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ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

Nair NU, Sahu AD, Bucher P, Moret BM.

PLoS One. 2012;7(8):e39573. doi: 10.1371/journal.pone.0039573. Epub 2012 Aug 3.


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.


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.


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.


ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity.

Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, Blewitt ME, Oshlack A, Majewski IJ.

Nucleic Acids Res. 2011 Sep 1;39(17):7415-27. doi: 10.1093/nar/gkr416. Epub 2011 Jun 7.


Identifying dispersed epigenomic domains from ChIP-Seq data.

Song Q, Smith AD.

Bioinformatics. 2011 Mar 15;27(6):870-1. doi: 10.1093/bioinformatics/btr030. Epub 2011 Feb 16.


A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.

Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W.

Bioinformatics. 2009 Aug 1;25(15):1952-8. doi: 10.1093/bioinformatics/btp340. Epub 2009 Jun 8.


H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome.

Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP.

Genome Res. 2009 Feb;19(2):221-33. doi: 10.1101/gr.080861.108. Epub 2008 Dec 1.


Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.

Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD.

Mol Cell Proteomics. 2012 May;11(5):128-37. doi: 10.1074/mcp.M111.015941. Epub 2012 Mar 21.


QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions.

Liu B, Yi J, Sv A, Lan X, Ma Y, Huang TH, Leone G, Jin VX.

BMC Genomics. 2013;14 Suppl 8:S3. doi: 10.1186/1471-2164-14-S8-S3. Epub 2013 Dec 9.


Inferring causal relationships among different histone modifications and gene expression.

Yu H, Zhu S, Zhou B, Xue H, Han JD.

Genome Res. 2008 Aug;18(8):1314-24. doi: 10.1101/gr.073080.107. Epub 2008 Jun 18. Erratum in: Genome Res. 2008 Sep;18(9):1544.


Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq.

Beck D, Brandl MB, Boelen L, Unnikrishnan A, Pimanda JE, Wong JW.

Bioinformatics. 2012 Apr 15;28(8):1062-9. doi: 10.1093/bioinformatics/bts085. Epub 2012 Feb 17.


Genome-wide evaluation of histone methylation changes associated with leaf senescence in Arabidopsis.

Brusslan JA, Rus Alvarez-Canterbury AM, Nair NU, Rice JC, Hitchler MJ, Pellegrini M.

PLoS One. 2012;7(3):e33151. doi: 10.1371/journal.pone.0033151. Epub 2012 Mar 12.


Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking.

Lee BM, Mahadevan LC.

J Cell Biochem. 2009 Sep 1;108(1):22-34. doi: 10.1002/jcb.22250.


diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates.

Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ.

PLoS One. 2013 Jun 10;8(6):e65598. doi: 10.1371/journal.pone.0065598. Print 2013.


Bivalent histone modifications in early embryogenesis.

Vastenhouw NL, Schier AF.

Curr Opin Cell Biol. 2012 Jun;24(3):374-86. doi: 10.1016/ Epub 2012 Apr 17. Review.


Genome-wide analysis of histone modifications by ChIP-on-chip.

Huebert DJ, Kamal M, O'Donovan A, Bernstein BE.

Methods. 2006 Dec;40(4):365-9.


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.


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.


Immunostaining of modified histones defines high-level features of the human metaphase epigenome.

Terrenoire E, McRonald F, Halsall JA, Page P, Illingworth RS, Taylor AM, Davison V, O'Neill LP, Turner BM.

Genome Biol. 2010;11(11):R110. doi: 10.1186/gb-2010-11-11-r110. Epub 2010 Nov 15.

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