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Items: 1 to 20 of 882

1.

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.

2.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
3.
4.

CONREAL web server: identification and visualization of conserved transcription factor binding sites.

Berezikov E, Guryev V, Cuppen E.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W447-50.

6.

CREME: Cis-Regulatory Module Explorer for the human genome.

Sharan R, Ben-Hur A, Loots GG, Ovcharenko I.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W253-6.

7.

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.

8.

DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.

Sebestyén E, Nagy T, Suhai S, Barta E.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S6. doi: 10.1186/1471-2105-10-S6-S6.

9.

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

Zambelli F, Pesole G, Pavesi G.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W247-52. doi: 10.1093/nar/gkp464.

10.

Exploring conservation of transcription factor binding sites with CONREAL.

Berezikov E, Guryev V, Cuppen E.

Methods Mol Biol. 2007;395:437-48.

PMID:
17993690
11.

TF Target Mapper: a BLAST search tool for the identification of Transcription Factor target genes.

Horsman S, Moorhouse MJ, de Jager VC, van der Spek P, Grosveld F, Strouboulis J, Katsantoni EZ.

BMC Bioinformatics. 2006 Mar 8;7:120.

12.

FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.

Corcoran DL, Feingold E, Benos PV.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.

13.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters.

Blanco E, Farré D, Albà MM, Messeguer X, Guigó R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D63-7.

14.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

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

15.

Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors.

Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ.

J Mol Biol. 2001 May 25;309(1):99-120.

PMID:
11491305
16.

DWE: discriminating word enumerator.

Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ.

Bioinformatics. 2005 Jan 1;21(1):31-8.

PMID:
15333453
17.

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.

18.

A tool-kit for cDNA microarray and promoter analysis.

Shah NH, King DC, Shah PN, Fedoroff NV.

Bioinformatics. 2003 Sep 22;19(14):1846-8.

PMID:
14512358
19.
20.

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites.

Qin ZS, McCue LA, Thompson W, Mayerhofer L, Lawrence CE, Liu JS.

Nat Biotechnol. 2003 Apr;21(4):435-9.

PMID:
12627170
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