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Items: 1 to 20 of 283

1.

Extracting transcription factor targets from ChIP-Seq data.

Tuteja G, White P, Schug J, Kaestner KH.

Nucleic Acids Res. 2009 Sep;37(17):e113. doi: 10.1093/nar/gkp536. Epub 2009 Jun 24.

2.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

3.

Modeling ChIP sequencing in silico with applications.

Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000158. doi: 10.1371/journal.pcbi.1000158.

4.

Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing.

Hoffman BG, Jones SJ.

J Endocrinol. 2009 Apr;201(1):1-13. doi: 10.1677/JOE-08-0526. Epub 2009 Jan 9. Review.

5.

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.

6.

Chromatin immunoprecipitation for identifying transcription factor targets in keratinocytes.

Ortt K, Sinha S.

Methods Mol Biol. 2010;585:159-70. doi: 10.1007/978-1-60761-380-0_12.

PMID:
19908003
7.
8.

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq.

Johannes F, Wardenaar R, Colomé-Tatché M, Mousson F, de Graaf P, Mokry M, Guryev V, Timmers HT, Cuppen E, Jansen RC.

Bioinformatics. 2010 Apr 15;26(8):1000-6. doi: 10.1093/bioinformatics/btq087. Epub 2010 Mar 5.

PMID:
20208068
9.

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.

10.

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
11.

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.

Rada-Iglesias A, Wallerman O, Koch C, Ameur A, Enroth S, Clelland G, Wester K, Wilcox S, Dovey OM, Ellis PD, Wraight VL, James K, Andrews R, Langford C, Dhami P, Carter N, Vetrie D, Pontén F, Komorowski J, Dunham I, Wadelius C.

Hum Mol Genet. 2005 Nov 15;14(22):3435-47. Epub 2005 Oct 12.

PMID:
16221759
12.

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing.

Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao Y, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA.

Nucleic Acids Res. 2008 Aug;36(14):4549-64. doi: 10.1093/nar/gkn382. Epub 2008 Jul 8.

13.

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
14.

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
15.

Genome-wide profiling of DNA-binding proteins using barcode-based multiplex Solexa sequencing.

Raghav SK, Deplancke B.

Methods Mol Biol. 2012;786:247-62. doi: 10.1007/978-1-61779-292-2_15.

PMID:
21938631
16.

Relative avidity, specificity, and sensitivity of transcription factor-DNA binding in genome-scale experiments.

Kuznetsov VA.

Methods Mol Biol. 2009;563:15-50. doi: 10.1007/978-1-60761-175-2_2.

PMID:
19597778
17.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
18.

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.

Szalkowski AM, Schmid CD.

Brief Bioinform. 2011 Nov;12(6):626-33. doi: 10.1093/bib/bbq068. Epub 2010 Nov 8.

PMID:
21059603
19.

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.

20.

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

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