarTosimilar toprns:sortOrdersort orderprns:uniquenessWeightuniqueness weightprns:yearyearAcademic ArticleArticleDocumentbibo:pmidPubMed IdentifierAddressvivo:address1address line 1vivo:address2address line 2vivo:address3address line 3vivo:addressCitycityvivo:addressPostalCodepostal codevivo:addressStatestate or provincevivo:authorInAuthorshipselected publicationsvivo:authorRankauthor rank in publicationAuthorshipDepartmentDivisionvivo:hasResearchArearesearch areasvivo:hrJobTitleHR job titleInformation Resourcevivo:linkedAuthorlinked authorvivo:linkedInformationResourcelinked information resourcevivo:mailingAddressmailing addressvivo:personInPositionpositionsvivo:phoneNumberphonePositionvivo:positionInOrganizationposition in organizationvivo:preferredTitlepreferred titlerdf:predicatepredicaterdf:typetyperdfs:labellabelConceptAgentfoaf:firstNamefirst namefoaf:lastNamelast nameOrganizationPerson19364822Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown MMolecular and cellular biologyCoactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol. 2009 Jun; 29(12):3413-23.Mol Cell Biol2009-04-13T00:00:002009Coactivator function defines the active estrogen receptor alpha cistrome.Authorship 103199222495509Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XSNucleic acids researchComputational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res. 2012 Aug; 40(14):6414-23.Nucleic Acids Res2012-04-10T00:00:002012Computational inference of mRNA stability from histone modification and transcriptome profiles.Authorship 107165114Authorship 1071543529868757Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XSBioinformatics (Oxford, England)Improved design and analysis of CRISPR knockout screens. Bioinformatics. 2018 Dec 01; 34(23):4095-4101.Bioinformatics2018-12-01T00:00:002018Improved design and analysis of CRISPR knockout screens.29863497Komura K, Yoshikawa Y, Shimamura T, Chakraborty G, Gerke TA, Hinohara K, Chadalavada K, Jeong SH, Armenia J, Du SY, Mazzu YZ, Taniguchi K, Ibuki N, Meyer CA, Nanjangud GJ, Inamoto T, Lee GM, Mucci LA, Azuma H, Sweeney CJ, Kantoff PWThe Journal of clinical investigationATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D. J Clin Invest. 2018 07 02; 128(7):2979-2995.J Clin Invest2018-06-04T00:00:002018ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.21532585Baba A, Ohtake F, Okuno Y, Yokota K, Okada M, Imai Y, Ni M, Meyer CA, Igarashi K, Kanno J, Brown M, Kato SNature cell biologyPKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B. Nat Cell Biol. 2011 Jun; 13(6):668-75.Nat Cell Biol2011-05-01T00:00:002011PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B.16769980Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky ASGenome researchGenomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul; 16(7):912-21.Genome Res2006-06-12T00:00:002006Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.21284836Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XSGenome biologyMM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol. 2011; 12(2):R11.Genome Biol2011-02-01T00:00:002011MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.21859476Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XSGenome biologyCistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011 Aug 22; 12(8):R83.Genome Biol2011-08-22T00:00:002011Cistrome: an integrative platform for transcriptional regulation studies.Authorship 1356272Authorship 11141941030462313Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XSNucleic acids researchCistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 2019 01 08; 47(D1):D729-D735.Nucleic Acids Res2019-01-08T00:00:002019Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis.16086846Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PAGenome biologyGenomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 2005; 6(8):R64.Genome Biol2005-07-15T00:00:002005Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells.17683528McKee AE, Neretti N, Carvalho LE, Meyer CA, Fox EA, Brodsky AS, Silver PAGenome biologyExon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biol. 2007; 8(8):R159.Genome Biol2007-01-01T00:00:002007Exon expression profiling reveals stimulus-mediated exon use in neural cells.15961467Li W, Meyer CA, Liu XSBioinformatics (Oxford, England)A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics. 2005 Jun; 21 Suppl 1:i274-82.Bioinformatics2005-06-01T00:00:002005A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.19129543Eeckhoute J, Lupien M, Meyer CA, Verzi MP, Shivdasani RA, Liu XS, Brown MGenome researchCell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 2009 Mar; 19(3):372-80.Genome Res2009-01-07T00:00:002009Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers.19488878Liu XS, Meyer CAMethods in molecular biology (Clifton, N.J.)ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol. 2009; 556:165-75.Methods Mol Biol2009-01-01T00:00:002009ChIP-Chip: algorithms for calling binding sites.21551136Meyer CA, He HH, Brown M, Liu XSBioinformatics (Oxford, England)BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics. 2011 Jul 01; 27(13):1867-8.Bioinformatics2011-05-05T00:00:002011BINOCh: binding inference from nucleosome occupancy changes.D001203Living Beings64800.920606AscomycotaD012984Activities & BehaviorsConcepts & IdeasObjectsOccupations196744230.352968SoftwareD002843AnatomyChemicals & DrugsPhysiology103828480.424879ChromatinD047369Procedures4648880.775384Chromatin ImmunoprecipitationD030562Concepts & Ideas2133820.819311Databases, ProteinAuthorship 1150901631053864Li S, Wan C, Zheng R, Fan J, Dong X, Meyer CA, Liu XSNucleic acids researchCistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. Nucleic Acids Res. 2019 07 02; 47(W1):W206-W211.Nucleic Acids Res2019-07-02T00:00:002019Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks.BiostatisticsGeneticsMedicinePathologyPediatricsHematology/OncologyAdult OncologyOncologyBoston Children's HospitalDana-Farber Cancer InstituteHarvard Medical SchoolHarvard T.H. Chan School of Public HealthMassachusetts General HospitalBEB3BradleyBernsteinBradley E. Bernstein, M.D., Ph.D.42.37730000000000-71.0525000000000086Bernstein, BradleyProfessor of PathologyNG59NilsGehlenborgNils Gehlenborg, Ph.D.94915Gehlenborg, NilsAssociate Professor of Biomedical InformaticsAuthorship 1223581REK1RobertKingstonRobert Edward Kingston, Ph.D.42.36241700000000-71.0689370000000073338Kingston, RobertProfessor of GeneticsKS26KevinStruhlKevin Struhl, Ph.D.42.33588600000000-71.1051460000000013584Struhl, KevinDavid Wesley Gaiser Professor of Biological Chemistry and Molecular PharmacologyMAB3MylesBrownMyles A. Brown, M.D.42.33789600000000-71.1072493000000036041Brown, MylesEmil Frei III Professor of MedicineDSN2DonnaNeubergDonna S. Neuberg, D.Sc.42.33789600000000-71.1072493000000028846Neuberg, DonnaSenior Lecturer on BiostatisticsSHO1StuartOrkinStuart Holland Orkin, M.D.42.33789600000000-71.1072493000000056992Orkin, StuartDavid G. Nathan Distinguished Professor of PediatricsHK60HaesookKimHaesook Teresa Kim, Ph.D.42.33789600000000-71.1072493000000041179Kim, HaesookPrincipal Research ScientistDPH5David P.HarringtonDavid P. Harrington, Ph.D.42.33789600000000-71.1072493000000011155Harrington, David P.Professor of Biostatistics, EmeritusAuthorship 1261872PJC4PaulCatalanoPaul J. Catalano, Sc.D.42.33789600000000-71.1072493000000054067Catalano, PaulSenior Lecturer on BiostatisticsZS28ZhuoxinSunZhuoxin Sun, Ph.D.42.33789600000000-71.1072493000000031801Sun, ZhuoxinSenior Research Scientist1167selected publications1.569340.00532659261research areas0.8516570.021313560coauthor of24.07597.4908560similar toPJP8PeterParkPeter Park, Ph.D.42.33837200000000-71.1032690000000062138Park, PeterProfessor of Biomedical InformaticsHWL7HenryLongHenry W Long, Ph.D.103408Long, HenryResearch Associate in MedicineQQ15QianQinQian Qin, Ph.D.183187Qin, QianResearch Fellow in Pathologytrue1Research Associate in MedicineResearch Associate in Medicinetrue1Emil Frei III Professor of MedicineEmil Frei III Professor of MedicineSL589SehiL'YiSehi L'Yi, Ph.D.187290L'Yi, SehiResearch Fellow in Biomedical InformaticsAuthorship 12230341032033573Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XSGenome biologyLisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol. 2020 02 07; 21(1):32.Genome Biol2020-02-07T00:00:002020Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data.Authorship 1244684532374402Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y, Weng QY, Fisher DE, Long HW, Brown M, Kim HJ, Wucherpfennig KWThe Journal of experimental medicineHdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. J Exp Med. 2020 07 06; 217(7).J Exp Med2020-07-06T00:00:002020Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.Authorship 124916310Authorship 1249361532441763Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y, Weng QY, Fisher DE, Long HW, Brown M, Kim HJ, Wucherpfennig KWThe Journal of experimental medicineCorrection: Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. J Exp Med. 2020 07 06; 217(7).J Exp Med2020-07-06T00:00:002020Correction: Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells.32424124Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XSNature communicationsDeterminants of transcription factor regulatory range. Nat Commun. 