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Results: 1 to 20 of 161

1.

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions.

Leleu M, Lefebvre G, Rougemont J.

Brief Funct Genomics. 2010 Dec;9(5-6):466-76. doi: 10.1093/bfgp/elq022. Epub 2010 Sep 22.

PMID:
20861161
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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. Epub 2010 Mar 1.

PMID:
20946807
[PubMed - indexed for MEDLINE]
3.

Mapping protein-DNA interactions using ChIP-sequencing.

Massie CE, Mills IG.

Methods Mol Biol. 2012;809:157-73. doi: 10.1007/978-1-61779-376-9_11.

PMID:
22113275
[PubMed - indexed for MEDLINE]
4.

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. Epub 2011 Jul 14.

PMID:
21779159
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
25128017
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22863112
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
21736739
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
19159457
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue.

Fanelli M, Amatori S, Barozzi I, Minucci S.

Nat Protoc. 2011 Nov 10;6(12):1905-19. doi: 10.1038/nprot.2011.406.

PMID:
22082985
[PubMed - indexed for MEDLINE]
10.

Computational analysis of protein-DNA interactions from ChIP-seq data.

Rougemont J, Naef F.

Methods Mol Biol. 2012;786:263-73. doi: 10.1007/978-1-61779-292-2_16.

PMID:
21938632
[PubMed - indexed for MEDLINE]
11.

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
[PubMed - indexed for MEDLINE]
12.

AREM: aligning short reads from ChIP-sequencing by expectation maximization.

Newkirk D, Biesinger J, Chon A, Yokomori K, Xie X.

J Comput Biol. 2011 Nov;18(11):1495-505. doi: 10.1089/cmb.2011.0185. Epub 2011 Oct 28.

PMID:
22035330
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

Jothi R, Cuddapah S, Barski A, Cui K, Zhao K.

Nucleic Acids Res. 2008 Sep;36(16):5221-31. doi: 10.1093/nar/gkn488. Epub 2008 Aug 6.

PMID:
18684996
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.

Taslim C, Huang K, Huang T, Lin S.

Methods Mol Biol. 2012;802:275-91. doi: 10.1007/978-1-61779-400-1_18.

PMID:
22130887
[PubMed - indexed for MEDLINE]
15.

Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.

Wei G, Hu G, Cui K, Zhao K.

Methods Enzymol. 2012;513:297-313. doi: 10.1016/B978-0-12-391938-0.00013-6.

PMID:
22929775
[PubMed - indexed for MEDLINE]
16.

Systematic bias in high-throughput sequencing data and its correction by BEADS.

Cheung MS, Down TA, Latorre I, Ahringer J.

Nucleic Acids Res. 2011 Aug;39(15):e103. doi: 10.1093/nar/gkr425. Epub 2011 Jun 6.

PMID:
21646344
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The analysis of ChIP-Seq data.

Ma W, Wong WH.

Methods Enzymol. 2011;497:51-73. doi: 10.1016/B978-0-12-385075-1.00003-2.

PMID:
21601082
[PubMed - indexed for MEDLINE]
18.

Genome-wide chromatin immunoprecipitation-sequencing in Plasmodium.

Lopez-Rubio JJ, Siegel TN, Scherf A.

Methods Mol Biol. 2013;923:321-33.

PMID:
22990789
[PubMed - indexed for MEDLINE]
19.

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]
20.

[Processing and analysis of ChIP-seq data].

Gao S, Zhang N, Li B, Xu S, Ye YB, Ruan JS.

Yi Chuan. 2012 Jun;34(6):773-83. Review. Chinese.

PMID:
22698750
[PubMed - indexed for MEDLINE]
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