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Results: 1 to 20 of 224

1.
2.

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
3.

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
4.

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.

Dermitzakis ET, Clark AG.

Mol Biol Evol. 2002 Jul;19(7):1114-21.

PMID:
12082130
[PubMed - indexed for MEDLINE]
Free Article
5.

A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas.

Stepanova M, Tiazhelova T, Skoblov M, Baranova A.

Bioinformatics. 2005 May 1;21(9):1789-96. Epub 2005 Feb 4.

PMID:
15699025
[PubMed - indexed for MEDLINE]
Free Article
6.

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing.

Ray P, Shringarpure S, Kolar M, Xing EP.

PLoS Comput Biol. 2008 Jun 6;4(6):e1000090. doi: 10.1371/journal.pcbi.1000090.

PMID:
18535663
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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]
8.

A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.

Li L, Cheng AS, Jin VX, Paik HH, Fan M, Li X, Zhang W, Robarge J, Balch C, Davuluri RV, Kim S, Huang TH, Nephew KP.

Bioinformatics. 2006 Sep 15;22(18):2210-6. Epub 2006 Jun 29.

PMID:
16809387
[PubMed - indexed for MEDLINE]
Free Article
9.

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.

Mahony S, Corcoran DL, Feingold E, Benos PV.

Genome Biol. 2007;8(5):R84.

PMID:
17506886
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

PMID:
15980535
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression.

Murakami K, Kojima T, Sakaki Y.

BMC Genomics. 2004 Feb 23;5(1):16.

PMID:
15053842
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

Berezikov E, Guryev V, Plasterk RH, Cuppen E.

Genome Res. 2004 Jan;14(1):170-8. Epub 2003 Dec 12.

PMID:
14672977
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

BLISS: binding site level identification of shared signal-modules in DNA regulatory sequences.

Meng H, Banerjee A, Zhou L.

BMC Bioinformatics. 2006 Jun 7;7:287.

PMID:
16756683
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

PromAn: an integrated knowledge-based web server dedicated to promoter analysis.

Lardenois A, Chalmel F, Bianchetti L, Sahel JA, Léveillard T, Poch O.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W578-83.

PMID:
16845074
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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. doi: 10.1186/1471-2164-9-226.

PMID:
18485226
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

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
18.

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
19.

Modeling promoter grammars with evolving hidden Markov models.

Won KJ, Sandelin A, Marstrand TT, Krogh A.

Bioinformatics. 2008 Aug 1;24(15):1669-75. doi: 10.1093/bioinformatics/btn254. Epub 2008 Jun 5.

PMID:
18535083
[PubMed - indexed for MEDLINE]
Free Article
20.

ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species.

Hooghe B, Hulpiau P, van Roy F, De Bleser P.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W128-32. doi: 10.1093/nar/gkn195. Epub 2008 May 3.

PMID:
18453628
[PubMed - indexed for MEDLINE]
Free PMC Article

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