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Items 1 - 20 of 114
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1:

cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers.

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF.

Genome Biol. 2007;8(5):R75.

PMID: 17490485 [PubMed - indexed for MEDLINE]

2:

Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers.

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF.

BMC Genomics. 2008 Aug 1;9:371.

PMID: 18673565 [PubMed - indexed for MEDLINE]

3:

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.

PMID: 18307801 [PubMed - indexed for MEDLINE]

4:

An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach.

Congdon CB, Aman JC, Nava GM, Gaskins HR, Mattingly CJ.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):1-14.

PMID: 18245871 [PubMed - indexed for MEDLINE]

5:

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA.

Genome Res. 2006 Jul;16(7):855-63. Epub 2006 Jun 12.

PMID: 16769978 [PubMed - indexed for MEDLINE]

6:

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.

Rastegar S, Hess I, Dickmeis T, Nicod JC, Ertzer R, Hadzhiev Y, Thies WG, Scherer G, Strähle U.

Dev Biol. 2008 Jun 15;318(2):366-77. Epub 2008 Apr 4.

PMID: 18455719 [PubMed - indexed for MEDLINE]

7:

Evolution of cis-regulatory sequence and function in Diptera.

Wittkopp PJ.

Heredity. 2006 Sep;97(3):139-47. Epub 2006 Jul 19. Review.

PMID: 16850038 [PubMed - indexed for MEDLINE]

8:

EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA.

Odenwald WF, Rasband W, Kuzin A, Brody T.

Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14700-5. Epub 2005 Oct 3.

PMID: 16203978 [PubMed - indexed for MEDLINE]

9:

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.

Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5. Epub 2005 Jul 5.

PMID: 15998734 [PubMed - indexed for MEDLINE]

10:

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.

Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G.

Genome Biol. 2007;8(2):R15.

PMID: 17274809 [PubMed - indexed for MEDLINE]

11:

Primate-specific evolution of an LDLR enhancer.

Wang QF, Prabhakar S, Wang Q, Moses AM, Chanan S, Brown M, Eisen MB, Cheng JF, Rubin EM, Boffelli D.

Genome Biol. 2006;7(8):R68. Epub 2006 Aug 2.

PMID: 16884525 [PubMed - indexed for MEDLINE]

12:

In vivo enhancer analysis of human conserved non-coding sequences.

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM.

Nature. 2006 Nov 23;444(7118):499-502. Epub 2006 Nov 5.

PMID: 17086198 [PubMed - indexed for MEDLINE]

13:

Locating potential enhancer elements by comparative genomics using the EEL software.

Palin K, Taipale J, Ukkonen E.

Nat Protoc. 2006;1(1):368-74.

PMID: 17406258 [PubMed - indexed for MEDLINE]

14:

Analysis of Fibroblast growth factor 15 cis-elements reveals two conserved enhancers which are closely related to cardiac outflow tract development.

Saitsu H, Shiota K, Ishibashi M.

Mech Dev. 2006 Sep;123(9):665-73. Epub 2006 Jul 15.

PMID: 16930954 [PubMed - indexed for MEDLINE]

15:

V1R promoters are well conserved and exhibit common putative regulatory motifs.

Stewart R, Lane RP.

BMC Genomics. 2007 Jul 25;8:253.

PMID: 17651493 [PubMed - indexed for MEDLINE]

16:

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F.

Genome Res. 2006 Dec;16(12):1596-604. Epub 2006 Oct 19.

PMID: 17053093 [PubMed - indexed for MEDLINE]

17:

Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer.

Grice EA, Rochelle ES, Green ED, Chakravarti A, McCallion AS.

Hum Mol Genet. 2005 Dec 15;14(24):3837-45. Epub 2005 Nov 3.

PMID: 16269442 [PubMed - indexed for MEDLINE]

18:

An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships.

Sumiyama K, Kim CB, Ruddle FH.

Genomics. 2001 Jan 15;71(2):260-2.

PMID: 11161821 [PubMed - indexed for MEDLINE]

19:

VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Visel A, Minovitsky S, Dubchak I, Pennacchio LA.

Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92. Epub 2006 Nov 27.

PMID: 17130149 [PubMed - indexed for MEDLINE]

20:

Strategies for characterising cis-regulatory elements in Xenopus.

Khokha MK, Loots GG.

Brief Funct Genomic Proteomic. 2005 May;4(1):58-68. Review.

PMID: 15975265 [PubMed - indexed for MEDLINE]

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