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The QTN program and the alleles that matter for evolution: all that's gold does not glitter.

Rockman MV.

Evolution. 2012 Jan;66(1):1-17. doi: 10.1111/j.1558-5646.2011.01486.x. Epub 2011 Nov 6.


Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB.

Lynch VJ, May G, Wagner GP.

Nature. 2011 Nov 13;480(7377):383-6. doi: 10.1038/nature10595.


Morphological evolution caused by many subtle-effect substitutions in regulatory DNA.

Frankel N, Erezyilmaz DF, McGregor AP, Wang S, Payre F, Stern DL.

Nature. 2011 Jun 29;474(7353):598-603. doi: 10.1038/nature10200.


Systematic detection of polygenic cis-regulatory evolution.

Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, Schadt EE.

PLoS Genet. 2011 Mar;7(3):e1002023. doi: 10.1371/journal.pgen.1002023. Epub 2011 Mar 31.


High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes.

Markova-Raina P, Petrov D.

Genome Res. 2011 Jun;21(6):863-74. doi: 10.1101/gr.115949.110. Epub 2011 Mar 10.


What are the genomic drivers of the rapid evolution of PRDM9?

Ponting CP.

Trends Genet. 2011 May;27(5):165-71. doi: 10.1016/j.tig.2011.02.001. Epub 2011 Mar 8.


webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.


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.


The role of nucleosome positioning in the evolution of gene regulation.

Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ.

PLoS Biol. 2010 Jul 6;8(7):e1000414. doi: 10.1371/journal.pbio.1000414.


Natural selection on cis and trans regulation in yeasts.

Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MY, Wu SH, Li WH.

Genome Res. 2010 Jun;20(6):826-36. doi: 10.1101/gr.101576.109. Epub 2010 May 5.


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.


Polygenic and directional regulatory evolution across pathways in Saccharomyces.

Bullard JH, Mostovoy Y, Dudoit S, Brem RB.

Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5058-63. doi: 10.1073/pnas.0912959107. Epub 2010 Mar 1.


Evidence for widespread adaptive evolution of gene expression in budding yeast.

Fraser HB, Moses AM, Schadt EE.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2977-82. doi: 10.1073/pnas.0912245107. Epub 2010 Jan 28.


Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population.

Rebeiz M, Pool JE, Kassner VA, Aquadro CF, Carroll SB.

Science. 2009 Dec 18;326(5960):1663-7. doi: 10.1126/science.1178357.


Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast.

Zhou L, Ma X, Arbeitman MN, Sun F.

PLoS One. 2009 Nov 30;4(11):e8086. doi: 10.1371/journal.pone.0008086.


Detecting positive selection in the budding yeast genome.

Li YD, Liang H, Gu Z, Lin Z, Guan W, Zhou L, Li YQ, Li WH.

J Evol Biol. 2009 Dec;22(12):2430-7. doi: 10.1111/j.1420-9101.2009.01851.x. Epub 2009 Oct 29.


Dissecting the pleiotropic consequences of a quantitative trait nucleotide.

Kim HS, Huh J, Fay JC.

FEMS Yeast Res. 2009 Aug;9(5):713-22. doi: 10.1111/j.1567-1364.2009.00516.x. Epub 2009 Apr 23.


Conservation of core gene expression in vertebrate tissues.

Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR.

J Biol. 2009;8(3):33. doi: 10.1186/jbiol130. Epub 2009 Apr 16.


Is genetic evolution predictable?

Stern DL, Orgogozo V.

Science. 2009 Feb 6;323(5915):746-51. doi: 10.1126/science.1158997. Review.


Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

Huang da W, Sherman BT, Lempicki RA.

Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.

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