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Items: 1 to 20 of 371

1.

Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data.

Xing H, Mo Y, Liao W, Zhang MQ.

PLoS Comput Biol. 2012;8(7):e1002613. doi: 10.1371/journal.pcbi.1002613. Epub 2012 Jul 26.

2.

A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types.

Xing H, Liao W, Mo Y, Zhang MQ.

J Vis Exp. 2012 Dec 10;(70):e4273. doi: 10.3791/4273.

3.

Integrative analyses for omics data: a Bayesian mixture model to assess the concordance of ChIP-chip and ChIP-seq measurements.

Schäfer M, Lkhagvasuren O, Klein HU, Elling C, Wüstefeld T, Müller-Tidow C, Zender L, Koschmieder S, Dugas M, Ickstadt K.

J Toxicol Environ Health A. 2012;75(8-10):461-70. doi: 10.1080/15287394.2012.674914.

PMID:
22686305
4.

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
5.

A fully Bayesian hidden Ising model for ChIP-seq data analysis.

Mo Q.

Biostatistics. 2012 Jan;13(1):113-28. doi: 10.1093/biostatistics/kxr029. Epub 2011 Sep 13.

PMID:
21914728
6.

WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.

Mitra A, Song J.

PLoS One. 2012;7(9):e45486. doi: 10.1371/journal.pone.0045486. Epub 2012 Sep 28.

7.

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
8.

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

Ashoor H, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V.

Bioinformatics. 2013 Dec 1;29(23):2979-86. doi: 10.1093/bioinformatics/btt524. Epub 2013 Sep 9.

9.

ChIPseqR: analysis of ChIP-seq experiments.

Humburg P, Helliwell CA, Bulger D, Stone G.

BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

10.

Evaluation of algorithm performance in ChIP-seq peak detection.

Wilbanks EG, Facciotti MT.

PLoS One. 2010 Jul 8;5(7):e11471. doi: 10.1371/journal.pone.0011471.

11.

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.

Xu H, Wei CL, Lin F, Sung WK.

Bioinformatics. 2008 Oct 15;24(20):2344-9. doi: 10.1093/bioinformatics/btn402. Epub 2008 Jul 29.

PMID:
18667444
12.

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.

13.

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments.

Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL.

BMC Genomics. 2009 Dec 18;10:618. doi: 10.1186/1471-2164-10-618.

14.

Studying the epigenome using next generation sequencing.

Ku CS, Naidoo N, Wu M, Soong R.

J Med Genet. 2011 Nov;48(11):721-30. doi: 10.1136/jmedgenet-2011-100242. Epub 2011 Aug 8. Review.

PMID:
21825079
15.

Identifying differential histone modification sites from ChIP-seq data.

Xu H, Sung WK.

Methods Mol Biol. 2012;802:293-303. doi: 10.1007/978-1-61779-400-1_19.

PMID:
22130888
16.

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.

17.
18.

BayesPeak: Bayesian analysis of ChIP-seq data.

Spyrou C, Stark R, Lynch AG, Tavaré S.

BMC Bioinformatics. 2009 Sep 21;10:299. doi: 10.1186/1471-2105-10-299.

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. doi: 10.4161/15384101.2014.949201. Review.

20.

The analysis of ChIP-Seq data.

Ma W, Wong WH.

Methods Enzymol. 2011;497:51-73. doi: 10.1016/B978-0-12-385075-1.00003-2.

PMID:
21601082

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