2020 05 18; 11(1):2472.Nat Commun2020-05-18T00:00:002020Determinants of transcription factor regulatory range.Authorship 12780371132767996Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, Liu XSGenome biologyIntegrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biol. 2020 08 07; 21(1):198.Genome Biol2020-08-07T00:00:002020Integrative analyses of single-cell transcriptome and regulome using MAESTRO.true1David Wesley Gaiser Professor of Biological Chemistry and Molecular PharmacologyDavid Wesley Gaiser Professor of Biological Chemistry and Molecular PharmacologyBCMPAuthorship 1295697133051080Meyer CA, Liu XSTrends in biochemical sciencesComputational Approaches to Modeling Transcription Factor Activity and Gene Regulation. Trends Biochem Sci. 2020 12; 45(12):1094-1095.Trends Biochem Sci2020-10-10T00:00:002020Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation.true1Professor of Biomedical InformaticsProfessor of Biomedical InformaticsAuthorship 13559921633997789Watt AC, Cejas P, DeCristo MJ, Metzger-Filho O, Lam EYN, Qiu X, BrinJones H, Kesten N, Coulson R, Font-Tello A, Lim K, Vadhi R, Daniels VW, Montero J, Taing L, Meyer CA, Gilan O, Bell CC, Korthauer KD, Giambartolomei C, Pasaniuc B, Seo JH, Freedman ML, Ma C, Ellis MJ, Krop I, Winer E, Letai A, Brown M, Dawson MA, Long HW, Zhao JJ, Goel SNature cancerCDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. Nat Cancer. 2021 01; 2(1):34-48.Nat Cancer2020-11-09T00:00:002020CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity.true1Associate Professor of Biomedical InformaticsAssociate Professor of Biomedical InformaticsAuthorship 14007401534582788Wang X, Tokheim C, Gu SS, Wang B, Tang Q, Li Y, Traugh N, Zeng Z, Zhang Y, Li Z, Zhang B, Fu J, Xiao T, Li W, Meyer CA, Chu J, Jiang P, Cejas P, Lim K, Long H, Brown M, Liu XSCellIn vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target. Cell. 2021 10 14; 184(21):5357-5374.e22.Cell2021-09-27T00:00:002021In vivo CRISPR screens identify the E3 ligase Cop1 as a modulator of macrophage infiltration and cancer immunotherapy target.Authorship 1413800634772935Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li HNature communicationsFast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. 2021 11 12; 12(1):6566.Nat Commun2021-11-12T00:00:002021Fast alignment and preprocessing of chromatin profiles with Chromap.35015684Schaefer EJ, Wang HC, Karp HQ, Meyer CA, Cejas P, Gearhart MD, Adelman ER, Fares I, Apffel A, Lim K, Xie Y, Gibson CJ, Schenone M, Murdock HM, Wang ES, Gondek LP, Carroll MP, Vedula RS, Winer ES, Garcia JS, Stone RM, Luskin MR, Carr SA, Long HW, Bardwell VJ, Figueroa ME, Lindsley RCBlood cancer discoveryBCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes. Blood Cancer Discov. 2022 03 01; 3(2):116-135.Blood Cancer Discov2022-03-01T00:00:002022BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes.Authorship 14258564Authorship 3652132Authorship 14864446Authorship 149339010Authorship 1492182636270276Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li XN, Meric-Bernstam F, Meyer CA, Mou H, Naegle KM, Pera MF, Perova Z, Politi KA, Raphael BJ, Robson P, Sears RC, Tabernero J, Tuveson DA, Welm AL, Welm BE, Willey CD, Salnikow K, Chuang JH, Shen XCancer cellA path to translation: How 3D patient tumor avatars enable next generation precision oncology. Cancer Cell. 2022 12 12; 40(12):1448-1453.Cancer Cell2022-10-20T00:00:002022A path to translation: How 3D patient tumor avatars enable next generation precision oncology.36130957Hu SS, Liu L, Li Q, Ma W, Guertin MJ, Meyer CA, Deng K, Zhang T, Zang CNature communicationsIntrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Nat Commun. 2022 09 21; 13(1):5533.Nat Commun2022-09-21T00:00:002022Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.36068320Lynch AW, Theodoris CV, Long HW, Brown M, Liu XS, Meyer CANature methodsMIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells. Nat Methods. 