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Items: 1 to 20 of 92

1.

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A, Lee K, Dorschner M, Dermitzakis ET, Antonarakis SE, Stamatoyannopoulos JA.

Genome Biol. 2008;9(12):R168. doi: 10.1186/gb-2008-9-12-r168.

2.
3.

A map of the cis-regulatory sequences in the mouse genome.

Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B.

Nature. 2012 Aug 2;488(7409):116-20. doi: 10.1038/nature11243.

4.

Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend.

McGaughey DM, Stine ZE, Huynh JL, Vinton RM, McCallion AS.

BMC Genomics. 2009 Jan 7;10:8. doi: 10.1186/1471-2164-10-8.

5.

Conserved non-coding elements and cis regulation: actions speak louder than words.

Nelson AC, Wardle FC.

Development. 2013 Apr;140(7):1385-95. doi: 10.1242/dev.084459. Review.

6.

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.

Wang QF, Prabhakar S, Chanan S, Cheng JF, Rubin EM, Boffelli D.

Genome Biol. 2007;8(1):R1.

7.

Cis-regulation and conserved non-coding elements in amphioxus.

Beaster-Jones L.

Brief Funct Genomics. 2012 Mar;11(2):118-30. doi: 10.1093/bfgp/els006. Review.

PMID:
22402505
8.

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.

PMID:
17086198
9.

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.

10.

Conserved distances between vertebrate highly conserved elements.

Sun H, Skogerbø G, Chen R.

Hum Mol Genet. 2006 Oct 1;15(19):2911-22.

PMID:
16923797
11.

Non-coding transcription at cis-regulatory elements: computational and experimental approaches.

Simonatto M, Barozzi I, Natoli G.

Methods. 2013 Sep 1;63(1):66-75. doi: 10.1016/j.ymeth.2013.03.021.

PMID:
23542771
12.

Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences.

De Silva DR, Nichols R, Elgar G.

PLoS One. 2014 Jul 25;9(7):e103357. doi: 10.1371/journal.pone.0103357.

13.

Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes.

Punnamoottil B, Herrmann C, Pascual-Anaya J, D'Aniello S, Garcia-FernĂ ndez J, Akalin A, Becker TS, Rinkwitz S.

Dev Biol. 2010 Apr 15;340(2):269-82. doi: 10.1016/j.ydbio.2010.01.035.

14.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium..

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

15.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.

16.

Human-specific loss of regulatory DNA and the evolution of human-specific traits.

McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM.

Nature. 2011 Mar 10;471(7337):216-9. doi: 10.1038/nature09774.

17.

Ancient noncoding elements conserved in the human genome.

Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S.

Science. 2006 Dec 22;314(5807):1892. Erratum in: Science. 2007 Feb 9;315(5813):766.

18.
19.

Divergence of conserved non-coding sequences: rate estimates and relative rate tests.

Wagner GP, Fried C, Prohaska SJ, Stadler PF.

Mol Biol Evol. 2004 Nov;21(11):2116-21.

PMID:
15282332
20.

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.

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