BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

775 related articles for article (PubMed ID: 18684996)

  • 1. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.
    Jothi R; Cuddapah S; Barski A; Cui K; Zhao K
    Nucleic Acids Res; 2008 Sep; 36(16):5221-31. PubMed ID: 18684996
    [TBL] [Abstract][Full Text] [Related]  

  • 2. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.
    Boeva V; Surdez D; Guillon N; Tirode F; Fejes AP; Delattre O; Barillot E
    Nucleic Acids Res; 2010 Jun; 38(11):e126. PubMed ID: 20375099
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.
    Chung D; Kuan PF; Li B; Sanalkumar R; Liang K; Bresnick EH; Dewey C; Keleş S
    PLoS Comput Biol; 2011 Jul; 7(7):e1002111. PubMed ID: 21779159
    [TBL] [Abstract][Full Text] [Related]  

  • 4. An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
    Mercier E; Droit A; Li L; Robertson G; Zhang X; Gottardo R
    PLoS One; 2011 Feb; 6(2):e16432. PubMed ID: 21358819
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.
    Robertson G; Hirst M; Bainbridge M; Bilenky M; Zhao Y; Zeng T; Euskirchen G; Bernier B; Varhol R; Delaney A; Thiessen N; Griffith OL; He A; Marra M; Snyder M; Jones S
    Nat Methods; 2007 Aug; 4(8):651-7. PubMed ID: 17558387
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.
    Valouev A; Johnson DS; Sundquist A; Medina C; Anton E; Batzoglou S; Myers RM; Sidow A
    Nat Methods; 2008 Sep; 5(9):829-34. PubMed ID: 19160518
    [TBL] [Abstract][Full Text] [Related]  

  • 7. T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets.
    Li Y; Umbach DM; Li L
    BMC Genomics; 2014 Jan; 15():27. PubMed ID: 24428924
    [TBL] [Abstract][Full Text] [Related]  

  • 8. ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.
    Narlikar L; Jothi R
    Methods Mol Biol; 2012; 802():305-22. PubMed ID: 22130889
    [TBL] [Abstract][Full Text] [Related]  

  • 9. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data.
    Qin ZS; Yu J; Shen J; Maher CA; Hu M; Kalyana-Sundaram S; Yu J; Chinnaiyan AM
    BMC Bioinformatics; 2010 Jul; 11():369. PubMed ID: 20598134
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.
    Wang X; Zhang X
    BMC Syst Biol; 2011; 5 Suppl 2(Suppl 2):S3. PubMed ID: 22784574
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. An effective approach for identification of in vivo protein-DNA binding sites from paired-end ChIP-Seq data.
    Wang C; Xu J; Zhang D; Wilson ZA; Zhang D
    BMC Bioinformatics; 2010 Feb; 11():81. PubMed ID: 20144209
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Evolutionary Conserved Motif Finder (ECMFinder) for genome-wide identification of clustered YY1- and CTCF-binding sites.
    Kang K; Chung JH; Kim J
    Nucleic Acids Res; 2009 Apr; 37(6):2003-13. PubMed ID: 19208640
    [TBL] [Abstract][Full Text] [Related]  

  • 14. MER41 repeat sequences contain inducible STAT1 binding sites.
    Schmid CD; Bucher P
    PLoS One; 2010 Jul; 5(7):e11425. PubMed ID: 20625510
    [TBL] [Abstract][Full Text] [Related]  

  • 15. MACE: model based analysis of ChIP-exo.
    Wang L; Chen J; Wang C; Uusküla-Reimand L; Chen K; Medina-Rivera A; Young EJ; Zimmermann MT; Yan H; Sun Z; Zhang Y; Wu ST; Huang H; Wilson MD; Kocher JP; Li W
    Nucleic Acids Res; 2014 Nov; 42(20):e156. PubMed ID: 25249628
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
    Mortazavi A; Leeper Thompson EC; Garcia ST; Myers RM; Wold B
    Genome Res; 2006 Oct; 16(10):1208-21. PubMed ID: 16963704
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Using CisGenome to analyze ChIP-chip and ChIP-seq data.
    Ji H; Jiang H; Ma W; Wong WH
    Curr Protoc Bioinformatics; 2011 Mar; Chapter 2():Unit2.13. PubMed ID: 21400695
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells.
    Liu T
    Methods Mol Biol; 2014; 1150():81-95. PubMed ID: 24743991
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.
    Mundade R; Ozer HG; Wei H; Prabhu L; Lu T
    Cell Cycle; 2014; 13(18):2847-52. PubMed ID: 25486472
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.
    Lefrançois P; Gallagher JE; Snyder M
    Methods Mol Biol; 2014; 1205():231-55. PubMed ID: 25213249
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 39.