PubMed

Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements.

Zhang Z, Gerstein M.

J Biol. 2003;2(2):11. Epub 2003 Jun 6. Review.PMID: 12814519 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying cis-regulatory elements by statistical analysis and phylogenetic footprinting and analyzing their coexistence and related gene ontology.

Shi W, Zhou W, Xu D.

Physiol Genomics. 2007 Nov 14;31(3):374-84. Epub 2007 Sep 11.PMID: 17848606 [PubMed - indexed for MEDLINE]Related articlesFree article

Searching for regulatory elements in human noncoding sequences.

Duret L, Bucher P.

Curr Opin Struct Biol. 1997 Jun;7(3):399-406. Review.PMID: 9204283 [PubMed - indexed for MEDLINE]Related articles

Algorithms for phylogenetic footprinting.

Blanchette M, Schwikowski B, Tompa M.

J Comput Biol. 2002;9(2):211-23.PMID: 12015878 [PubMed - indexed for MEDLINE]Related articles

Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes.

von Bubnoff A, Peiffer DA, Blitz IL, Hayata T, Ogata S, Zeng Q, Trunnell M, Cho KW.

Dev Biol. 2005 May 15;281(2):210-26.PMID: 15893974 [PubMed - indexed for MEDLINE]Related articles

Phylogenetic footprinting reveals extensive conservation of Sonic Hedgehog (SHH) regulatory elements.

Lemos B, Yunes JA, Vargas FR, Moreira MA, Cardoso AA, Seuánez HN.

Genomics. 2004 Sep;84(3):511-23.PMID: 15498458 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

Grad YH, Roth FP, Halfon MS, Church GM.

Bioinformatics. 2004 Nov 1;20(16):2738-50. Epub 2004 May 14.PMID: 15145800 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational prediction of conserved operons and phylogenetic footprinting of transcription regulatory elements in the metal-reducing bacterial family Geobacteraceae.

Yan B, Methé BA, Lovley DR, Krushkal J.

J Theor Biol. 2004 Sep 7;230(1):133-44.PMID: 15276006 [PubMed - indexed for MEDLINE]Related articles

AGenDA: gene prediction by cross-species sequence comparison.

Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W305-8.PMID: 15215399 [PubMed - indexed for MEDLINE]Related articlesFree article

Cracking the genome's second code: enhancer detection by combined phylogenetic footprinting and transgenic fish and frog embryos.

Allende ML, Manzanares M, Tena JJ, Feijóo CG, Gómez-Skarmeta JL.

Methods. 2006 Jul;39(3):212-9.PMID: 16806968 [PubMed - indexed for MEDLINE]Related articles

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

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications.

Prohaska SJ, Fried C, Flamm C, Wagner GP, Stadler PF.

Mol Phylogenet Evol. 2004 May;31(2):581-604.PMID: 15062796 [PubMed - indexed for MEDLINE]Related articles

Phylogenetic footprinting reveals evolutionarily conserved regions of the gonadotropin-releasing hormone gene that enhance cell-specific expression.

Givens ML, Kurotani R, Rave-Harel N, Miller NL, Mellon PL.

Mol Endocrinol. 2004 Dec;18(12):2950-66. Epub 2004 Aug 19.PMID: 15319450 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogenetic footprinting to find functional DNA elements.

Ganley AR, Kobayashi T.

Methods Mol Biol. 2007;395:367-80.PMID: 17993686 [PubMed - indexed for MEDLINE]Related articles

Prediction of synergistic transcription factors by function conservation.

Hu Z, Hu B, Collins JF.

Genome Biol. 2007;8(12):R257.PMID: 18053230 [PubMed - indexed for MEDLINE]Related articlesFree article

Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting.

Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, Okey AB.

Biochem Biophys Res Commun. 2004 Aug 27;321(3):707-15.PMID: 15358164 [PubMed - indexed for MEDLINE]Related articles

The identification and functional characterisation of conserved regulatory elements in developmental genes.

Dickmeis T, Müller F.

Brief Funct Genomic Proteomic. 2005 Feb;3(4):332-50. Review.PMID: 15814024 [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

Activation of CRABS CLAW in the Nectaries and Carpels of Arabidopsis.

Lee JY, Baum SF, Alvarez J, Patel A, Chitwood DH, Bowman JL.

Plant Cell. 2005 Jan;17(1):25-36. Epub 2004 Dec 14.PMID: 15598802 [PubMed - indexed for MEDLINE]Related articlesFree article