BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

193 related articles for article (PubMed ID: 22228832)

  • 1. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.
    Ma X; Kulkarni A; Zhang Z; Xuan Z; Serfling R; Zhang MQ
    Nucleic Acids Res; 2012 Apr; 40(7):e50. PubMed ID: 22228832
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Inferring direct DNA binding from ChIP-seq.
    Bailey TL; Machanick P
    Nucleic Acids Res; 2012 Sep; 40(17):e128. PubMed ID: 22610855
    [TBL] [Abstract][Full Text] [Related]  

  • 3. SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
    Ding J; Hu H; Li X
    Nucleic Acids Res; 2014 Mar; 42(5):e35. PubMed ID: 24322294
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
    Kulakovskiy I; Levitsky V; Oshchepkov D; Bryzgalov L; Vorontsov I; Makeev V
    J Bioinform Comput Biol; 2013 Feb; 11(1):1340004. PubMed ID: 23427986
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
    Castro-Mondragon JA; Rioualen C; Contreras-Moreira B; van Helden J
    Methods Mol Biol; 2016; 1482():297-322. PubMed ID: 27557775
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. 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]  

  • 10. A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets.
    Zhang Y; Wang P
    Biomed Res Int; 2015; 2015():218068. PubMed ID: 26236718
    [TBL] [Abstract][Full Text] [Related]  

  • 11. A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
    Jia C; Carson MB; Wang Y; Lin Y; Lu H
    PLoS One; 2014; 9(1):e86044. PubMed ID: 24475069
    [TBL] [Abstract][Full Text] [Related]  

  • 12. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.
    Thomas-Chollier M; Herrmann C; Defrance M; Sand O; Thieffry D; van Helden J
    Nucleic Acids Res; 2012 Feb; 40(4):e31. PubMed ID: 22156162
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space.
    Karnik R; Beer MA
    PLoS One; 2015; 10(10):e0140557. PubMed ID: 26465884
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection.
    Sun H; Guns T; Fierro AC; Thorrez L; Nijssen S; Marchal K
    Nucleic Acids Res; 2012 Jul; 40(12):e90. PubMed ID: 22422841
    [TBL] [Abstract][Full Text] [Related]  

  • 15. De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.
    Niu M; Tabari ES; Su Z
    BMC Genomics; 2014 Dec; 15():1047. PubMed ID: 25442502
    [TBL] [Abstract][Full Text] [Related]  

  • 16. DREME: motif discovery in transcription factor ChIP-seq data.
    Bailey TL
    Bioinformatics; 2011 Jun; 27(12):1653-9. PubMed ID: 21543442
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Integrative analysis of ChIP-chip and ChIP-seq dataset.
    Zhu LJ
    Methods Mol Biol; 2013; 1067():105-24. PubMed ID: 23975789
    [TBL] [Abstract][Full Text] [Related]  

  • 18. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.
    Thomas-Chollier M; Darbo E; Herrmann C; Defrance M; Thieffry D; van Helden J
    Nat Protoc; 2012 Jul; 7(8):1551-68. PubMed ID: 22836136
    [TBL] [Abstract][Full Text] [Related]  

  • 19. EXTREME: an online EM algorithm for motif discovery.
    Quang D; Xie X
    Bioinformatics; 2014 Jun; 30(12):1667-73. PubMed ID: 24532725
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Motif-based analysis of large nucleotide data sets using MEME-ChIP.
    Ma W; Noble WS; Bailey TL
    Nat Protoc; 2014; 9(6):1428-50. PubMed ID: 24853928
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.