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Items: 1 to 20 of 80

1.

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

2.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, Taipale J.

Genome Res. 2010 Jun;20(6):861-73. doi: 10.1101/gr.100552.109. Epub 2010 Apr 8.

3.

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.

Orenstein Y, Shamir R.

Nucleic Acids Res. 2014 Apr;42(8):e63. doi: 10.1093/nar/gku117. Epub 2014 Feb 5.

4.

Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data.

Zamanighomi M, Lin Z, Wang Y, Jiang R, Wong WH.

Nucleic Acids Res. 2017 Jun 2;45(10):5666-5677. doi: 10.1093/nar/gkx358.

5.

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.

6.

[DNA-binding profiles of mammalian transcription factors].

Gu GM, Wang JK.

Yi Chuan. 2012 Aug;34(8):950-68. Review. Chinese.

PMID:
22917900
7.

In vitro DNA-binding profile of transcription factors: methods and new insights.

Wang J, Lu J, Gu G, Liu Y.

J Endocrinol. 2011 Jul;210(1):15-27. doi: 10.1530/JOE-11-0010. Epub 2011 Mar 9. Review.

8.

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J.

Elife. 2015 Mar 17;4. doi: 10.7554/eLife.04837.

9.

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.

10.

A feature-based approach to modeling protein-DNA interactions.

Sharon E, Lubliner S, Segal E.

PLoS Comput Biol. 2008 Aug 22;4(8):e1000154. doi: 10.1371/journal.pcbi.1000154.

11.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

12.

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J.

Nature. 2015 Nov 19;527(7578):384-8. doi: 10.1038/nature15518. Epub 2015 Nov 9.

PMID:
26550823
13.

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.

Kazemian M, Pham H, Wolfe SA, Brodsky MH, Sinha S.

Nucleic Acids Res. 2013 Sep;41(17):8237-52. doi: 10.1093/nar/gkt598. Epub 2013 Jul 11.

14.

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.

15.

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.

16.

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
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.

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.

Jolma A, Taipale J.

Subcell Biochem. 2011;52:155-73. doi: 10.1007/978-90-481-9069-0_7. Review.

PMID:
21557082
19.

Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9.

20.

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.

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