Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 232

1.

Inferring transcription factor complexes from ChIP-seq data.

Whitington T, Frith MC, Johnson J, Bailey TL.

Nucleic Acids Res. 2011 Aug;39(15):e98. doi: 10.1093/nar/gkr341. Epub 2011 May 20.

2.

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.

3.

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. Epub 2015 May 7.

PMID:
25957350
4.

Inferring direct DNA binding from ChIP-seq.

Bailey TL, Machanick P.

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

5.

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.

6.

DREME: motif discovery in transcription factor ChIP-seq data.

Bailey TL.

Bioinformatics. 2011 Jun 15;27(12):1653-9. doi: 10.1093/bioinformatics/btr261. Epub 2011 May 4.

7.

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.

8.

PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. doi: 10.1093/nar/gkt448. Epub 2013 Jun 7.

9.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

10.

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.

11.

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. Epub 2013 Aug 24.

12.

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
13.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

14.

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis.

Rautio S, Lähdesmäki H.

BMC Bioinformatics. 2015 Dec 24;16:413. doi: 10.1186/s12859-015-0834-3.

15.

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.

16.

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.

Najafabadi HS, Albu M, Hughes TR.

Bioinformatics. 2015 Sep 1;31(17):2879-81. doi: 10.1093/bioinformatics/btv284. Epub 2015 May 6.

17.

Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data.

Goi C, Little P, Xie C.

BMC Genomics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2164-14-S5-S2. Epub 2013 Oct 16.

18.

LASAGNA: a novel algorithm for transcription factor binding site alignment.

Lee C, Huang CH.

BMC Bioinformatics. 2013 Mar 24;14:108. doi: 10.1186/1471-2105-14-108.

19.

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.

20.

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.

Supplemental Content

Support Center