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Results: 1 to 20 of 107

1.

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.

Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB.

Genome Biol. 2004;5(12):R98. Epub 2004 Nov 30.

PMID:
15575972
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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]
Free PMC Article
3.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

PMID:
17914226
[PubMed - indexed for MEDLINE]
Free Article
4.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

PMID:
19293946
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Conservation and evolution of cis-regulatory systems in ascomycete fungi.

Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB.

PLoS Biol. 2004 Dec;2(12):e398. Epub 2004 Nov 9.

PMID:
15534694
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Yeast general transcription factor GFI: sequence requirements for binding to DNA and evolutionary conservation.

Dorsman JC, van Heeswijk WC, Grivell LA.

Nucleic Acids Res. 1990 May 11;18(9):2769-76.

PMID:
2187179
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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]
Free PMC Article
8.

Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer.

Eisermann K, Tandon S, Bazarov A, Brett A, Fraizer G, Piontkivska H.

BMC Genomics. 2008 Jul 16;9:337. doi: 10.1186/1471-2164-9-337.

PMID:
18631392
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes.

Hestand MS, van Galen M, Villerius MP, van Ommen GJ, den Dunnen JT, 't Hoen PA.

BMC Bioinformatics. 2008 Nov 26;9:495. doi: 10.1186/1471-2105-9-495.

PMID:
19036135
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Context specific transcription factor prediction.

Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.

Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.

PMID:
17377845
[PubMed - indexed for MEDLINE]
11.

An evolutionary approach for identifying potential transcription factor binding sites: the renin gene as an example.

Mrowka R, Steinhage K, Patzak A, Persson PB.

Am J Physiol Regul Integr Comp Physiol. 2003 Apr;284(4):R1147-50.

PMID:
12626372
[PubMed - indexed for MEDLINE]
12.

Evolution of transcription factor binding sites in mammalian gene regulatory regions: handling counterintuitive results.

Balmer JE, Blomhoff R.

J Mol Evol. 2009 Jun;68(6):654-64. doi: 10.1007/s00239-009-9238-1. Epub 2009 May 29.

PMID:
19479175
[PubMed - indexed for MEDLINE]
13.

A discriminative model for identifying spatial cis-regulatory modules.

Segal E, Sharan R.

J Comput Biol. 2005 Jul-Aug;12(6):822-34.

PMID:
16108719
[PubMed - indexed for MEDLINE]
14.

Combinatorial repression of the hypoxic genes of Saccharomyces cerevisiae by DNA binding proteins Rox1 and Mot3.

Klinkenberg LG, Mennella TA, Luetkenhaus K, Zitomer RS.

Eukaryot Cell. 2005 Apr;4(4):649-60.

PMID:
15821125
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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]
Free Article
16.

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1998-2003. Epub 2005 Jan 31.

PMID:
15684073
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Identifying target sites for cooperatively binding factors.

GuhaThakurta D, Stormo GD.

Bioinformatics. 2001 Jul;17(7):608-21.

PMID:
11448879
[PubMed - indexed for MEDLINE]
Free Article
18.

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]
Free PMC Article
19.

Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity.

Raviscioni M, Gu P, Sattar M, Cooney AJ, Lichtarge O.

J Mol Biol. 2005 Jul 15;350(3):402-15.

PMID:
15946684
[PubMed - indexed for MEDLINE]
20.

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]

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