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Items: 1 to 20 of 145

1.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

2.

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.

3.

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E.

Nucleic Acids Res. 2010 Jun;38(11):e126. doi: 10.1093/nar/gkq217. Epub 2010 Apr 7.

4.

MEME-ChIP: motif analysis of large DNA datasets.

Machanick P, Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1696-7. doi: 10.1093/bioinformatics/btr189. Epub 2011 Apr 12.

5.

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.

6.

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.

7.

Inferring direct DNA binding from ChIP-seq.

Bailey TL, Machanick P.

Nucleic Acids Res. 2012 Sep 1;40(17):e128. Epub 2012 May 18.

8.

Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq.

Jiao S, Bailey CP, Zhang S, Ladunga I.

Methods Mol Biol. 2010;674:161-77. doi: 10.1007/978-1-60761-854-6_10.

PMID:
20827591
9.

High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.

Chumsakul O, Nakamura K, Kurata T, Sakamoto T, Hobman JL, Ogasawara N, Oshima T, Ishikawa S.

DNA Res. 2013 Aug;20(4):325-38. doi: 10.1093/dnares/dst013. Epub 2013 Apr 11.

10.

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.

11.

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B.

Genome Res. 2006 Oct;16(10):1208-21. Epub 2006 Sep 8.

12.

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.

13.

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
14.

Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.

Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.

BMC Genomics. 2014 Jun 13;15:472. doi: 10.1186/1471-2164-15-472.

15.

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.

16.

dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data.

Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S.

PLoS Comput Biol. 2013;9(10):e1003246. doi: 10.1371/journal.pcbi.1003246. Epub 2013 Oct 17.

17.

Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors.

Muiño JM, Angenent GC, Kaufmann K.

Methods Mol Biol. 2011;754:293-305. doi: 10.1007/978-1-61779-154-3_17. Review.

PMID:
21720960
18.

Design and analysis of ChIP-seq experiments for DNA-binding proteins.

Kharchenko PV, Tolstorukov MY, Park PJ.

Nat Biotechnol. 2008 Dec;26(12):1351-9. doi: 10.1038/nbt.1508. Epub 2008 Nov 16.

19.

A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques.

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M.

PLoS One. 2010 Dec 29;5(12):e15898. doi: 10.1371/journal.pone.0015898.

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