PubMed

Identification of conserved regulatory elements by comparative genome analysis.

Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman WW.

J Biol. 2003;2(2):13. Epub 2003 May 22.PMID: 12760745 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Enrichment of regulatory signals in conserved non-coding genomic sequence.

Levy S, Hannenhalli S, Workman C.

Bioinformatics. 2001 Oct;17(10):871-7.PMID: 11673231 [PubMed - indexed for MEDLINE]Related articlesFree article

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.PMID: 15590941 [PubMed - indexed for MEDLINE]Related articlesFree article

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(1):24.PMID: 15723697 [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

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.PMID: 15865625 [PubMed - indexed for MEDLINE]Related articlesFree article

ConSite: web-based prediction of regulatory elements using cross-species comparison.

Sandelin A, Wasserman WW, Lenhard B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W249-52.PMID: 15215389 [PubMed - indexed for MEDLINE]Related articlesFree article

NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans and C. briggsae.

Rambaldi D, Guffanti A, Morandi P, Cassata G.

BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S22.PMID: 16351749 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 15980509 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals.

Cheremushkin E, Kel A.

Pac Symp Biocomput. 2003:291-302.PMID: 12603036 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE.

Genome Biol. 2004;5(9):R61. Epub 2004 Aug 20.PMID: 15345045 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.PMID: 15790569 [PubMed - indexed for MEDLINE]Related articlesFree article

MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes.

Marinescu VD, Kohane IS, Riva A.

BMC Bioinformatics. 2005 Mar 30;6:79.PMID: 15799782 [PubMed - indexed for MEDLINE]Related articlesFree article

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.PMID: 15655071 [PubMed - indexed for MEDLINE]Related articlesFree article

Evaluating phylogenetic footprinting for human-rodent comparisons.

Sauer T, Shelest E, Wingender E.

Bioinformatics. 2006 Feb 15;22(4):430-7. Epub 2005 Dec 6.PMID: 16332706 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ.

Bioinformatics. 2008 Jul 1;24(13):i165-71.PMID: 18586710 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article