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Results: 1 to 20 of 100

1.

EpiExplorer: live exploration and global analysis of large epigenomic datasets.

Halachev K, Bast H, Albrecht F, Lengauer T, Bock C.

Genome Biol. 2012 Oct 3;13(10):R96. doi: 10.1186/gb-2012-13-10-r96.

PMID:
23034089
[PubMed - in process]
Free PMC Article
2.

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy.

Bock C, Von Kuster G, Halachev K, Taylor J, Nekrutenko A, Lengauer T.

Methods Mol Biol. 2010;628:275-96. doi: 10.1007/978-1-60327-367-1_15.

PMID:
20238087
[PubMed - indexed for MEDLINE]
3.

Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.

Chen CC, Xiao S, Xie D, Cao X, Song CX, Wang T, He C, Zhong S.

PLoS Comput Biol. 2013;9(12):e1003367. doi: 10.1371/journal.pcbi.1003367. Epub 2013 Dec 5.

PMID:
24339764
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

Bock C, Halachev K, Büch J, Lengauer T.

Genome Biol. 2009 Feb 10;10(2):R14. doi: 10.1186/gb-2009-10-2-r14.

PMID:
19208250
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser.

Zhou X, Li D, Lowdon RF, Costello JF, Wang T.

Bioinformatics. 2014 Aug 1;30(15):2206-7. doi: 10.1093/bioinformatics/btu191. Epub 2014 Apr 10.

PMID:
24728854
[PubMed - in process]
6.

CpG island mapping by epigenome prediction.

Bock C, Walter J, Paulsen M, Lengauer T.

PLoS Comput Biol. 2007 Jun;3(6):e110. Epub 2007 May 2.

PMID:
17559301
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

A method for finding consensus breakpoints in the cancer genome from copy number data.

Toloşi L, Theißen J, Halachev K, Hero B, Berthold F, Lengauer T.

Bioinformatics. 2013 Jul 15;29(14):1793-800. doi: 10.1093/bioinformatics/btt300. Epub 2013 May 28.

PMID:
23716195
[PubMed - indexed for MEDLINE]
Free Article
8.

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database.

Tecle IY, Menda N, Buels RM, van der Knaap E, Mueller LA.

BMC Bioinformatics. 2010 Oct 21;11:525. doi: 10.1186/1471-2105-11-525.

PMID:
20964836
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.

Derrien T, André C, Galibert F, Hitte C.

Bioinformatics. 2007 Feb 15;23(4):498-9. Epub 2006 Dec 4.

PMID:
17145741
[PubMed - indexed for MEDLINE]
Free Article
10.

The USC Epigenome Center.

Laird PW.

Epigenomics. 2009 Oct;1(1):29-31. doi: 10.2217/epi.09.12.

PMID:
22122635
[PubMed - indexed for MEDLINE]
Free Article
11.

Lep-MAP: fast and accurate linkage map construction for large SNP datasets.

Rastas P, Paulin L, Hanski I, Lehtonen R, Auvinen P.

Bioinformatics. 2013 Dec 15;29(24):3128-34. doi: 10.1093/bioinformatics/btt563. Epub 2013 Sep 26.

PMID:
24078685
[PubMed - indexed for MEDLINE]
12.

MIRPIPE: quantification of microRNAs in niche model organisms.

Kuenne C, Preussner J, Herzog M, Braun T, Looso M.

Bioinformatics. 2014 Aug 26. pii: btu573. [Epub ahead of print]

PMID:
25165094
[PubMed - as supplied by publisher]
Free Article
13.

Ontology-driven indexing of public datasets for translational bioinformatics.

Shah NH, Jonquet C, Chiang AP, Butte AJ, Chen R, Musen MA.

BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S1. doi: 10.1186/1471-2105-10-S2-S1.

PMID:
19208184
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

MethylAid: visual and interactive quality control of large Illumina 450k datasets.

van Iterson M, Tobi EW, Slieker RC, den Hollander W, Luijk R, Slagboom PE, Heijmans BT.

Bioinformatics. 2014 Aug 21. pii: btu566. [Epub ahead of print]

PMID:
25147358
[PubMed - as supplied by publisher]
15.

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives.

Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W501-7. doi: 10.1093/nar/gku457. Epub 2014 May 29.

PMID:
24875479
[PubMed - in process]
Free Article
16.

e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences.

Krüger J, Sczyrba A, Kurtz S, Giegerich R.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W301-4.

PMID:
15215398
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Enabling interspecies epigenomic comparison with CEpBrowser.

Cao X, Zhong S.

Bioinformatics. 2013 May 1;29(9):1223-5. doi: 10.1093/bioinformatics/btt114. Epub 2013 Mar 29.

PMID:
23543396
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.

PMID:
19654113
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

ChIPseek, a web-based analysis tool for ChIP data.

Chen TW, Li HP, Lee CC, Gan RC, Huang PJ, Wu TH, Lee CY, Chang YF, Tang P.

BMC Genomics. 2014 Jun 30;15:539. doi: 10.1186/1471-2164-15-539.

PMID:
24974934
[PubMed - in process]
Free PMC Article
20.

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.

Jombart T, Ahmed I.

Bioinformatics. 2011 Nov 1;27(21):3070-1. doi: 10.1093/bioinformatics/btr521. Epub 2011 Sep 16.

PMID:
21926124
[PubMed - indexed for MEDLINE]
Free PMC Article

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