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Results: 1 to 20 of 144

1.

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
[PubMed - indexed for MEDLINE]
Free Article
2.

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.

PMID:
22936215
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19061503
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23029045
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23762400
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

An integrated ChIP-seq analysis platform with customizable workflows.

Giannopoulou EG, Elemento O.

BMC Bioinformatics. 2011 Jul 7;12:277. doi: 10.1186/1471-2105-12-277.

PMID:
21736739
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.

Kornacker K, Rye MB, Håndstad T, Drabløs F.

BMC Bioinformatics. 2012 Jul 24;13:176. doi: 10.1186/1471-2105-13-176.

PMID:
22827163
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22844240
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21325299
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
19505939
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

PeakRanger: a cloud-enabled peak caller for ChIP-seq data.

Feng X, Grossman R, Stein L.

BMC Bioinformatics. 2011 May 9;12:139. doi: 10.1186/1471-2105-12-139.

PMID:
21554709
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Inferring nucleosome positions with their histone mark annotation from ChIP data.

Mammana A, Vingron M, Chung HR.

Bioinformatics. 2013 Oct 15;29(20):2547-54. doi: 10.1093/bioinformatics/btt449. Epub 2013 Aug 26.

PMID:
23981350
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Characterising ChIP-seq binding patterns by model-based peak shape deconvolution.

Mendoza-Parra MA, Nowicka M, Van Gool W, Gronemeyer H.

BMC Genomics. 2013 Nov 26;14:834. doi: 10.1186/1471-2164-14-834.

PMID:
24279297
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21356108
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.

Kim NK, Jayatillake RV, Spouge JL.

BMC Genomics. 2013 May 25;14:349. doi: 10.1186/1471-2164-14-349.

PMID:
23706083
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Integrative analysis of ChIP-chip and ChIP-seq dataset.

Zhu LJ.

Methods Mol Biol. 2013;1067:105-24. doi: 10.1007/978-1-62703-607-8_8.

PMID:
23975789
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
22863112
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions.

Bolouri H, Ruzzo WL.

J Comput Biol. 2012 Sep;19(9):989-97. doi: 10.1089/cmb.2012.0100. Epub 2012 Aug 16.

PMID:
22897152
[PubMed - indexed for MEDLINE]
19.

Picking ChIP-seq peak detectors for analyzing chromatin modification experiments.

Micsinai M, Parisi F, Strino F, Asp P, Dynlacht BD, Kluger Y.

Nucleic Acids Res. 2012 May;40(9):e70. doi: 10.1093/nar/gks048. Epub 2012 Feb 3.

PMID:
22307239
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

seqMINER: an integrated ChIP-seq data interpretation platform.

Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L.

Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.

PMID:
21177645
[PubMed - indexed for MEDLINE]
Free PMC Article

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