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Items: 1 to 20 of 70

1.

Identification and characterization of multi-species conserved sequences.

Margulies EH, Blanchette M; NISC Comparative Sequencing Program., Haussler D, Green ED.

Genome Res. 2003 Dec;13(12):2507-18.

2.

Enrichment of regulatory signals in conserved non-coding genomic sequence.

Levy S, Hannenhalli S, Workman C.

Bioinformatics. 2001 Oct;17(10):871-7.

PMID:
11673231
3.

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. Epub 2004 Feb 12.

4.

Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer.

Portnoy ME, McDermott KJ, Antonellis A, Margulies EH, Prasad AB; NISC Comparative Sequencing Program., Kingsley DM, Green ED, Mortlock DP.

Genomics. 2005 Sep;86(3):295-305.

PMID:
15979840
5.
6.

Genome-wide identification of coding and non-coding conserved sequence tags in human and mouse genomes.

Mignone F, Anselmo A, Donvito G, Maggi GP, Grillo G, Pesole G.

BMC Genomics. 2008 Jun 11;9:277. doi: 10.1186/1471-2164-9-277.

7.

Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences.

Sironi M, Menozzi G, Comi GP, Cagliani R, Bresolin N, Pozzoli U.

Hum Mol Genet. 2005 Sep 1;14(17):2533-46. Epub 2005 Jul 21.

PMID:
16037065
8.

Identification of transcription factor binding sites in the human genome sequence.

Levy S, Hannenhalli S.

Mamm Genome. 2002 Sep;13(9):510-4.

PMID:
12370781
9.

Comparative genomic analysis of vertebrate Hox3 and Hox4 genes.

Hadrys T, Prince V, Hunter M, Baker R, Rinkwitz S.

J Exp Zool B Mol Dev Evol. 2004 Mar 15;302(2):147-64.

PMID:
15054858
10.

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
11.

Identification of estrogen-responsive genes using a genome-wide analysis of promoter elements for transcription factor binding sites.

Kamalakaran S, Radhakrishnan SK, Beck WT.

J Biol Chem. 2005 Jun 3;280(22):21491-7. Epub 2005 Mar 24.

12.

Identification and characterization of new long conserved noncoding sequences in vertebrates.

Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi KR, Toyoda A, Fukumura R, Murata T, Sakaki Y, Yamamura M, Wakana S, Noda T, Shiroishi T, Gondo Y.

Mamm Genome. 2008 Oct-Dec;19(10-12):703-12. doi: 10.1007/s00335-008-9152-7. Epub 2008 Nov 18.

PMID:
19015917
13.

SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approach.

McCauley JL, Kenealy SJ, Margulies EH, Schnetz-Boutaud N, Gregory SG, Hauser SL, Oksenberg JR, Pericak-Vance MA, Haines JL, Mortlock DP.

BMC Genomics. 2007 Aug 6;8:266.

14.

Exploring transcription factor binding properties of several non-coding DNA sequence elements in the human NF-IL6 gene.

Pares-Matos EI, Milligan JS, Bina M.

J Mol Biol. 2006 Mar 31;357(3):732-47. Epub 2006 Jan 6.

PMID:
16458921
15.

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. Epub 2007 Nov 14.

16.

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.

Washietl S, Hofacker IL, Lukasser M, Hüttenhofer A, Stadler PF.

Nat Biotechnol. 2005 Nov;23(11):1383-90.

PMID:
16273071
17.

Ultraconserved elements in the human genome.

Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D.

Science. 2004 May 28;304(5675):1321-5. Epub 2004 May 6.

19.

Into the heart of darkness: large-scale clustering of human non-coding DNA.

Bejerano G, Haussler D, Blanchette M.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i40-8.

PMID:
15262779
20.

Biocomputational prediction of non-coding RNAs in model cyanobacteria.

Voss B, Georg J, Schön V, Ude S, Hess WR.

BMC Genomics. 2009 Mar 23;10:123. doi: 10.1186/1471-2164-10-123.

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