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Items: 1 to 20 of 530

1.

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP.

BMC Bioinformatics. 2014 Aug 15;15:280. doi: 10.1186/1471-2105-15-280.

2.

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.

3.

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
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.

5.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

Giurato G, De Filippo MR, Rinaldi A, Hashim A, Nassa G, Ravo M, Rizzo F, Tarallo R, Weisz A.

BMC Bioinformatics. 2013 Dec 13;14:362. doi: 10.1186/1471-2105-14-362.

6.

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.

Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.

Bioinformatics. 2014 Sep 15;30(18):2568-75. doi: 10.1093/bioinformatics/btu372.

7.

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
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.

9.

Cell-type specificity of ChIP-predicted transcription factor binding sites.

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P.

BMC Genomics. 2012 Aug 3;13:372. doi: 10.1186/1471-2164-13-372.

10.

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.

Nakato R, Itoh T, Shirahige K.

Genes Cells. 2013 Jul;18(7):589-601. doi: 10.1111/gtc.12058.

11.

Optimizing detection of transcription factor-binding sites in ChIP-seq experiments.

Kallio A, Elo LL.

Methods Mol Biol. 2013;1038:181-91. doi: 10.1007/978-1-62703-514-9_11.

PMID:
23872976
12.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

13.

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond.

Mundade R, Ozer HG, Wei H, Prabhu L, Lu T.

Cell Cycle. 2014;13(18):2847-52. doi: 10.4161/15384101.2014.949201. Review.

14.

Statistical analysis of ChIP-seq data with MOSAiCS.

Sun G, Chung D, Liang K, Keleş S.

Methods Mol Biol. 2013;1038:193-212. doi: 10.1007/978-1-62703-514-9_12.

PMID:
23872977
15.

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J.

Nat Protoc. 2012 Jul 26;7(8):1551-68. doi: 10.1038/nprot.2012.088.

PMID:
22836136
16.

ChIP-Seq using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites.

Lefrançois P, Zheng W, Snyder M.

Methods Enzymol. 2010;470:77-104. doi: 10.1016/S0076-6879(10)70004-5.

PMID:
20946807
17.

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.

18.

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.

19.
20.

Optimized detection of transcription factor-binding sites in ChIP-seq experiments.

Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T.

Nucleic Acids Res. 2012 Jan;40(1):e1. doi: 10.1093/nar/gkr839.

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