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Items: 1 to 20 of 102

1.

Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data.

Palumbo MJ, Newberg LA.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W268-74. doi: 10.1093/nar/gkq330. Epub 2010 Apr 30.

2.

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.

3.

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. Epub 2009 May 31.

4.

Gibbs Recursive Sampler: finding transcription factor binding sites.

Thompson W, Rouchka EC, Lawrence CE.

Nucleic Acids Res. 2003 Jul 1;31(13):3580-5.

5.

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.

The Gibbs Centroid Sampler.

Thompson WA, Newberg LA, Conlan S, McCue LA, Lawrence CE.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W232-7. Epub 2007 May 5.

7.

Comparative promoter region analysis powered by CORG.

Dieterich C, Grossmann S, Tanzer A, Röpcke S, Arndt PF, Stadler PF, Vingron M.

BMC Genomics. 2005 Feb 21;6:24.

8.

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.

9.
10.

PhyloScan: identification of transcription factor binding sites using cross-species evidence.

Carmack CS, McCue LA, Newberg LA, Lawrence CE.

Algorithms Mol Biol. 2007 Jan 23;2:1.

11.

SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences.

Boardman PE, Oliver SG, Hubbard SJ.

Nucleic Acids Res. 2003 Jul 1;31(13):3572-5.

12.

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.

13.

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.

Edwards YJ, Carver TJ, Vavouri T, Frith M, Bishop MJ, Elgar G.

Nucleic Acids Res. 2003 Jul 1;31(13):3510-7.

14.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

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

PMID:
16362910
15.

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes.

Pavesi G, Mereghetti P, Zambelli F, Stefani M, Mauri G, Pesole G.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W566-70.

16.

Using Weeder, Pscan, and PscanChIP for the Discovery of Enriched Transcription Factor Binding Site Motifs in Nucleotide Sequences.

Zambelli F, Pesole G, Pavesi G.

Curr Protoc Bioinformatics. 2014 Sep 8;47:2.11.1-31. doi: 10.1002/0471250953.bi0211s47.

PMID:
25199791
17.

CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

BMC Bioinformatics. 2008 Oct 27;9:455. doi: 10.1186/1471-2105-9-455.

18.

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.

19.

POBO, transcription factor binding site verification with bootstrapping.

Kankainen M, Holm L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W222-9.

20.

Ab initio identification of putative human transcription factor binding sites by comparative genomics.

Corà D, Herrmann C, Dieterich C, Di Cunto F, Provero P, Caselle M.

BMC Bioinformatics. 2005 May 2;6:110.

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