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Items: 1 to 20 of 167

1.

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.

Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H.

Bioinformatics. 2013 May 1;29(9):1182-9. doi: 10.1093/bioinformatics/btt108.

2.

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.

Wu G, Ji H.

BMC Bioinformatics. 2013 Jun 10;14:188. doi: 10.1186/1471-2105-14-188.

3.

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.

4.

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
5.

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Qin J, Li MJ, Wang P, Zhang MQ, Wang J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6. doi: 10.1093/nar/gkr332.

6.
7.

Identification of transcription factor binding sites from ChIP-seq data at high resolution.

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A.

Bioinformatics. 2013 Nov 1;29(21):2705-13. doi: 10.1093/bioinformatics/btt470.

8.

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data.

Yang JH, Li JH, Jiang S, Zhou H, Qu LH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. doi: 10.1093/nar/gks1060.

9.

Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.

Brdlik CM, Niu W, Snyder M.

Methods Enzymol. 2014;539:89-111. doi: 10.1016/B978-0-12-420120-0.00007-4.

PMID:
24581441
10.

Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.

Worsley Hunt R, Wasserman WW.

Genome Biol. 2014 Jul 29;15(7):412. doi: 10.1186/s13059-014-0412-4.

11.

Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.

Lefrançois P, Gallagher JE, Snyder M.

Methods Mol Biol. 2014;1205:231-55. doi: 10.1007/978-1-4939-1363-3_15.

12.

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.

13.

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP).

Kaufmann K, Muiño JM, Østerås M, Farinelli L, Krajewski P, Angenent GC.

Nat Protoc. 2010 Mar;5(3):457-72. doi: 10.1038/nprot.2009.244.

PMID:
20203663
14.

Optimization of transcription factor binding map accuracy utilizing knockout-mouse models.

Krebs W, Schmidt SV, Goren A, De Nardo D, Labzin L, Bovier A, Ulas T, Theis H, Kraut M, Latz E, Beyer M, Schultze JL.

Nucleic Acids Res. 2014 Dec 1;42(21):13051-60. doi: 10.1093/nar/gku1078.

15.

Analyzing transcription factor occupancy during embryo development using ChIP-seq.

Ghavi-Helm Y, Furlong EE.

Methods Mol Biol. 2012;786:229-45. doi: 10.1007/978-1-61779-292-2_14.

PMID:
21938630
16.

The comprehensive transcriptional analysis in Caenorhabditis elegans by integrating ChIP-seq and gene expression data.

He K, Shao J, Zhao Z, Liu D.

Genet Res (Camb). 2014;96:e005. doi: 10.1017/S0016672314000081.

PMID:
25023089
17.

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data.

Kähärä J, Lähdesmäki H.

Bioinformatics. 2015 Sep 1;31(17):2852-9. doi: 10.1093/bioinformatics/btv294.

PMID:
25957350
18.

Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome.

Kuznetsov VA, Singh O, Jenjaroenpun P.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S12. doi: 10.1186/1471-2164-11-S1-S12.

19.

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.

20.

Chromatin immunoprecipitation for ChIP-chip and ChIP-seq.

Schulz S, Häussler S.

Methods Mol Biol. 2014;1149:591-605. doi: 10.1007/978-1-4939-0473-0_45.

PMID:
24818935

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