Harvard Catalyst Profiles

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Clifford Meyer, Ph.D.

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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.
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  1. Li S, Wan C, Zheng R, Fan J, Dong X, Meyer CA, Liu XS. Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. Nucleic Acids Res. 2019 May 04. PMID: 31053864.
    Citations:    
  2. Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 2019 Jan 08; 47(D1):D729-D735. PMID: 30462313.
    Citations:    Fields:    
  3. Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS. Improved design and analysis of CRISPR knockout screens. Bioinformatics. 2018 Dec 01; 34(23):4095-4101. PMID: 29868757.
    Citations:    Fields:    
  4. Komura 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 PW. ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D. J Clin Invest. 2018 Jul 02; 128(7):2979-2995. PMID: 29863497.
    Citations:    Fields:    
  5. Mei 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 XS. Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer. Cancer Res. 2017 11 01; 77(21):e19-e22. PMID: 29092931.
    Citations:    Fields:    Translation:HumansCells
  6. Mei 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 XS. Cistrome 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. PMID: 27789702.
    Citations: 22     Fields:    Translation:HumansAnimals
  7. Qin 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 XS. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics. 2016 Oct 03; 17(1):404. PMID: 27716038.
    Citations: 7     Fields:    Translation:Humans
  8. Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li X, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res. 2016 10; 26(10):1417-1429. PMID: 27466232.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  9. Zang 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 XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun. 2016 Apr 13; 7:11305. PMID: 27072482.
    Citations: 4     Fields:    Translation:HumansCells
  10. Shu 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 K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417. PMID: 26735014.
    Citations: 90     Fields:    Translation:HumansAnimalsCells
  11. Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015 Aug; 25(8):1147-57. PMID: 26063738.
    Citations: 83     Fields:    Translation:HumansCells
  12. Li 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 P. Cyclin C is a haploinsufficient tumour suppressor. Nat Cell Biol. 2014 Nov; 16(11):1080-91. PMID: 25344755.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  13. Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014 Nov; 15(11):709-21. PMID: 25223782.
    Citations: 62     Fields:    Translation:Cells
  14. Zheng 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 XS. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014 Aug 07; 15(8):419. PMID: 25103624.
    Citations: 21     Fields:    Translation:HumansCells
  15. He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2014 Jan; 11(1):73-78. PMID: 24317252.
    Citations: 62     Fields:    Translation:HumansCells
  16. Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013 Dec; 8(12):2502-15. PMID: 24263090.
    Citations: 60     Fields:    Translation:Cells
  17. Wang H, Meyer CA, Fei T, Wang G, Zhang F, Liu XS. A 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. PMID: 24093963.
    Citations: 12     Fields:    Translation:HumansCells
  18. Schwartzman A, Jaffe A, Gavrilov Y, Meyer CA. MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN CHIP-SEQ DATA. Ann Appl Stat. 2013; 7(1):471-494. PMID: 25411587.
    Citations: 1     
  19. Meyer CA, Tang Q, Liu XS. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol. 2012 Oct; 26(10):1651-9. PMID: 22930692.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  20. Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics. 2012 Nov 01; 28(21):2782-8. PMID: 22923299.
    Citations: 92     Fields:    Translation:HumansCells
  21. He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012 Jun; 22(6):1015-25. PMID: 22508765.
    Citations: 80     Fields:    Translation:HumansCells
  22. Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res. 2012 Aug; 40(14):6414-23. PMID: 22495509.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  23. Liu 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 XS. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011 Aug 22; 12(8):R83. PMID: 21859476.
    Citations: 228     Fields:    Translation:Humans
  24. Meyer CA, He HH, Brown M, Liu XS. BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics. 2011 Jul 01; 27(13):1867-8. PMID: 21551136.
    Citations: 9     Fields:    Translation:HumansCells
  25. Baba A, Ohtake F, Okuno Y, Yokota K, Okada M, Imai Y, Ni M, Meyer CA, Igarashi K, Kanno J, Brown M, Kato S. PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B. Nat Cell Biol. 2011 Jun; 13(6):668-75. PMID: 21532585.
    Citations: 54     Fields:    Translation:HumansAnimalsCells
  26. Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol. 2011; 12(2):R11. PMID: 21284836.
    Citations: 10     Fields:    Translation:HumansCells
  27. Verzi MP, Shin H, He HH, Sulahian R, Meyer CA, Montgomery RK, Fleet JC, Brown M, Liu XS, Shivdasani RA. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell. 2010 Nov 16; 19(5):713-26. PMID: 21074721.
    Citations: 85     Fields:    Translation:HumansAnimalsCells
  28. Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec; 20(12):1730-9. PMID: 21045080.
    Citations: 22     Fields:    Translation:HumansCells
  29. Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D968-74. PMID: 20972221.
    Citations: 12     Fields:    Translation:Humans
  30. Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown M. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev. 2010 Oct 01; 24(19):2219-27. PMID: 20889718.
    Citations: 61     Fields:    Translation:HumansCells
  31. He 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 XS. Nucleosome dynamics define transcriptional enhancers. Nat Genet. 2010 Apr; 42(4):343-7. PMID: 20208536.
    Citations: 235     Fields:    Translation:HumansCells
  32. Wolfer 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 S. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703. PMID: 20133671.
    Citations: 72     Fields:    Translation:Humans
  33. Bienvenu 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 P. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21; 463(7279):374-8. PMID: 20090754.
    Citations: 101     Fields:    Translation:AnimalsCells
  34. Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. Elucidation 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. PMID: 19687146.
    Citations: 56     Fields:    Translation:HumansCells
  35. Wang 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 M. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56. PMID: 19632176.
    Citations: 352     Fields:    Translation:HumansCells
  36. Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol. 2009 Jun; 29(12):3413-23. PMID: 19364822.
    Citations: 33     Fields:    Translation:HumansCells
  37. Eeckhoute J, Lupien M, Meyer CA, Verzi MP, Shivdasani RA, Liu XS, Brown M. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 2009 Mar; 19(3):372-80. PMID: 19129543.
    Citations: 55     Fields:    Translation:HumansCells
  38. Liu XS, Meyer CA. ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol. 2009; 556:165-75. PMID: 19488878.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  39. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. PMID: 18798982.
    Citations: 2870     Fields:    Translation:HumansCells
  40. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell. 2008 Mar 21; 132(6):958-70. PMID: 18358809.
    Citations: 410     Fields:    Translation:HumansCells
  41. McKee AE, Neretti N, Carvalho LE, Meyer CA, Fox EA, Brodsky AS, Silver PA. Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biol. 2007; 8(8):R159. PMID: 17683528.
    Citations: 26     Fields:    Translation:HumansCells
  42. Carroll 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 M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97. PMID: 17013392.
    Citations: 615     Fields:    Translation:HumansCells
  43. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62. PMID: 16895995.
    Citations: 246     Fields:    Translation:Humans
  44. Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul; 16(7):912-21. PMID: 16769980.
    Citations: 22     Fields:    Translation:HumansCells
  45. Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 2005; 6(8):R64. PMID: 16086846.
    Citations: 46     Fields:    Translation:HumansCells
  46. Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005 Jul 15; 122(1):33-43. PMID: 16009131.
    Citations: 542     Fields:    Translation:HumansAnimalsCells
  47. Li W, Meyer CA, Liu XS. 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. PMID: 15961467.
    Citations: 41     Fields:    Translation:HumansCells
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.