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Results: 1 to 20 of 105

1.

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.

Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.

PMID:
21993624
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.

Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M.

Genome Res. 2011 Nov;21(11):1916-28. doi: 10.1101/gr.108753.110. Epub 2011 Oct 12.

PMID:
21994248
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Distribution and intensity of constraint in mammalian genomic sequence.

Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow A.

Genome Res. 2005 Jul;15(7):901-13. Epub 2005 Jun 17.

PMID:
15965027
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.

Lowe CB, Haussler D.

PLoS One. 2012;7(8):e43128. doi: 10.1371/journal.pone.0043128. Epub 2012 Aug 27.

PMID:
22952639
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. doi: 10.1371/journal.pcbi.1001025.

PMID:
21152010
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

PMID:
17567995
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

PMID:
22955616
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.

Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A.

Genome Res. 2010 Mar;20(3):301-10. doi: 10.1101/gr.102210.109. Epub 2010 Jan 12.

PMID:
20067941
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Mammalian BEX, WEX and GASP genes: coding and non-coding chimaerism sustained by gene conversion events.

Winter EE, Ponting CP.

BMC Evol Biol. 2005 Oct 12;5:54.

PMID:
16221301
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
17201929
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

Khachane AN, Harrison PM.

BMC Genomics. 2009 Sep 15;10:435. doi: 10.1186/1471-2164-10-435.

PMID:
19754956
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Massive turnover of functional sequence in human and other mammalian genomes.

Meader S, Ponting CP, Lunter G.

Genome Res. 2010 Oct;20(10):1335-43. doi: 10.1101/gr.108795.110. Epub 2010 Aug 6.

PMID:
20693480
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.

Margulies EH, Vinson JP; NISC Comparative Sequencing Program, Miller W, Jaffe DB, Lindblad-Toh K, Chang JL, Green ED, Lander ES, Mullikin JC, Clamp M.

Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4795-800. Epub 2005 Mar 18.

PMID:
15778292
[PubMed - indexed for MEDLINE]
Free PMC Article
14.
15.

[Conserved non-coding elements in human genome].

TIAN J, ZHAO ZH, CHEN HP.

Yi Chuan. 2009 Nov;31(11):1067-76. Review. Chinese.

PMID:
19933086
[PubMed - indexed for MEDLINE]
16.

Genome-wide identification of human functional DNA using a neutral indel model.

Lunter G, Ponting CP, Hein J.

PLoS Comput Biol. 2006 Jan;2(1):e5. Epub 2006 Jan 13.

PMID:
16410828
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B.

Nucleic Acids Res. 2010 Mar;38(4):1071-85. doi: 10.1093/nar/gkp1124. Epub 2009 Dec 6.

PMID:
19969543
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Comparative genomic analysis of eutherian ribonuclease A genes.

Premzl M.

Mol Genet Genomics. 2014 Apr;289(2):161-7. doi: 10.1007/s00438-013-0801-5. Epub 2013 Dec 15.

PMID:
24337645
[PubMed - indexed for MEDLINE]
19.
20.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.

PMID:
17994088
[PubMed - indexed for MEDLINE]
Free PMC Article

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