2022 09; 19(9):1097-1108.Nat Methods2022-09-06T00:00:002022MIRA: joint regulatory modeling of multimodal expression and chromatin accessibility in single cells.Authorship 1519013736688700L'Yi S, Keller MS, Dandawate A, Taing L, Chen CH, Brown M, Meyer CA, Gehlenborg NBioinformatics (Oxford, England)Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data. Bioinformatics. 2023 02 03; 39(2).Bioinformatics2023-02-03T00:00:002023Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data.Authorship 24479313Authorship 15256012836745048Sahu A, Wang X, Munson P, Klomp JPG, Wang X, Gu SS, Han Y, Qian G, Nicol P, Zeng Z, Wang C, Tokheim C, Zhang W, Fu J, Wang J, Nair NU, Rens JAP, Bourajjaj M, Jansen B, Leenders I, Lemmers J, Musters M, van Zanten S, van Zelst L, Worthington J, Liu JS, Juric D, Meyer CA, Oubrie A, Liu XS, Fisher DE, Flaherty KTCancer discoveryDiscovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha. Cancer Discov. 2023 03 01; 13(3):672-701.Cancer Discov2023-03-01T00:00:002023Discovery of Targets for Immune-Metabolic Antitumor Drugs Identifies Estrogen-Related Receptor Alpha.Authorship 15545723Authorship 155619015Authorship 15714501037149682Zhang Y, Xiang G, Jiang AY, Lynch A, Zeng Z, Wang C, Zhang W, Fan J, Kang J, Gu SS, Wan C, Zhang B, Liu XS, Brown M, Meyer CANature communicationsMetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment. Nat Commun. 2023 05 06; 14(1):2634.Nat Commun2023-05-06T00:00:002023MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.37433791Lynch AW, Brown M, Meyer CANature communicationsMulti-batch single-cell comparative atlas construction by deep learning disentanglement. Nat Commun. 2023 07 12; 14(1):4126.Nat Commun2023-07-12T00:00:002023Multi-batch single-cell comparative atlas construction by deep learning disentanglement.37333088Jiang Y, Hu Z, Lynch AW, Jiang J, Zhu A, Zhang Y, Xie Y, Li R, Zhou N, Meyer CA, Cejas P, Brown M, Long HW, Qiu XbioRxiv : the preprint server for biologyscATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data. bioRxiv. 2024 Jan 11.bioRxiv2024-01-11T00:00:002024scATAnno: Automated Cell Type Annotation for single-cell ATAC Sequencing Data.true1Research Fellow in PathologyResearch Fellow in Pathologytrue1Professor of GeneticsProfessor of Geneticstrue1Professor of PathologyProfessor of Pathologytrue1Research Fellow in Biomedical InformaticsResearch Fellow in Biomedical InformaticsAuthorship 1610541637971305Taing L, Dandawate A, L'Yi S, Gehlenborg N, Brown M, Meyer CANucleic acids researchCistrome Data Browser: integrated search, analysis and visualization of chromatin data. Nucleic Acids Res. 2024 Jan 05; 52(D1):D61-D66.Nucleic Acids Res2024-01-05T00:00:002024Cistrome Data Browser: integrated search, analysis and visualization of chromatin data.Authorship 16231531238260422Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Gomez MM, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RAbioRxiv : the preprint server for biologyTranscription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. bioRxiv. 2024 Jan 09.bioRxiv2024-01-09T00:00:002024Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation.true1Principal Research ScientistPrincipal Research Scientisttrue1Senior Research ScientistSenior Research Scientisttrue1Senior Lecturer on BiostatisticsSenior Lecturer on Biostatisticstrue1David G. Nathan Distinguished Professor of PediatricsDavid G. Nathan Distinguished Professor of Pediatricstrue1Professor of Biostatistics, EmeritusProfessor of Biostatistics, Emeritustrue1Senior Lecturer on BiostatisticsSenior Lecturer on Biostatisticstrue1Senior Research ScientistSenior Research ScientistAuthorship 3714133Authorship 2302724Authorship 354950224093963Wang H, Meyer CA, Fei T, Wang G, Zhang F, Liu XSBMC genomicsA systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. BMC Genomics. 2013 Oct 04; 14:680.BMC Genomics2013-10-04T00:00:002013A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer.Authorship 367161224317252He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown MNature methodsRefined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2014 Jan; 11(1):73-78.Nat Methods2013-12-08T00:00:002013Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification.Authorship 2630214Authorship 722704224263090Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XSNature protocolsTarget analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013 Dec; 8(12):2502-15.Nat Protoc2013-11-21T00:00:002013Target analysis by integration of transcriptome and