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Journal Abstract Search

334 related items for PubMed ID: 28334916

  • 1. 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]

  • 2. Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility.
    Liu S, Zibetti C, Wan J, Wang G, Blackshaw S, Qian J.
    BMC Bioinformatics; 2017 Jul 27; 18(1):355. PubMed ID: 28750606
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. 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]

  • 5. 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]

  • 6. COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.
    Ha N, Polychronidou M, Lohmann I.
    PLoS One; 2012 Aug 03; 7(12):e52055. PubMed ID: 23272209
    [Abstract] [Full Text] [Related]

  • 7. Sequence and chromatin determinants of cell-type-specific transcription factor binding.
    Arvey A, Agius P, Noble WS, Leslie C.
    Genome Res; 2012 Sep 03; 22(9):1723-34. PubMed ID: 22955984
    [Abstract] [Full Text] [Related]

  • 8. Anchor: trans-cell type prediction of transcription factor binding sites.
    Li H, Quang D, Guan Y.
    Genome Res; 2019 Feb 03; 29(2):281-292. PubMed ID: 30567711
    [Abstract] [Full Text] [Related]

  • 9. 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]

  • 10. 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]

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  • 12. TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
    Ouyang N, Boyle AP.
    Genome Res; 2020 Jul 01; 30(7):1040-1046. PubMed ID: 32660981
    [Abstract] [Full Text] [Related]

  • 13. Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species.
    Huang L, Li X, Dong L, Wang B, Pan L.
    BMC Biol; 2021 Sep 06; 19(1):189. PubMed ID: 34488759
    [Abstract] [Full Text] [Related]

  • 14. REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data.
    Yang Y, Pe'er D.
    Bioinformatics; 2024 Jun 28; 40(Suppl 1):i567-i575. PubMed ID: 38940155
    [Abstract] [Full Text] [Related]

  • 15. Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.
    Kuznetsov VA, Singh O, Jenjaroenpun P.
    BMC Genomics; 2010 Feb 10; 11 Suppl 1(Suppl 1):S12. PubMed ID: 20158869
    [Abstract] [Full Text] [Related]

  • 16. MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
    Xuan Lin QX, Sian S, An O, Thieffry D, Jha S, Benoukraf T.
    Nucleic Acids Res; 2019 Jan 08; 47(D1):D145-D154. PubMed ID: 30380113
    [Abstract] [Full Text] [Related]

  • 17. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.
    Tsai ZT, Shiu SH, Tsai HK.
    PLoS Comput Biol; 2015 Aug 08; 11(8):e1004418. PubMed ID: 26291518
    [Abstract] [Full Text] [Related]

  • 18. Modeling co-occupancy of transcription factors using chromatin features.
    Liu L, Zhao W, Zhou X.
    Nucleic Acids Res; 2016 Mar 18; 44(5):e49. PubMed ID: 26590261
    [Abstract] [Full Text] [Related]

  • 19. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.
    Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dehghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH.
    Nucleic Acids Res; 2017 Jan 09; 45(1):54-66. PubMed ID: 27899623
    [Abstract] [Full Text] [Related]

  • 20. Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.
    Grau J, Schmidt F, Schulz MH.
    Nucleic Acids Res; 2023 Oct 13; 51(18):e95. PubMed ID: 37650641
    [Abstract] [Full Text] [Related]

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