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Large-scale discovery and validation of functional elements in the human genome.

Bernstein BE, Kellis M.

Genome Biol. 2005;6(3):312. Epub 2005 Mar 1.PMID: 15774039 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational identification of transcriptional regulatory elements in DNA sequence.

GuhaThakurta D.

Nucleic Acids Res. 2006 Jul 19;34(12):3585-98. Print 2006. Review.PMID: 16855295 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating sequence, evolution and functional genomics in regulatory genomics.

Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.

Genome Biol. 2009;10(1):202. Epub 2009 Jan 30. Review.PMID: 19226437 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis.

Loots GG.

Adv Genet. 2008;61:269-93. Review.PMID: 18282510 [PubMed - indexed for MEDLINE]Related articles

Identifying pattern-defined regulatory islands in mammalian genomes.

Cheung TH, Barthel KK, Kwan YL, Liu X.

Proc Natl Acad Sci U S A. 2007 Jun 12;104(24):10116-21. Epub 2007 May 29.PMID: 17535887 [PubMed - indexed for MEDLINE]Related articlesFree article

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

Young JA, Johnson JR, Benner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA.

BMC Genomics. 2008 Feb 7;9:70.PMID: 18257930 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome.

Wang T, Stormo GD.

Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17400-5. Epub 2005 Nov 21.PMID: 16301543 [PubMed - indexed for MEDLINE]Related articlesFree article

CoMoDis: composite motif discovery in mammalian genomes.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2007;35(1):e1. Epub 2006 Nov 27.PMID: 17130158 [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

Computational method for discovery of estrogen responsive genes.

Tang S, Tan SL, Ramadoss SK, Kumar AP, Tang MH, Bajic VB.

Nucleic Acids Res. 2004 Dec 1;32(21):6212-7. Print 2004.PMID: 15576347 [PubMed - indexed for MEDLINE]Related articlesFree article

TFBScluster web server for the identification of mammalian composite regulatory elements.

Donaldson IJ, Göttgens B.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W524-8.PMID: 16845063 [PubMed - indexed for MEDLINE]Related articlesFree article

Systematic identification of mammalian regulatory motifs' target genes and functions.

Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. Epub 2008 Mar 2.PMID: 18311145 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of muscle-specific regulatory modules in Caenorhabditis elegans.

Zhao G, Schriefer LA, Stormo GD.

Genome Res. 2007 Mar;17(3):348-57. Epub 2007 Feb 6.PMID: 17284674 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop.

Brazma A, Freeman T, Gardiner K, Weissman S, Werner T, Korn B.

Cytogenet Genome Res. 2004;105(1):11-7. No abstract available. PMID: 15218252 [PubMed - indexed for MEDLINE]Related articles

Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.

Linhart C, Elkon R, Shiloh Y, Shamir R.

Cell Cycle. 2005 Dec;4(12):1788-97. Epub 2005 Dec 13.PMID: 16294034 [PubMed - indexed for MEDLINE]Related articlesFree article

A primer on regression methods for decoding cis-regulatory logic.

Das D, Pellegrini M, Gray JW.

PLoS Comput Biol. 2009 Jan;5(1):e1000269. Epub 2009 Jan 30. No abstract available. PMID: 19180174 [PubMed - indexed for MEDLINE]Related articlesFree article

Unravelling the world of cis-regulatory elements.

Wang Z, Wei GH, Liu DP, Liang CC.

Med Biol Eng Comput. 2007 Aug;45(8):709-18. Epub 2007 May 31. Review.PMID: 17541666 [PubMed - indexed for MEDLINE]Related articles

Methods for identification of epigenetic elements in mammalian long multigenic genome sequences.

Akopov SB, Chernov IP, Bulanenkova SS, Skvortsova YV, Vetchinova AS, Nikolaev LG.

Biochemistry (Mosc). 2007 Jun;72(6):589-94. Review.PMID: 17630903 [PubMed - indexed for MEDLINE]Related articles