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    Results: 1 to 20 of 126

    1.

    ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

    Buck MJ, Nobel AB, Lieb JD.

    Genome Biol. 2005;6(11):R97. Epub 2005 Oct 19.

    PMID:
    16277752
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.

    Scacheri PC, Crawford GE, Davis S.

    Methods Enzymol. 2006;411:270-82. Review.

    PMID:
    16939795
    [PubMed - indexed for MEDLINE]
    3.

    An integrated software system for analyzing ChIP-chip and ChIP-seq data.

    Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

    Nat Biotechnol. 2008 Nov;26(11):1293-300. Epub 2008 Nov 2.

    PMID:
    18978777
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    ChIP-chip: data, model, and analysis.

    Zheng M, Barrera LO, Ren B, Wu YN.

    Biometrics. 2007 Sep;63(3):787-96.

    PMID:
    17825010
    [PubMed - indexed for MEDLINE]
    5.

    Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

    Kuznetsov VA, Orlov YL, Wei CL, Ruan Y.

    Genome Inform. 2007;19:83-94.

    PMID:
    18546507
    [PubMed - indexed for MEDLINE]
    6.

    Use of SNP-arrays for ChIP assays: computational aspects.

    Muro EM, McCann JA, Rudnicki MA, Andrade-Navarro MA.

    Methods Mol Biol. 2009;567:145-54. Review.

    PMID:
    19588091
    [PubMed - indexed for MEDLINE]
    7.

    GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.

    Danford T, Rolfe A, Gifford D.

    Pac Symp Biocomput. 2008:539-50.

    PMID:
    18229714
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure.

    Kuan PF, Chun H, Keleş S.

    Pac Symp Biocomput. 2008:515-26.

    PMID:
    18229712
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Analyzing ChIP-chip data using bioconductor.

    Toedling J, Huber W.

    PLoS Comput Biol. 2008 Nov;4(11):e1000227. Epub 2008 Nov 28. No abstract available.

    PMID:
    19043553
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.

    Ghosh S, Hirsch HA, Sekinger E, Struhl K, Gingeras TR.

    BMC Bioinformatics. 2006 Oct 5;7:434.

    PMID:
    17022824
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Modeling and analysis of ChIP-chip experiments.

    Gottardo R.

    Methods Mol Biol. 2009;567:133-43. Review.

    PMID:
    19588090
    [PubMed - indexed for MEDLINE]
    12.

    BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments.

    Wang LY, Snyder M, Gerstein M.

    Genome Biol. 2006;7(11):R102.

    PMID:
    17078876
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    CAPweb: a bioinformatics CGH array Analysis Platform.

    Liva S, Hupé P, Neuvial P, Brito I, Viara E, La Rosa P, Barillot E.

    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W477-81.

    PMID:
    16845053
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    WebArray: an online platform for microarray data analysis.

    Xia X, McClelland M, Wang Y.

    BMC Bioinformatics. 2005 Dec 21;6:306.

    PMID:
    16371165
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    Modeling ChIP sequencing in silico with applications.

    Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

    PLoS Comput Biol. 2008 Aug 22;4(8):e1000158.

    PMID:
    18725927
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data.

    Watson M, Dukes J, Abu-Median AB, King DP, Britton P.

    Genome Biol. 2007;8(9):R190.

    PMID:
    17868443
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.

    Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W.

    BMC Bioinformatics. 2007 Jun 26;8:221. Erratum in: BMC Bioinformatics. 2007;8:443. Sklyar, Oleg [corrected to Skylar, Oleg]; Krueger, Tammo [added]; Fischer, JJ [added]; Sperling, Silke [added].

    PMID:
    17594472
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    A physical model for tiling array analysis.

    Chung HR, Kostka D, Vingron M.

    Bioinformatics. 2007 Jul 1;23(13):i80-6.

    PMID:
    17646349
    [PubMed - indexed for MEDLINE]
    Free Article
    20.

    W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.

    Jin VX, Apostolos J, Nagisetty NS, Farnham PJ.

    Bioinformatics. 2009 Dec 1;25(23):3191-3. Epub 2009 Oct 1.

    PMID:
    19797408
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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