ChIP-seq data with BETA.Authorship 2902413Authorship 763309125223782Meyer CA, Liu XSNature reviews. GeneticsIdentifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014 Nov; 15(11):709-21.Nat Rev Genet2014-09-16T00:00:002014Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.Authorship 7660711725344755Li N, Fassl A, Chick J, Inuzuka H, Li X, Mansour MR, Liu L, Wang H, King B, Shaik S, Gutierrez A, Ordureau A, Otto T, Kreslavsky T, Baitsch L, Bury L, Meyer CA, Ke N, Mulry KA, Kluk MJ, Roy M, Kim S, Zhang X, Geng Y, Zagozdzon A, Jenkinson S, Gale RE, Linch DC, Zhao JJ, Mullighan CG, Harper JW, Aster JC, Aifantis I, von Boehmer H, Gygi SP, Wei W, Look AT, Sicinski PNature cell biologyCyclin C is a haploinsufficient tumour suppressor. Nat Cell Biol. 2014 Nov; 16(11):1080-91.Nat Cell Biol2014-10-26T00:00:002014Cyclin C is a haploinsufficient tumour suppressor.Authorship 560562Authorship 824512Authorship 3032052Authorship 5366384Authorship 2513804Authorship 2768013Biomedical InformaticsAuthorship 822281526063738Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XSGenome researchSequence determinants of improved CRISPR sgRNA design. Genome Res. 2015 Aug; 25(8):1147-57.Genome Res2015-06-10T00:00:002015Sequence determinants of improved CRISPR sgRNA design.Authorship 996377Authorship 433059226735014Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Huh SJ, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Brown J, D'Santos C, Krop IE, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Wu SY, Chiang CM, Anders L, Young RA, Winer E, Letai A, Barry WT, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak KNatureResponse and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417.Nature2016-01-06T00:00:002016Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer.Authorship 85868337Authorship 3896255Authorship 877258927072482Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XSNature communicationsHigh-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun. 2016 Apr 13; 7:11305.Nat Commun2016-04-13T00:00:002016High-dimensional genomic data bias correction and data integration using MANCIE.Authorship 41388151Associate Professor6Fellow or Post Doc0Full Professor3Lecturer5Other FacultyAuthorship 924486425411587Schwartzman A, Jaffe A, Gavrilov Y, Meyer CAThe annals of applied statisticsMULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA. Ann Appl Stat. 2013; 7(1):471-494.Ann Appl Stat2013-01-01T00:00:002013MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA.27466232Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li X, Xu K, He HH, Brown M, Meyer CA, Liu XSGenome researchModeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res. 2016 10; 26(10):1417-1429.Genome Res2016-07-27T00:00:002016Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles.Authorship 5503613Authorship 2726891Authorship 572180527789702Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XSNucleic acids researchCistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 2017 01 04; 45(D1):D658-D662.Nucleic Acids Res2016-10-26T00:00:002016Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.27716038Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XSBMC bioinformaticsChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics. 2016 Oct 03; 17(1):404.BMC Bioinformatics2016-10-03T00:00:002016ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.25103624Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P, Zhang Y, Liu XSGenome biologyMethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014 Aug 07; 15(8):419.Genome Biol2014-08-07T00:00:002014MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes.22930692Meyer CA, Tang Q, Liu XSMolecular endocrinology (Baltimore, Md.)Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol. 2012 Oct; 26(10):1651-9.Mol Endocrinol2012-08-28T00:00:002012Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function.20972221Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XSNucleic acids researchCaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D968-74.Nucleic Acids Res2010-10-23T00:00:002010CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data.16895995Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XSProceedings of the National Academy of Sciences of the United States of AmericaModel-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62.Proc Natl Acad Sci U S A2006-08-08T00:00:002006Model-based analysis of tiling-arrays