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Items: 1 to 20 of 135

1.

Large-scale turnover of functional transcription factor binding sites in Drosophila.

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB.

PLoS Comput Biol. 2006 Oct;2(10):e130. Epub 2006 Aug 21.

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Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

He BZ, Holloway AK, Maerkl SJ, Kreitman M.

PLoS Genet. 2011 Apr;7(4):e1002053. doi: 10.1371/journal.pgen.1002053. Epub 2011 Apr 28.

5.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

6.

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.

7.

Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers.

Lusk RW, Eisen MB.

PLoS Genet. 2010 Jan 22;6(1):e1000829. doi: 10.1371/journal.pgen.1000829.

8.

Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.

Martinez C, Rest JS, Kim AR, Ludwig M, Kreitman M, White K, Reinitz J.

Mol Biol Evol. 2014 Apr;31(4):903-16. doi: 10.1093/molbev/msu042. Epub 2014 Jan 9.

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.

Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo.

Hodar C, Zuñiga A, Pulgar R, Travisany D, Chacon C, Pino M, Maass A, Cambiazo V.

Gene. 2014 Feb 10;535(2):210-7. doi: 10.1016/j.gene.2013.11.032. Epub 2013 Dec 7.

PMID:
24321690
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Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila.

Ho MC, Johnsen H, Goetz SE, Schiller BJ, Bae E, Tran DA, Shur AS, Allen JM, Rau C, Bender W, Fisher WW, Celniker SE, Drewell RA.

PLoS Genet. 2009 Nov;5(11):e1000709. doi: 10.1371/journal.pgen.1000709. Epub 2009 Nov 6.

13.

Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species.

Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M.

PLoS Biol. 2008 Oct 28;6(10):e261. doi: 10.1371/journal.pbio.0060261.

14.

Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila.

Halligan DL, Eyre-Walker A, Andolfatto P, Keightley PD.

Genome Res. 2004 Feb;14(2):273-9.

15.

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

Dermitzakis ET, Bergman CM, Clark AG.

Mol Biol Evol. 2003 May;20(5):703-14. Epub 2003 Apr 2.

PMID:
12679540
16.

Simulations of enhancer evolution provide mechanistic insights into gene regulation.

Duque T, Samee MA, Kazemian M, Pham HN, Brodsky MH, Sinha S.

Mol Biol Evol. 2014 Jan;31(1):184-200. doi: 10.1093/molbev/mst170. Epub 2013 Oct 4.

17.

Comparative genomics of Drosophila mtDNA: Novel features of conservation and change across functional domains and lineages.

Montooth KL, Abt DN, Hofmann JW, Rand DM.

J Mol Evol. 2009 Jul;69(1):94-114. doi: 10.1007/s00239-009-9255-0. Epub 2009 Jun 16.

18.

Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?

Venkataram S, Fay JC.

Genome Biol Evol. 2010;2:851-8. doi: 10.1093/gbe/evq066. Epub 2010 Nov 10.

19.

Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S.

Mol Biol Evol. 2015 Sep;32(9):2441-55. doi: 10.1093/molbev/msv107. Epub 2015 May 4.

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