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Journal Abstract Search

1002 related items for PubMed ID: 22955990

  • 1. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
    Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.
    Genome Res; 2012 Sep; 22(9):1798-812. PubMed ID: 22955990
    [Abstract] [Full Text] [Related]

  • 2. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
    Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.
    Nucleic Acids Res; 2013 Jan; 41(Database issue):D171-6. PubMed ID: 23203885
    [Abstract] [Full Text] [Related]

  • 3. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
    Arvey A, Agius P, Noble WS, Leslie C.
    Genome Res; 2012 Sep; 22(9):1723-34. PubMed ID: 22955984
    [Abstract] [Full Text] [Related]

  • 4. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.
    He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.
    BMC Genomics; 2013 Jun 28; 14():428. PubMed ID: 23805837
    [Abstract] [Full Text] [Related]

  • 5. Mapping nucleosome positions using DNase-seq.
    Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ.
    Genome Res; 2016 Mar 28; 26(3):351-64. PubMed ID: 26772197
    [Abstract] [Full Text] [Related]

  • 6. Nucleosome organization in the vicinity of transcription factor binding sites in the human genome.
    Nie Y, Cheng X, Chen J, Sun X.
    BMC Genomics; 2014 Jun 19; 15(1):493. PubMed ID: 24942981
    [Abstract] [Full Text] [Related]

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  • 9. Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes.
    Sethi I, Sinha S, Buck MJ.
    BMC Genomics; 2014 Nov 29; 15(1):1042. PubMed ID: 25433490
    [Abstract] [Full Text] [Related]

  • 10. Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.
    Worsley Hunt R, Wasserman WW.
    Genome Biol; 2014 Jul 29; 15(7):412. PubMed ID: 25070602
    [Abstract] [Full Text] [Related]

  • 11. Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.
    Yu CP, Kuo CH, Nelson CW, Chen CA, Soh ZT, Lin JJ, Hsiao RX, Chang CY, Li WH.
    Proc Natl Acad Sci U S A; 2021 May 18; 118(20):. PubMed ID: 33975951
    [Abstract] [Full Text] [Related]

  • 12. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.
    Goh WS, Orlov Y, Li J, Clarke ND.
    PLoS Comput Biol; 2010 Jan 22; 6(1):e1000649. PubMed ID: 20098497
    [Abstract] [Full Text] [Related]

  • 13. A map of direct TF-DNA interactions in the human genome.
    Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A.
    Nucleic Acids Res; 2019 Feb 28; 47(4):e21. PubMed ID: 30517703
    [Abstract] [Full Text] [Related]

  • 14. PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
    Zambelli F, Pesole G, Pavesi G.
    Nucleic Acids Res; 2013 Jul 28; 41(Web Server issue):W535-43. PubMed ID: 23748563
    [Abstract] [Full Text] [Related]

  • 15. Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types.
    Ernst J, Kellis M.
    Genome Res; 2013 Jul 28; 23(7):1142-54. PubMed ID: 23595227
    [Abstract] [Full Text] [Related]

  • 16. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.
    Kumar S, Bucher P.
    BMC Bioinformatics; 2016 Jan 11; 17 Suppl 1(Suppl 1):4. PubMed ID: 26818008
    [Abstract] [Full Text] [Related]

  • 17. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.
    Chen X, Yu B, Carriero N, Silva C, Bonneau R.
    Nucleic Acids Res; 2017 May 05; 45(8):4315-4329. PubMed ID: 28334916
    [Abstract] [Full Text] [Related]

  • 18. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.
    Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA.
    Nat Methods; 2014 Jan 05; 11(1):66-72. PubMed ID: 24185839
    [Abstract] [Full Text] [Related]

  • 19. Predicting cell-type-specific gene expression from regions of open chromatin.
    Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U.
    Genome Res; 2012 Sep 05; 22(9):1711-22. PubMed ID: 22955983
    [Abstract] [Full Text] [Related]

  • 20. Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
    Yardımcı GG, Frank CL, Crawford GE, Ohler U.
    Nucleic Acids Res; 2014 Oct 29; 42(19):11865-78. PubMed ID: 25294828
    [Abstract] [Full Text] [Related]

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