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Journal Abstract Search

404 related items for PubMed ID: 25070602

  • 1. 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]

  • 2. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
    Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.
    BMC Genomics; 2014 Jun 13; 15(1):472. PubMed ID: 24927817
    [Abstract] [Full Text] [Related]

  • 3. 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 13; 22(9):1798-812. PubMed ID: 22955990
    [Abstract] [Full Text] [Related]

  • 4. ChIPulate: A comprehensive ChIP-seq simulation pipeline.
    Datta V, Hannenhalli S, Siddharthan R.
    PLoS Comput Biol; 2019 Mar 13; 15(3):e1006921. PubMed ID: 30897079
    [Abstract] [Full Text] [Related]

  • 5. Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data.
    Levitsky V, Oshchepkov D, Zemlyanskaya E, Merkulova T.
    Int J Mol Sci; 2020 Aug 21; 21(17):. PubMed ID: 32825662
    [Abstract] [Full Text] [Related]

  • 6. Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans.
    Tahara S, Tsuchiya T, Matsumoto H, Ozaki H.
    BMC Genomics; 2023 Oct 07; 24(1):597. PubMed ID: 37805453
    [Abstract] [Full Text] [Related]

  • 7. MEME-ChIP: motif analysis of large DNA datasets.
    Machanick P, Bailey TL.
    Bioinformatics; 2011 Jun 15; 27(12):1696-7. PubMed ID: 21486936
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.
    Agius P, Arvey A, Chang W, Noble WS, Leslie C.
    PLoS Comput Biol; 2010 Sep 09; 6(9):. PubMed ID: 20838582
    [Abstract] [Full Text] [Related]

  • 10. Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data.
    Goi C, Little P, Xie C.
    BMC Genomics; 2013 Sep 09; 14 Suppl 5(Suppl 5):S2. PubMed ID: 24564528
    [Abstract] [Full Text] [Related]

  • 11. Cell-type specificity of ChIP-predicted transcription factor binding sites.
    Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.
    BMC Genomics; 2012 Aug 03; 13():372. PubMed ID: 22863112
    [Abstract] [Full Text] [Related]

  • 12. 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
    Ibn-Salem J, Andrade-Navarro MA.
    BMC Genomics; 2019 Oct 25; 20(1):777. PubMed ID: 31653198
    [Abstract] [Full Text] [Related]

  • 13. Differential motif enrichment analysis of paired ChIP-seq experiments.
    Lesluyes T, Johnson J, Machanick P, Bailey TL.
    BMC Genomics; 2014 Sep 02; 15(1):752. PubMed ID: 25179504
    [Abstract] [Full Text] [Related]

  • 14. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
    Ozaki H, Iwasaki W.
    Comput Biol Chem; 2016 Aug 02; 63():62-72. PubMed ID: 26971251
    [Abstract] [Full Text] [Related]

  • 15. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.
    He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.
    PLoS One; 2009 Dec 01; 4(12):e8155. PubMed ID: 19956545
    [Abstract] [Full Text] [Related]

  • 16. FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets.
    Zhang S, Liang Y, Wang X, Su Z, Chen Y.
    DNA Res; 2019 Jun 01; 26(3):231-242. PubMed ID: 30957858
    [Abstract] [Full Text] [Related]

  • 17. 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 01; 41(Web Server issue):W535-43. PubMed ID: 23748563
    [Abstract] [Full Text] [Related]

  • 18. An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example.
    Cheng CY, Chu CH, Hsu HW, Hsu FR, Tang CY, Wang WC, Kung HJ, Chang PC.
    BMC Genomics; 2014 Jul 01; 15 Suppl 1(Suppl 1):S1. PubMed ID: 24564277
    [Abstract] [Full Text] [Related]

  • 19. Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA.
    Nagy G, Czipa E, Steiner L, Nagy T, Pongor S, Nagy L, Barta E.
    BMC Genomics; 2016 Aug 15; 17(1):637. PubMed ID: 27526722
    [Abstract] [Full Text] [Related]

  • 20. Inferring transcription factor complexes from ChIP-seq data.
    Whitington T, Frith MC, Johnson J, Bailey TL.
    Nucleic Acids Res; 2011 Aug 15; 39(15):e98. PubMed ID: 21602262
    [Abstract] [Full Text] [Related]

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