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Results: 1 to 20 of 84

1.

jMOSAiCS: joint analysis of multiple ChIP-seq datasets.

Zeng X, Sanalkumar R, Bresnick EH, Li H, Chang Q, Keleş S.

Genome Biol. 2013 Apr 29;14(4):R38. doi: 10.1186/gb-2013-14-4-r38.

PMID:
23844871
[PubMed - in process]
Free PMC Article
2.

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
[PubMed - indexed for MEDLINE]
Free Article
3.

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data.

Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS.

Genome Biol. 2011;12(2):R11. doi: 10.1186/gb-2011-12-2-r11. Epub 2011 Feb 1.

PMID:
21284836
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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
[PubMed - indexed for MEDLINE]
5.

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
6.

SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles.

Wong KC, Li Y, Peng C, Zhang Z.

Bioinformatics. 2014 Sep 5. pii: btu604. [Epub ahead of print]

PMID:
25192742
[PubMed - as supplied by publisher]
7.

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
8.

A statistical framework for power calculations in ChIP-seq experiments.

Zuo C, Keleş S.

Bioinformatics. 2014 Mar 15;30(6):753-60. doi: 10.1093/bioinformatics/btt200. Epub 2013 May 10.

PMID:
23665773
[PubMed - indexed for MEDLINE]
9.

dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.

Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S.

PLoS Comput Biol. 2013;9(10):e1003246. doi: 10.1371/journal.pcbi.1003246. Epub 2013 Oct 17.

PMID:
24146601
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets.

Wei Y, Li X, Wang QF, Ji H.

BMC Genomics. 2012 Nov 29;13:681. doi: 10.1186/1471-2164-13-681.

PMID:
23194258
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets.

Schweikert G, Cseke B, Clouaire T, Bird A, Sanguinetti G.

BMC Genomics. 2013 Nov 24;14:826. doi: 10.1186/1471-2164-14-826.

PMID:
24267901
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
[PubMed - indexed for MEDLINE]
13.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

PMID:
20158869
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Normalization of ChIP-seq data with control.

Liang K, Keleş S.

BMC Bioinformatics. 2012 Aug 10;13:199. doi: 10.1186/1471-2105-13-199.

PMID:
22883957
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20628599
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Use model-based Analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells.

Liu T.

Methods Mol Biol. 2014;1150:81-95. doi: 10.1007/978-1-4939-0512-6_4.

PMID:
24743991
[PubMed - in process]
17.

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
18.

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
19.

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

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