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Items: 1 to 20 of 392

1.

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. doi: 10.1186/1471-2105-9-523.

2.

Using combined evidence from replicates to evaluate ChIP-seq peaks.

Jalili V, Matteucci M, Masseroli M, Morelli MJ.

Bioinformatics. 2015 Sep 1;31(17):2761-9. doi: 10.1093/bioinformatics/btv293. Epub 2015 May 7.

PMID:
25957351
3.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

4.

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. doi: 10.4161/15384101.2014.949201. Review.

5.

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. doi: 10.1186/1471-2164-12-134.

6.

Identifying ChIP-seq enrichment using MACS.

Feng J, Liu T, Qin B, Zhang Y, Liu XS.

Nat Protoc. 2012 Sep;7(9):1728-40. doi: 10.1038/nprot.2012.101. Epub 2012 Aug 30.

7.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

8.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

9.

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. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

10.

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.

Taslim C, Huang K, Huang T, Lin S.

Methods Mol Biol. 2012;802:275-91. doi: 10.1007/978-1-61779-400-1_18.

PMID:
22130887
11.

A signal-noise model for significance analysis of ChIP-seq with negative control.

Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.

Bioinformatics. 2010 May 1;26(9):1199-204. doi: 10.1093/bioinformatics/btq128. Epub 2010 Apr 5.

PMID:
20371496
12.

Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments.

Jain D, Baldi S, Zabel A, Straub T, Becker PB.

Nucleic Acids Res. 2015 Aug 18;43(14):6959-68. doi: 10.1093/nar/gkv637. Epub 2015 Jun 27.

13.

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data.

Wu S, Wang J, Zhao W, Pounds S, Cheng C.

Theor Biol Med Model. 2010 Jun 3;7:18. doi: 10.1186/1742-4682-7-18.

14.

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

Wang J, Lunyak VV, Jordan IK.

Bioinformatics. 2013 Feb 15;29(4):492-3. doi: 10.1093/bioinformatics/bts722. Epub 2013 Jan 7.

PMID:
23300134
15.

Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

Angelini C, Heller R, Volkinshtein R, Yekutieli D.

BMC Bioinformatics. 2015 May 9;16:150. doi: 10.1186/s12859-015-0579-z.

16.

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

Chen L, Wang C, Qin ZS, Wu H.

Bioinformatics. 2015 Jun 15;31(12):1889-96. doi: 10.1093/bioinformatics/btv094. Epub 2015 Feb 13.

17.

Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-Seq.

Hitchler MJ, Rice JC.

Methods Mol Biol. 2011;767:253-67. doi: 10.1007/978-1-61779-201-4_19.

PMID:
21822881
18.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

19.

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. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.

PMID:
20208068
20.

Epigenetic analysis: ChIP-chip and ChIP-seq.

Pellegrini M, Ferrari R.

Methods Mol Biol. 2012;802:377-87. doi: 10.1007/978-1-61779-400-1_25.

PMID:
22130894

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