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    Results: 1 to 20 of 103

    1.

    Model-based analysis of ChIP-Seq (MACS).

    Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS.

    Genome Biol. 2008;9(9):R137. Epub 2008 Sep 17.

    PMID:
    18798982
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    PICS: probabilistic inference for ChIP-seq.

    Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R.

    Biometrics. 2011 Mar;67(1):151-63. doi: 10.1111/j.1541-0420.2010.01441.x.

    PMID:
    20528864
    [PubMed - indexed for MEDLINE]
    3.

    Using MACS to identify peaks from ChIP-Seq data.

    Feng J, Liu T, Zhang Y.

    Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:Unit 2.14.

    PMID:
    21633945
    [PubMed - indexed for MEDLINE]
    4.

    ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

    Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

    BMC Bioinformatics. 2010 May 11;11:237.

    PMID:
    20459804
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    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]
    6.

    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.

    PMID:
    21400695
    [PubMed - indexed for MEDLINE]
    7.

    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 9;11:81.

    PMID:
    20144209
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    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 16;6(2):e16432.

    PMID:
    21358819
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    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 2;11:369.

    PMID:
    20598134
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

    Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ.

    BMC Genomics. 2011 Feb 28;12:134.

    PMID:
    21356108
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.

    Nix DA, Courdy SJ, Boucher KM.

    BMC Bioinformatics. 2008 Dec 5;9:523.

    PMID:
    19061503
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Extracting transcription factor targets from ChIP-Seq data.

    Tuteja G, White P, Schug J, Kaestner KH.

    Nucleic Acids Res. 2009 Sep;37(17):e113. Epub 2009 Jun 24.

    PMID:
    19553195
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    High-resolution computational models of genome binding events.

    Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

    Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

    PMID:
    16900145
    [PubMed - indexed for MEDLINE]
    14.

    Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

    Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

    BMC Genomics. 2009 Jan 21;10:37.

    PMID:
    19159457
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

    Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

    Bioinformatics. 2010 Apr 15;26(8):1000-6. Epub 2010 Mar 5.

    PMID:
    20208068
    [PubMed - indexed for MEDLINE]
    Free Article
    16.

    Modeling and analysis of ChIP-chip experiments.

    Gottardo R.

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

    PMID:
    19588090
    [PubMed - indexed for MEDLINE]
    17.

    Model-based deconvolution of genome-wide DNA binding.

    Reiss DJ, Facciotti MT, Baliga NS.

    Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.

    PMID:
    18056063
    [PubMed - indexed for MEDLINE]
    Free Article
    18.

    Evaluation of algorithm performance in ChIP-seq peak detection.

    Wilbanks EG, Facciotti MT.

    PLoS One. 2010 Jul 8;5(7):e11471.

    PMID:
    20628599
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    CoCAS: a ChIP-on-chip analysis suite.

    Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P.

    Bioinformatics. 2009 Apr 1;25(7):954-5. Epub 2009 Feb 4.

    PMID:
    19193731
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    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

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