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Items: 1 to 20 of 222

1.

The functional consequences of variation in transcription factor binding.

Cusanovich DA, Pavlovic B, Pritchard JK, Gilad Y.

PLoS Genet. 2014 Mar 6;10(3):e1004226. doi: 10.1371/journal.pgen.1004226. eCollection 2014 Mar.

2.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold B, Willard HF, Myers RM.

Genome Res. 2012 May;22(5):860-9. doi: 10.1101/gr.131201.111. Epub 2012 Feb 2.

3.

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.

4.

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.

5.

Chromatin properties of regulatory DNA probed by manipulation of transcription factors.

Sharov AA, Nishiyama A, Qian Y, Dudekula DB, Longo DL, Schlessinger D, Ko MS.

J Comput Biol. 2014 Aug;21(8):569-77. doi: 10.1089/cmb.2013.0126. Epub 2014 Jun 11.

6.

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.

Chen CY, Morris Q, Mitchell JA.

BMC Genomics. 2012 Apr 26;13:152. doi: 10.1186/1471-2164-13-152.

7.

A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.

Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K.

Plant Cell. 2014 Oct;26(10):3894-910. doi: 10.1105/tpc.114.130591. Epub 2014 Oct 31.

8.

Transcription factors: specific DNA binding and specific gene regulation.

Todeschini AL, Georges A, Veitia RA.

Trends Genet. 2014 Jun;30(6):211-9. doi: 10.1016/j.tig.2014.04.002. Epub 2014 Apr 26. Review.

PMID:
24774859
9.

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements.

Rye M, Sætrom P, Håndstad T, Drabløs F.

BMC Biol. 2011 Nov 24;9:80. doi: 10.1186/1741-7007-9-80.

10.

Modeling gene regulation from paired expression and chromatin accessibility data.

Duren Z, Chen X, Jiang R, Wang Y, Wong WH.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):E4914-E4923. doi: 10.1073/pnas.1704553114. Epub 2017 Jun 2.

11.

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

He A, Kong SW, Ma Q, Pu WT.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5632-7. doi: 10.1073/pnas.1016959108. Epub 2011 Mar 17.

13.

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.

14.

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
15.

Defining specificity of transcription factor regulatory activities.

Eeckhoute J, Métivier R, Salbert G.

J Cell Sci. 2009 Nov 15;122(Pt 22):4027-34. doi: 10.1242/jcs.054916.

16.

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features.

Kumar S, Bucher P.

BMC Bioinformatics. 2016 Jan 11;17 Suppl 1:4. doi: 10.1186/s12859-015-0846-z.

17.

Transcription factor-DNA binding: beyond binding site motifs.

Inukai S, Kock KH, Bulyk ML.

Curr Opin Genet Dev. 2017 Apr;43:110-119. doi: 10.1016/j.gde.2017.02.007. Epub 2017 Mar 27. Review.

18.

Sequence and chromatin determinants of cell-type-specific transcription factor binding.

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

Genome Res. 2012 Sep;22(9):1723-34. doi: 10.1101/gr.127712.111.

19.

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.

20.

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX.

Nucleic Acids Res. 2012 Sep;40(16):7690-704. Epub 2012 Jun 6.

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