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Results: 1 to 20 of 120

1.

Cistrome: an integrative platform for transcriptional regulation studies.

Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS.

Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

PMID:
21859476
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data.

Barozzi I, Termanini A, Minucci S, Natoli G.

Biol Direct. 2011 Oct 6;6:51. doi: 10.1186/1745-6150-6-51.

PMID:
21978789
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

Nebula--a web-server for advanced ChIP-seq data analysis.

Boeva V, Lermine A, Barette C, Guillouf C, Barillot E.

Bioinformatics. 2012 Oct 1;28(19):2517-9. Epub 2012 Jul 24.

PMID:
22829625
[PubMed - indexed for MEDLINE]
Free Article
5.

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.

Cesaroni M, Cittaro D, Brozzi A, Pelicci PG, Luzi L.

Bioinformatics. 2008 Dec 15;24(24):2918-20. doi: 10.1093/bioinformatics/btn542. Epub 2008 Oct 21.

PMID:
18945685
[PubMed - indexed for MEDLINE]
Free Article
6.

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse.

Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS, Zhang Y.

Nucleic Acids Res. 2014 Jan;42(Database issue):D450-8. doi: 10.1093/nar/gkt1151. Epub 2013 Nov 18.

PMID:
24253304
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

NTAP: for NimbleGen tiling array ChIP-chip data analysis.

He K, Li X, Zhou J, Deng XW, Zhao H, Luo J.

Bioinformatics. 2009 Jul 15;25(14):1838-40. doi: 10.1093/bioinformatics/btp320. Epub 2009 May 25.

PMID:
19468055
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.

PMID:
17683565
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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]
10.

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.

MuiƱo JM, Hoogstraat M, van Ham RC, van Dijk AD.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W524-7. doi: 10.1093/nar/gkr373. Epub 2011 May 24.

PMID:
21609962
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Analyzing ChIP-chip data using bioconductor.

Toedling J, Huber W.

PLoS Comput Biol. 2008 Nov;4(11):e1000227. doi: 10.1371/journal.pcbi.1000227. Epub 2008 Nov 28. No abstract available.

PMID:
19043553
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

CoCAS: a ChIP-on-chip analysis suite.

Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC, Spicuglia S, Ferrier P.

Bioinformatics. 2009 Apr 1;25(7):954-5. doi: 10.1093/bioinformatics/btp075. Epub 2009 Feb 4.

PMID:
19193731
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.

Droit A, Cheung C, Gottardo R.

Bioinformatics. 2010 Mar 1;26(5):678-9. doi: 10.1093/bioinformatics/btq023. Epub 2010 Jan 19.

PMID:
20089513
[PubMed - indexed for MEDLINE]
Free Article
14.

Epigenetic analysis: ChIP-chip and ChIP-seq.

Pellegrini M, Ferrari R.

Methods Mol Biol. 2012;802:377-87. doi: 10.1007/978-1-61779-400-1_25.

PMID:
22130894
[PubMed - indexed for MEDLINE]
15.

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Kawaji H, Severin J, Lizio M, Waterhouse A, Katayama S, Irvine KM, Hume DA, Forrest AR, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.

Genome Biol. 2009;10(4):R40. doi: 10.1186/gb-2009-10-4-r40. Epub 2009 Apr 19.

PMID:
19374775
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Use of SNP-arrays for ChIP assays: computational aspects.

Muro EM, McCann JA, Rudnicki MA, Andrade-Navarro MA.

Methods Mol Biol. 2009;567:145-54. doi: 10.1007/978-1-60327-414-2_10. Review.

PMID:
19588091
[PubMed - indexed for MEDLINE]
17.

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]
18.

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.

Wu G, Ji H.

BMC Bioinformatics. 2013 Jun 10;14:188. doi: 10.1186/1471-2105-14-188.

PMID:
23758851
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.

Girardot C, Sklyar O, Grosz S, Huber W, Furlong EE.

Bioinformatics. 2007 Mar 15;23(6):771-3. Epub 2007 Jan 17.

PMID:
17234641
[PubMed - indexed for MEDLINE]
Free Article
20.

Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-seq).

Zhu JY, Sun Y, Wang ZY.

Methods Mol Biol. 2012;876:173-88. doi: 10.1007/978-1-61779-809-2_14.

PMID:
22576095
[PubMed - indexed for MEDLINE]

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