BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

385 related articles for article (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; 15(7):412. PubMed ID: 25070602
    [TBL] [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; 15(1):472. PubMed ID: 24927817
    [TBL] [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; 22(9):1798-812. PubMed ID: 22955990
    [TBL] [Abstract][Full Text] [Related]  

  • 4. ChIPulate: A comprehensive ChIP-seq simulation pipeline.
    Datta V; Hannenhalli S; Siddharthan R
    PLoS Comput Biol; 2019 Mar; 15(3):e1006921. PubMed ID: 30897079
    [TBL] [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(17):. PubMed ID: 32825662
    [TBL] [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; 24(1):597. PubMed ID: 37805453
    [TBL] [Abstract][Full Text] [Related]  

  • 7. MEME-ChIP: motif analysis of large DNA datasets.
    Machanick P; Bailey TL
    Bioinformatics; 2011 Jun; 27(12):1696-7. PubMed ID: 21486936
    [TBL] [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; 47(4):e21. PubMed ID: 30517703
    [TBL] [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; 6(9):. PubMed ID: 20838582
    [TBL] [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; 14 Suppl 5(Suppl 5):S2. PubMed ID: 24564528
    [TBL] [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; 13():372. PubMed ID: 22863112
    [TBL] [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; 20(1):777. PubMed ID: 31653198
    [TBL] [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; 15(1):752. PubMed ID: 25179504
    [TBL] [Abstract][Full Text] [Related]  

  • 14. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.
    Ozaki H; Iwasaki W
    Comput Biol Chem; 2016 Aug; 63():62-72. PubMed ID: 26971251
    [TBL] [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; 4(12):e8155. PubMed ID: 19956545
    [TBL] [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; 26(3):231-242. PubMed ID: 30957858
    [TBL] [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; 41(Web Server issue):W535-43. PubMed ID: 23748563
    [TBL] [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; 15 Suppl 1(Suppl 1):S1. PubMed ID: 24564277
    [TBL] [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; 17(1):637. PubMed ID: 27526722
    [TBL] [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; 39(15):e98. PubMed ID: 21602262
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 20.