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Results: 1 to 20 of 84

1.

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

Buck MJ, Nobel AB, Lieb JD.

Genome Biol. 2005;6(11):R97. Epub 2005 Oct 19.

PMID:
16277752
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.

Scacheri PC, Crawford GE, Davis S.

Methods Enzymol. 2006;411:270-82. Review.

PMID:
16939795
[PubMed - indexed for MEDLINE]
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.

ChIP-chip: data, model, and analysis.

Zheng M, Barrera LO, Ren B, Wu YN.

Biometrics. 2007 Sep;63(3):787-96.

PMID:
17825010
[PubMed - indexed for MEDLINE]
5.

Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

Kuznetsov VA, Orlov YL, Wei CL, Ruan Y.

Genome Inform. 2007;19:83-94.

PMID:
18546507
[PubMed - indexed for MEDLINE]
6.

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
7.

Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part B: ChIP-chip data analysis.

Göbel U, Reimer J, Turck F.

Methods Mol Biol. 2010;631:161-84. doi: 10.1007/978-1-60761-646-7_13.

PMID:
20204875
[PubMed - indexed for MEDLINE]
8.

WebArray: an online platform for microarray data analysis.

Xia X, McClelland M, Wang Y.

BMC Bioinformatics. 2005 Dec 21;6:306.

PMID:
16371165
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

PMID:
18725927
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

Normalization and experimental design for ChIP-chip data.

Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ.

BMC Bioinformatics. 2007 Jun 25;8:219.

PMID:
17592629
[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.

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Narlikar L, Jothi R.

Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.

PMID:
22130889
[PubMed - indexed for MEDLINE]
14.

PATIKAmad: putting microarray data into pathway context.

Babur O, Colak R, Demir E, Dogrusoz U.

Proteomics. 2008 Jun;8(11):2196-8. doi: 10.1002/pmic.200700769.

PMID:
18452226
[PubMed - indexed for MEDLINE]
15.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

PMID:
19036135
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Parameter estimation for robust HMM analysis of ChIP-chip data.

Humburg P, Bulger D, Stone G.

BMC Bioinformatics. 2008 Aug 18;9:343. doi: 10.1186/1471-2105-9-343.

PMID:
18706106
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Nancarrow DJ, Handoko HY, Stark MS, Whiteman DC, Hayward NK.

PLoS One. 2007 Oct 31;2(10):e1093.

PMID:
17971856
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

Sun H, Palaniswamy SK, Pohar TT, Jin VX, Huang TH, Davuluri RV.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D98-103.

PMID:
16381984
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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]
20.

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.

Tsai HK, Chou MY, Shih CH, Huang GT, Chang TH, Li WH.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W221-6. Epub 2007 May 30.

PMID:
17537814
[PubMed - indexed for MEDLINE]
Free PMC Article

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