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Results: 1 to 20 of 55

1.

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

Elemento O, Tavazoie S.

Genome Biol. 2005;6(2):R18. Epub 2005 Jan 26.

PMID:
15693947
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Discovery of regulatory elements in vertebrates through comparative genomics.

Prakash A, Tompa M.

Nat Biotechnol. 2005 Oct;23(10):1249-56.

PMID:
16211068
[PubMed - indexed for MEDLINE]
3.

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements.

Venkatesh B, Yap WH.

Bioessays. 2005 Jan;27(1):100-7. Review.

PMID:
15612032
[PubMed - indexed for MEDLINE]
4.

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]
5.

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.

Yavatkar AS, Lin Y, Ross J, Fann Y, Brody T, Odenwald WF.

BMC Genomics. 2008 Feb 28;9:106. doi: 10.1186/1471-2164-9-106.

PMID:
18307801
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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]
Free PMC Article
7.

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.

PMID:
16716228
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S.

Genome Res. 2004 Mar;14(3):451-8.

PMID:
14993210
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.

Elemento O, Tavazoie S.

Methods Mol Biol. 2007;395:349-66.

PMID:
17993685
[PubMed - indexed for MEDLINE]
10.

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.

Sosinsky A, Honig B, Mann RS, Califano A.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10. Epub 2007 Mar 29.

PMID:
17395715
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D.

Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.

PMID:
16024819
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs.

Jegga AG, Chen J, Gowrisankar S, Deshmukh MA, Gudivada R, Kong S, Kaimal V, Aronow BJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D116-21. Epub 2006 Dec 18.

PMID:
17178752
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

PMID:
19478016
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.

Hazelett DJ, Lakeland DL, Weiss JB.

Bioinformatics. 2009 Jul 1;25(13):1617-24. doi: 10.1093/bioinformatics/btp282. Epub 2009 Apr 28.

PMID:
19401399
[PubMed - indexed for MEDLINE]
Free PMC Article
15.
16.

Annotating non-coding regions of the genome.

Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB.

Nat Rev Genet. 2010 Aug;11(8):559-71. doi: 10.1038/nrg2814. Epub 2010 Jul 13. Review.

PMID:
20628352
[PubMed - indexed for MEDLINE]
17.

Comparative genomic analysis of allatostatin-encoding (Ast) genes in Drosophila species and prediction of regulatory elements by phylogenetic footprinting.

Bowser PR, Tobe SS.

Peptides. 2007 Jan;28(1):83-93. Epub 2006 Dec 15.

PMID:
17175069
[PubMed - indexed for MEDLINE]
18.

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]
Free PMC Article
19.

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops.

Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH.

Plant Physiol. 2006 Apr;140(4):1183-91.

PMID:
16607031
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

jPREdictor: a versatile tool for the prediction of cis-regulatory elements.

Fiedler T, Rehmsmeier M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W546-50.

PMID:
16845067
[PubMed - indexed for MEDLINE]
Free PMC Article

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