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Items: 1 to 20 of 61

1.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.

Cell. 2013 Aug 1;154(3):530-40. doi: 10.1016/j.cell.2013.07.007.

2.

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.

Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P.

Genome Res. 2015 Feb;25(2):167-78. doi: 10.1101/gr.177840.114. Epub 2014 Nov 13.

3.

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.

4.

Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399. doi: 10.1186/1471-2164-9-399.

5.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.

Elife. 2014 Oct 3;3:e02626. doi: 10.7554/eLife.02626.

6.

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.

Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A.

Genome Res. 2012 Oct;22(10):2018-30. doi: 10.1101/gr.132811.111. Epub 2012 Apr 25.

7.

Regulatory network structure as a dominant determinant of transcription factor evolutionary rate.

Coulombe-Huntington J, Xia Y.

PLoS Comput Biol. 2012;8(10):e1002734. doi: 10.1371/journal.pcbi.1002734. Epub 2012 Oct 18.

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.

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J.

BMC Genomics. 2015 Feb 14;16:87. doi: 10.1186/s12864-015-1245-6.

10.

Towards an evolutionary model of transcription networks.

Xie D, Chen CC, He X, Cao X, Zhong S.

PLoS Comput Biol. 2011 Jun;7(6):e1002064. doi: 10.1371/journal.pcbi.1002064. Epub 2011 Jun 9.

11.

Molecular dissection of cis-regulatory modules at the Drosophila bithorax complex reveals critical transcription factor signature motifs.

Starr MO, Ho MC, Gunther EJ, Tu YK, Shur AS, Goetz SE, Borok MJ, Kang V, Drewell RA.

Dev Biol. 2011 Nov 15;359(2):290-302. doi: 10.1016/j.ydbio.2011.07.028. Epub 2011 Jul 28.

12.

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.

Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT.

Science. 2010 May 21;328(5981):1036-40. doi: 10.1126/science.1186176. Epub 2010 Apr 8.

13.

CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.

Jiang P, Singh M.

Nucleic Acids Res. 2014 Mar;42(5):2833-47. doi: 10.1093/nar/gkt1302. Epub 2013 Dec 23.

14.

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.

Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112.

15.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.

16.

Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster.

Slattery M, Nègre N, White KP.

Brief Funct Genomics. 2012 Sep;11(5):336-46. doi: 10.1093/bfgp/els034.

17.

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB.

PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343.

18.

Conservation of transcription factor binding events predicts gene expression across species.

Hemberg M, Kreiman G.

Nucleic Acids Res. 2011 Sep 1;39(16):7092-102. doi: 10.1093/nar/gkr404. Epub 2011 May 26.

19.

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.

20.

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

Vandenbon A, Kumagai Y, Akira S, Standley DM.

BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11. Epub 2012 Dec 13.

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