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Items: 1 to 20 of 155

1.

MochiView: versatile software for genome browsing and DNA motif analysis.

Homann OR, Johnson AD.

BMC Biol. 2010 Apr 21;8:49. doi: 10.1186/1741-7007-8-49.

2.

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.

3.

MPDA: microarray pooled DNA analyzer.

Yang HC, Huang MC, Li LH, Lin CH, Yu AL, Diccianni MB, Wu JY, Chen YT, Fann CS.

BMC Bioinformatics. 2008 Apr 15;9:196. doi: 10.1186/1471-2105-9-196.

4.

TF Target Mapper: a BLAST search tool for the identification of Transcription Factor target genes.

Horsman S, Moorhouse MJ, de Jager VC, van der Spek P, Grosveld F, Strouboulis J, Katsantoni EZ.

BMC Bioinformatics. 2006 Mar 8;7:120.

5.

SNP-PHAGE--High throughput SNP discovery pipeline.

Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP.

BMC Bioinformatics. 2006 Oct 23;7:468.

6.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL.

BMC Genomics. 2006 Dec 27;7:324.

7.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

8.

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
9.

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].

10.

Development of software facilities to characterize regulatory binding motifs and application to streptococcaceae.

Pons N, Batto JM, Ehrlich SD, Renault P.

J Mol Microbiol Biotechnol. 2008;14(1-3):67-73.

PMID:
17957112
11.

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.

BMC Bioinformatics. 2010 Aug 6;11:415. doi: 10.1186/1471-2105-11-415.

12.

VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.

La Rosa P, Viara E, Hupé P, Pierron G, Liva S, Neuvial P, Brito I, Lair S, Servant N, Robine N, Manié E, Brennetot C, Janoueix-Lerosey I, Raynal V, Gruel N, Rouveirol C, Stransky N, Stern MH, Delattre O, Aurias A, Radvanyi F, Barillot E.

Bioinformatics. 2006 Sep 1;22(17):2066-73. Epub 2006 Jul 4.

PMID:
16820431
13.

Quantitative analysis of genome-wide chromatin remodeling.

Baek S, Sung MH, Hager GL.

Methods Mol Biol. 2012;833:433-41. doi: 10.1007/978-1-61779-477-3_26.

PMID:
22183609
14.

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.

Han BW, Wang W, Zamore PD, Weng Z.

Bioinformatics. 2015 Feb 15;31(4):593-5. doi: 10.1093/bioinformatics/btu647. Epub 2014 Oct 17.

15.

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators.

Piechota M, Korostynski M, Ficek J, Tomski A, Przewlocki R.

BMC Bioinformatics. 2016 Feb 12;17:85. doi: 10.1186/s12859-016-0938-4.

16.

High-resolution computational models of genome binding events.

Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

Nat Biotechnol. 2006 Aug;24(8):963-70. Erratum in: Nat Biotechnol. 2006 Oct;24(10):1293.

PMID:
16900145
17.

A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets.

Zuo C, Chen K, Keleş S.

J Comput Biol. 2017 Jun;24(6):472-485. doi: 10.1089/cmb.2016.0138. Epub 2016 Nov 11.

PMID:
27835030
18.

ChIP-chip comes of age for genome-wide functional analysis.

Wu J, Smith LT, Plass C, Huang TH.

Cancer Res. 2006 Jul 15;66(14):6899-902. Review.

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