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Results: 1 to 20 of 149

1.

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
2.

CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures.

Hentrich T, Schulze JM, Emberly E, Kobor MS.

Bioinformatics. 2012 Mar 1;28(5):717-8. doi: 10.1093/bioinformatics/bts007. Epub 2012 Jan 11.

PMID:
22238257
[PubMed - indexed for MEDLINE]
Free Article
3.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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]
5.

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
6.

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]
7.

Using CisGenome to analyze ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Wong WH.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13. doi: 10.1002/0471250953.bi0213s33.

PMID:
21400695
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keleş S.

PLoS Comput Biol. 2011 Jul;7(7):e1002111. doi: 10.1371/journal.pcbi.1002111. Epub 2011 Jul 14.

PMID:
21779159
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

GeneTrack--a genomic data processing and visualization framework.

Albert I, Wachi S, Jiang C, Pugh BF.

Bioinformatics. 2008 May 15;24(10):1305-6. doi: 10.1093/bioinformatics/btn119. Epub 2008 Apr 3.

PMID:
18388141
[PubMed - indexed for MEDLINE]
Free Article
10.

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
11.

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.

Szalkowski AM, Schmid CD.

Brief Bioinform. 2011 Nov;12(6):626-33. doi: 10.1093/bib/bbq068. Epub 2010 Nov 8.

PMID:
21059603
[PubMed - indexed for MEDLINE]
Free Article
12.

Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.

Gupta R, Wikramasinghe P, Bhattacharyya A, Perez FA, Pal S, Davuluri RV.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S65. doi: 10.1186/1471-2105-11-S1-S65.

PMID:
20122241
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M.

PLoS One. 2010 Dec 29;5(12):e15898. doi: 10.1371/journal.pone.0015898.

PMID:
21209968
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
15.

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite.

Wang X, Zhang X.

BMC Syst Biol. 2011 Dec 14;5 Suppl 2:S3. doi: 10.1186/1752-0509-5-S2-S3. Epub 2011 Dec 14.

PMID:
22784574
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.

Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W.

BMC Bioinformatics. 2007 Jun 26;8:221. Erratum in: BMC Bioinformatics. 2007;8:443. Sklyar, Oleg [corrected to Skylar, Oleg]; Krueger, Tammo [added]; Fischer, JJ [added]; Sperling, Silke [added].

PMID:
17594472
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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
18.

An integrated software system for analyzing ChIP-chip and ChIP-seq data.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH.

Nat Biotechnol. 2008 Nov;26(11):1293-300. doi: 10.1038/nbt.1505. Epub 2008 Nov 2.

PMID:
18978777
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237.

PMID:
20459804
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Combining chromatin immunoprecipitation and oligonucleotide tiling arrays (ChIP-Chip) for functional genomic studies.

Eeckhoute J, Lupien M, Brown M.

Methods Mol Biol. 2009;556:155-64. doi: 10.1007/978-1-60327-192-9_11.

PMID:
19488877
[PubMed - indexed for MEDLINE]

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