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Items: 1 to 20 of 218

1.

Bioinformatics for the 'bench biologist': how to find regulatory regions in genomic DNA.

Nardone J, Lee DU, Ansel KM, Rao A.

Nat Immunol. 2004 Aug;5(8):768-74. Review.

PMID:
15282556
2.
3.

Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.

Meireles-Filho AC, Stark A.

Curr Opin Genet Dev. 2009 Dec;19(6):565-70. doi: 10.1016/j.gde.2009.10.006. Review.

PMID:
19913403
4.

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

5.

Discovery of regulatory elements in vertebrates through comparative genomics.

Prakash A, Tompa M.

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

PMID:
16211068
6.

Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.

Frazer KA, Tao H, Osoegawa K, de Jong PJ, Chen X, Doherty MF, Cox DR.

Genome Res. 2004 Mar;14(3):367-72.

7.

A multistep bioinformatic approach detects putative regulatory elements in gene promoters.

Bortoluzzi S, Coppe A, Bisognin A, Pizzi C, Danieli GA.

BMC Bioinformatics. 2005 May 18;6:121.

8.

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
9.

Numerous potentially functional but non-genic conserved sequences on human chromosome 21.

Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, Deutsch S, Stevenson BJ, Flegel V, Bucher P, Jongeneel CV, Antonarakis SE.

Nature. 2002 Dec 5;420(6915):578-82.

PMID:
12466853
10.

Comparative genomics: a tool to functionally annotate human DNA.

Cheng JF, Priest JR, Pennacchio LA.

Methods Mol Biol. 2007;366:229-51.

PMID:
17568128
11.

Dissecting the transcription networks of a cell using computational genomics.

Li H, Wang W.

Curr Opin Genet Dev. 2003 Dec;13(6):611-6. Review.

PMID:
14638323
12.

New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences.

Gómez-Skarmeta JL, Lenhard B, Becker TS.

Dev Dyn. 2006 Apr;235(4):870-85. Review.

13.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Brown CT, Xie Y, Davidson EH, Cameron RA.

BMC Bioinformatics. 2005 Mar 24;6:70.

14.

PLATCOM: a Platform for Computational Comparative Genomics.

Choi K, Ma Y, Choi JH, Kim S.

Bioinformatics. 2005 May 15;21(10):2514-6.

PMID:
15731206
15.

Evidence for turnover of functional noncoding DNA in mammalian genome evolution.

Smith NG, Brandström M, Ellegren H.

Genomics. 2004 Nov;84(5):806-13.

PMID:
15475259
16.

Comparative analyses of multi-species sequences from targeted genomic regions.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED.

Nature. 2003 Aug 14;424(6950):788-93.

PMID:
12917688
17.

Genomic regions with distinct genomic distance conservation in vertebrate genomes.

Sun H, Skogerbø G, Zheng X, Liu W, Li Y.

BMC Genomics. 2009 Mar 27;10:133. doi: 10.1186/1471-2164-10-133.

18.

Functional and bioinformatics analyses reveal conservation of cis-regulatory elements between sciaridae and drosophilidae.

Lecci MS, Malta TM, Flausino VT, Gitaí DL, Ruiz JC, Monesi N.

Genesis. 2008 Jan;46(1):43-51. doi: 10.1002/dvg.20364.

PMID:
18196600
19.

Analysis of sequence conservation at nucleotide resolution.

Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.

PLoS Comput Biol. 2007 Dec;3(12):e254. doi: 10.1371/journal.pcbi.0030254.

20.

Computational approaches to finding and analyzing cis-regulatory elements.

Brown CT.

Methods Cell Biol. 2008;87:337-65. doi: 10.1016/S0091-679X(08)00218-5. Review.

PMID:
18485306
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