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Clifford Meyer, Ph.D.


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. Schaefer 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 RC. BCOR 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. PMID: 35015684.
    Citations:    Fields:    Translation:HumansCells
  2. Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. 2021 11 12; 12(1):6566. PMID: 34772935; PMCID: PMC8589834.
    Citations: 2     Fields:    Translation:HumansCells
  3. Wang 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 XS. In 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. PMID: 34582788; PMCID: PMC9136996.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  4. Watt 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 S. CDK4/6 inhibition reprograms the breast cancer enhancer landscape by stimulating AP-1 transcriptional activity. Nat Cancer. 2021 01; 2(1):34-48. PMID: 33997789; PMCID: PMC8115221.
    Citations: 10     Translation:HumansAnimals
  5. Meyer CA, Liu XS. Computational Approaches to Modeling Transcription Factor Activity and Gene Regulation. Trends Biochem Sci. 2020 12; 45(12):1094-1095. PMID: 33051080.
    Citations:    Fields:    
  6. Wang 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 XS. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biol. 2020 08 07; 21(1):198. PMID: 32767996.
    Citations: 29     Fields:    Translation:HumansCells
  7. Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y, Weng QY, Fisher DE, Long HW, Brown M, Kim HJ, Wucherpfennig KW. Correction: Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. J Exp Med. 2020 07 06; 217(7). PMID: 32441763; PMCID: PMC7336308.
    Citations: 2     Fields:    
  8. Tay RE, Olawoyin O, Cejas P, Xie Y, Meyer CA, Ito Y, Weng QY, Fisher DE, Long HW, Brown M, Kim HJ, Wucherpfennig KW. Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. J Exp Med. 2020 07 06; 217(7). PMID: 32374402.
    Citations: 9     Fields:    Translation:AnimalsCells
  9. Chen CH, Zheng R, Tokheim C, Dong X, Fan J, Wan C, Tang Q, Brown M, Liu JS, Meyer CA, Liu XS. Determinants of transcription factor regulatory range. Nat Commun. 2020 05 18; 11(1):2472. PMID: 32424124.
    Citations: 12     Fields:    Translation:AnimalsCells
  10. Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XS. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol. 2020 02 07; 21(1):32. PMID: 32033573.
    Citations: 42     Fields:    Translation:HumansAnimalsCells
  11. 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 07 02; 47(W1):W206-W211. PMID: 31053864; PMCID: PMC6602521.
    Citations: 24     Fields:    Translation:HumansAnimals
  12. 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 01 08; 47(D1):D729-D735. PMID: 30462313; PMCID: PMC6324081.
    Citations: 182     Fields:    Translation:HumansAnimalsCells
  13. 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 12 01; 34(23):4095-4101. PMID: 29868757.
    Citations: 17     Fields:    
  14. 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 07 02; 128(7):2979-2995. PMID: 29863497; PMCID: PMC6025984.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  15. 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; PMCID: PMC5826647.
    Citations: 80     Fields:    Translation:HumansCells
  16. 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; PMCID: PMC5210658.
    Citations: 207     Fields:    Translation:HumansAnimals
  17. 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: 52     Fields:    Translation:Humans
  18. 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; PMCID: PMC5052056.
    Citations: 35     Fields:    Translation:HumansAnimalsCells
  19. 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: 13     Fields:    Translation:HumansCells
  20. 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: 253     Fields:    Translation:HumansAnimalsCells
  21. 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; PMCID: PMC4509999.
    Citations: 215     Fields:    Translation:HumansCells
  22. 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; PMCID: PMC4235773.
    Citations: 56     Fields:    Translation:HumansAnimalsCells
  23. 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: 124     Fields:    Translation:Cells
  24. 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: 38     Fields:    Translation:HumansCells
  25. 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: 115     Fields:    Translation:HumansCells
  26. 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: 192     Fields:    Translation:Cells
  27. 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: 31     Fields:    Translation:HumansCells
  28. 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; PMCID: PMC4233463.
    Citations: 3     
  29. 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
  30. 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: 199     Fields:    Translation:HumansCells
  31. 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: 111     Fields:    Translation:HumansCells
  32. 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: 11     Fields:    Translation:HumansAnimalsCells
  33. 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: 382     Fields:    Translation:Humans
  34. 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: 12     Fields:    Translation:HumansCells
  35. 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: 82     Fields:    Translation:HumansAnimalsCells
  36. 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: 11     Fields:    Translation:HumansCells
  37. 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: 116     Fields:    Translation:HumansAnimalsCells
  38. 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: 25     Fields:    Translation:HumansCells
  39. 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: 14     Fields:    Translation:Humans
  40. 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; PMCID: PMC2947773.
    Citations: 93     Fields:    Translation:HumansCells
  41. 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; PMCID: PMC2932437.
    Citations: 281     Fields:    Translation:HumansCells
  42. 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: 101     Fields:    Translation:Humans
  43. 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: 136     Fields:    Translation:AnimalsCells
  44. 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: 77     Fields:    Translation:HumansCells
  45. 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: 475     Fields:    Translation:HumansCells
  46. 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: 43     Fields:    Translation:HumansCells
  47. 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: 64     Fields:    Translation:HumansCells
  48. 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
  49. 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: 6536     Fields:    Translation:HumansCells
  50. 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: 527     Fields:    Translation:HumansCells
  51. 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; PMCID: PMC2374990.
    Citations: 28     Fields:    Translation:HumansCells
  52. 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: 734     Fields:    Translation:HumansCells
  53. 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; PMCID: PMC1567901.
    Citations: 266     Fields:    Translation:Humans
  54. 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; PMCID: PMC1484458.
    Citations: 28     Fields:    Translation:HumansCells
  55. 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: 693     Fields:    Translation:HumansAnimalsCells
  56. 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; PMCID: PMC1273631.
    Citations: 54     Fields:    Translation:HumansCells
  57. 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 National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.