PubMed

Position specific variation in the rate of evolution in transcription factor binding sites.

Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB.

BMC Evol Biol. 2003 Aug 28;3:19. Epub 2003 Aug 28.PMID: 12946282 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.PMID: 16362910 [PubMed - indexed for MEDLINE]Related articles

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA.

Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK.

BMC Genomics. 2008 May 17;9:226.PMID: 18485226 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites.

Raijman D, Shamir R, Tanay A.

PLoS Comput Biol. 2008 Jan;4(1):e7.PMID: 18193940 [PubMed - indexed for MEDLINE]Related articlesFree article

Functional characterization of variations on regulatory motifs.

Lapidot M, Mizrahi-Man O, Pilpel Y.

PLoS Genet. 2008 Mar 7;4(3):e1000018. Erratum in: PLoS Genet. 2008 Jun;4(6). doi: 10.1371/annotation/99662172-8f18-4bfb-ad0f-79ed1d69fffd. Michal, Lapidot [corrected to Lapidot, Michal]. PMID: 18369443 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of functional transcription factor binding sites using closely related Saccharomyces species.

Doniger SW, Huh J, Fay JC.

Genome Res. 2005 May;15(5):701-9. Epub 2005 Apr 18.PMID: 15837806 [PubMed - indexed for MEDLINE]Related articlesFree article

Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.

Lusk RW, Eisen MB.

Pac Symp Biocomput. 2008:489-500.PMID: 18229710 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequencing and comparison of yeast species to identify genes and regulatory elements.

Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES.

Nature. 2003 May 15;423(6937):241-54.PMID: 12748633 [PubMed - indexed for MEDLINE]Related articles

Divergence of transcription factor binding sites across related yeast species.

Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M.

Science. 2007 Aug 10;317(5839):815-9.PMID: 17690298 [PubMed - indexed for MEDLINE]Related articlesFree article

A global view of the selection forces in the evolution of yeast cis-regulation.

Tanay A, Gat-Viks I, Shamir R.

Genome Res. 2004 May;14(5):829-34.PMID: 15123582 [PubMed - indexed for MEDLINE]Related articlesFree article

Expression studies and promoter analysis of the nuclear gene for mitochondrial transcription factor 1 (MTF1) in yeast.

Jan PS, Stein T, Hehl S, Lisowsky T.

Curr Genet. 1999 Aug;36(1-2):37-48.PMID: 10447593 [PubMed - indexed for MEDLINE]Related articles

Combined analysis of expression data and transcription factor binding sites in the yeast genome.

Nagaraj VH, O'Flanagan RA, Bruning AR, Mathias JR, Vershon AK, Sengupta AM.

BMC Genomics. 2004 Aug 26;5(1):59.PMID: 15331021 [PubMed - indexed for MEDLINE]Related articlesFree article

Frequent gain and loss of functional transcription factor binding sites.

Doniger SW, Fay JC.

PLoS Comput Biol. 2007 May;3(5):e99. Epub 2007 Apr 19. Erratum in: PLoS Comput Biol. 2009 Feb;5(2). doi: 10.1371/annotation/363b6074-caec-4238-b88f-acbf45de498f. PMID: 17530920 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of regulatory sequences in 12 Drosophila species.

Kim J, He X, Sinha S.

PLoS Genet. 2009 Jan;5(1):e1000330. Epub 2009 Jan 9.PMID: 19132088 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs.

Corà D, Di Cunto F, Provero P, Silengo L, Caselle M.

BMC Bioinformatics. 2004 May 11;5:57.PMID: 15137914 [PubMed - indexed for MEDLINE]Related articlesFree article

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.PMID: 15113405 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution of a glucose-regulated ADH gene in the genus Saccharomyces.

Young ET, Sloan J, Miller B, Li N, van Riper K, Dombek KM.

Gene. 2000 Mar 21;245(2):299-309.PMID: 10717481 [PubMed - indexed for MEDLINE]Related articles

Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.

Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB.

Genome Biol. 2003;4(7):R43. Epub 2003 Jun 26.PMID: 12844359 [PubMed - indexed for MEDLINE]Related articlesFree article

Whole-genome discovery of transcription factor binding sites by network-level conservation.

Pritsker M, Liu YC, Beer MA, Tavazoie S.

Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.PMID: 14672978 [PubMed - indexed for MEDLINE]Related articlesFree article