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Results: 1 to 20 of 124

1.

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J.

Nucleic Acids Res. 2012 Feb;40(4):e31. doi: 10.1093/nar/gkr1104. Epub 2011 Dec 8.

PMID:
22156162
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J.

Nat Protoc. 2012 Jul 26;7(8):1551-68. doi: 10.1038/nprot.2012.088.

PMID:
22836136
[PubMed - indexed for MEDLINE]
3.

MEME-ChIP: motif analysis of large DNA datasets.

Machanick P, Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1696-7. doi: 10.1093/bioinformatics/btr189. Epub 2011 Apr 12.

PMID:
21486936
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Inferring direct DNA binding from ChIP-seq.

Bailey TL, Machanick P.

Nucleic Acids Res. 2012 Sep 1;40(17):e128. Epub 2012 May 18.

PMID:
22610855
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.

Ha N, Polychronidou M, Lohmann I.

PLoS One. 2012;7(12):e52055. doi: 10.1371/journal.pone.0052055. Epub 2012 Dec 18.

PMID:
23272209
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

DREME: motif discovery in transcription factor ChIP-seq data.

Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1653-9. doi: 10.1093/bioinformatics/btr261. Epub 2011 May 4.

PMID:
21543442
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

RSAT 2011: regulatory sequence analysis tools.

Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. doi: 10.1093/nar/gkr377.

PMID:
21715389
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.

Ding J, Hu H, Li X.

Nucleic Acids Res. 2014 Mar;42(5):e35. doi: 10.1093/nar/gkt1288. Epub 2013 Dec 9.

PMID:
24322294
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ.

Nucleic Acids Res. 2012 Apr;40(7):e50. doi: 10.1093/nar/gkr1135. Epub 2012 Jan 6.

PMID:
22228832
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

PMID:
23748563
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

PMID:
18950538
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ.

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.

PMID:
19906703
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis.

Klepper K, Drabløs F.

BMC Bioinformatics. 2013 Jan 16;14:9. doi: 10.1186/1471-2105-14-9.

PMID:
23323883
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

PMID:
21690655
[PubMed - indexed for MEDLINE]
15.

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

Sand O, Thomas-Chollier M, Vervisch E, van Helden J.

Nat Protoc. 2008;3(10):1604-15. doi: 10.1038/nprot.2008.99.

PMID:
18802441
[PubMed - indexed for MEDLINE]
16.

Identification of context-dependent motifs by contrasting ChIP binding data.

Mason MJ, Plath K, Zhou Q.

Bioinformatics. 2010 Nov 15;26(22):2826-32. doi: 10.1093/bioinformatics/btq546. Epub 2010 Sep 23.

PMID:
20870645
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.

Kheradpour P, Kellis M.

Nucleic Acids Res. 2014 Mar;42(5):2976-87. doi: 10.1093/nar/gkt1249. Epub 2013 Dec 13.

PMID:
24335146
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.

van Heeringen SJ, Veenstra GJ.

Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636. Epub 2010 Nov 15.

PMID:
21081511
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.

Mercier E, Droit A, Li L, Robertson G, Zhang X, Gottardo R.

PLoS One. 2011 Feb 16;6(2):e16432. doi: 10.1371/journal.pone.0016432.

PMID:
21358819
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

D-peaks: a visual tool to display ChIP-seq peaks along the genome.

Brohée S, Bontempi G.

Transcription. 2012 Sep-Oct;3(5):255-9. doi: 10.4161/trns.22457. Epub 2012 Sep 1.

PMID:
23132505
[PubMed - indexed for MEDLINE]
Free PMC Article

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