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Results: 1 to 20 of 53

1.

Regulatory divergence in Drosophila revealed by mRNA-seq.

McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ.

Genome Res. 2010 Jun;20(6):816-25. doi: 10.1101/gr.102491.109. Epub 2010 Mar 30. Erratum in: Genome Res. 2014 Jun;24(6):1051.

PMID:
20354124
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
20194736
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The role of DNA shape in protein-DNA recognition.

Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B.

Nature. 2009 Oct 29;461(7268):1248-53. doi: 10.1038/nature08473.

PMID:
19865164
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

DiProGB: the dinucleotide properties genome browser.

Friedel M, Nikolajewa S, Sühnel J, Wilhelm T.

Bioinformatics. 2009 Oct 1;25(19):2603-4. doi: 10.1093/bioinformatics/btp436. Epub 2009 Jul 15.

PMID:
19605418
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A yeast hybrid provides insight into the evolution of gene expression regulation.

Tirosh I, Reikhav S, Levy AA, Barkai N.

Science. 2009 May 1;324(5927):659-62. doi: 10.1126/science.1169766.

PMID:
19407207
[PubMed - indexed for MEDLINE]
Free Article
6.

Nuance in the double-helix and its role in protein-DNA recognition.

Rohs R, West SM, Liu P, Honig B.

Curr Opin Struct Biol. 2009 Apr;19(2):171-7. doi: 10.1016/j.sbi.2009.03.002. Epub 2009 Apr 10. Review.

PMID:
19362815
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Local DNA topography correlates with functional noncoding regions of the human genome.

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH.

Science. 2009 Apr 17;324(5925):389-92. doi: 10.1126/science.1169050. Epub 2009 Mar 12.

PMID:
19286520
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Intrinsic variability of gene expression encoded in nucleosome positioning sequences.

Choi JK, Kim YJ.

Nat Genet. 2009 Apr;41(4):498-503. doi: 10.1038/ng.319. Epub 2009 Mar 1.

PMID:
19252489
[PubMed - indexed for MEDLINE]
9.

Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization.

Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal E.

Nat Genet. 2009 Apr;41(4):438-45. doi: 10.1038/ng.324. Epub 2009 Mar 1.

PMID:
19252487
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.

Venters BJ, Pugh BF.

Genome Res. 2009 Mar;19(3):360-71. doi: 10.1101/gr.084970.108. Epub 2009 Jan 5.

PMID:
19124666
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The DNA-encoded nucleosome organization of a eukaryotic genome.

Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E.

Nature. 2009 Mar 19;458(7236):362-6. doi: 10.1038/nature07667. Epub 2008 Dec 17.

PMID:
19092803
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Chance and necessity in chromosomal gene distributions.

Hermsen R, ten Wolde PR, Teichmann S.

Trends Genet. 2008 May;24(5):216-9. doi: 10.1016/j.tig.2008.02.004. Epub 2008 Apr 2. Review.

PMID:
18378035
[PubMed - indexed for MEDLINE]
13.

Regulatory changes underlying expression differences within and between Drosophila species.

Wittkopp PJ, Haerum BK, Clark AG.

Nat Genet. 2008 Mar;40(3):346-50. doi: 10.1038/ng.77. Epub 2008 Feb 17.

PMID:
18278046
[PubMed - indexed for MEDLINE]
14.

Evolution of gene sequence and gene expression are not correlated in yeast.

Tirosh I, Barkai N.

Trends Genet. 2008 Mar;24(3):109-13. doi: 10.1016/j.tig.2007.12.004. Epub 2008 Feb 4.

PMID:
18249461
[PubMed - indexed for MEDLINE]
15.

Epigenetic regulation and the variability of gene expression.

Choi JK, Kim YJ.

Nat Genet. 2008 Feb;40(2):141-7. doi: 10.1038/ng.2007.58.

PMID:
18227874
[PubMed - indexed for MEDLINE]
16.

On the relation between promoter divergence and gene expression evolution.

Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N.

Mol Syst Biol. 2008;4:159. doi: 10.1038/msb4100198. Epub 2008 Jan 15.

PMID:
18197176
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Generic eukaryotic core promoter prediction using structural features of DNA.

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y.

Genome Res. 2008 Feb;18(2):310-23. Epub 2007 Dec 20.

PMID:
18096745
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes.

Heger A, Ponting CP.

Genome Res. 2007 Dec;17(12):1837-49. Epub 2007 Nov 7.

PMID:
17989258
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A high-resolution atlas of nucleosome occupancy in yeast.

Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C.

Nat Genet. 2007 Oct;39(10):1235-44. Epub 2007 Sep 16.

PMID:
17873876
[PubMed - indexed for MEDLINE]
20.

Natural history and evolutionary principles of gene duplication in fungi.

Wapinski I, Pfeffer A, Friedman N, Regev A.

Nature. 2007 Sep 6;449(7158):54-61.

PMID:
17805289
[PubMed - indexed for MEDLINE]
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