for ChIP-chip.17013392Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown MNature geneticsGenome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97.Nat Genet2006-10-01T00:00:002006Genome-wide analysis of estrogen receptor binding sites.22508765He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XSGenome researchDifferential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012 Jun; 22(6):1015-25.Genome Res2012-04-16T00:00:002012Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.16009131Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown MCellChromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005 Jul 15; 122(1):33-43.Cell2005-07-15T00:00:002005Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.19687146Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks ADGenome researchElucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 2009 Nov; 19(11):1963-73.Genome Res2009-08-17T00:00:002009Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.20889718Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown MGenes & developmentGrowth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev. 2010 Oct 01; 24(19):2219-27.Genes Dev2010-10-01T00:00:002010Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance.44 Binney StDana Farber Cancer InstituteBiostatistics & Computational Biology44 Binney StBoston02115MA21074721Verzi MP, Shin H, He HH, Sulahian R, Meyer CA, Montgomery RK, Fleet JC, Brown M, Liu XS, Shivdasani RADevelopmental cellDifferentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell. 2010 Nov 16; 19(5):713-26.Dev Cell2010-11-16T00:00:002010Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2.20090754Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski PNatureTranscriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21; 463(7279):374-8.Nature2010-01-21T00:00:002010Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen.Authorship 10139548Authorship 101420613Authorship 10142653Authorship 10135266Authorship 10142642Authorship 10144387Authorship 10151098Authorship 101341213Authorship 1013413222923299Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang YBioinformatics (Oxford, England)GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012 Nov 01; 28(21):2782-8.Bioinformatics2012-08-24T00:00:002012GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.Authorship 1023816229092931Mei S, Meyer CA, Zheng R, Qin Q, Wu Q, Jiang P, Li B, Shi X, Wang B, Fan J, Shih C, Brown M, Zang C, Liu XSCancer researchCistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer. Cancer Res. 2017 11 01; 77(21):e19-e22.Cancer Res2017-11-01T00:00:002017Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer.21045080Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XSGenome researchGene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec; 20(12):1730-9.Genome Res2010-11-02T00:00:002010Gene expression profiling of human breast tissue samples using SAGE-Seq.18358809Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown MCellFoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell. 2008 Mar 21; 132(6):958-70.Cell2008-03-21T00:00:002008FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.20133671Wolfer A, Wittner BS, Irimia D, Flavin RJ, Lupien M, Gunawardane RN, Meyer CA, Lightcap ES, Tamayo P, Mesirov JP, Liu XS, Shioda T, Toner M, Loda M, Brown M, Brugge JS, Ramaswamy SProceedings of the National Academy of Sciences of the United States of AmericaMYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703.Proc Natl Acad Sci U S A2010-02-04T00:00:002010MYC regulation of a "poor-prognosis" metastatic cancer cell state.20208536He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XSNature geneticsNucleosome dynamics define transcriptional enhancers. Nat Genet. 2010 Apr; 42(4):343-7.Nat Genet2010-03-07T00:00:002010Nucleosome dynamics define transcriptional enhancers.18798982Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XSGenome biologyModel-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137.Genome Biol2008-09-17T00:00:002008Model-based analysis of ChIP-Seq (MACS).19632176Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, Jänne OA, Balk SP, Mehra R, Han B, Chinnaiyan AM, Rubin MA, True L, Fiorentino M, Fiore C, Loda M, Kantoff PW, Liu XS, Brown MCellAndrogen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56.Cell2009-07-23T00:00:002009Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer.Authorship 103723212