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Items: 1 to 20 of 102

1.

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.

2.

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.

3.

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.

4.

8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.

Rands CM, Meader S, Ponting CP, Lunter G.

PLoS Genet. 2014 Jul 24;10(7):e1004525. doi: 10.1371/journal.pgen.1004525. eCollection 2014 Jul.

5.

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.

6.

Detection of nonneutral substitution rates on mammalian phylogenies.

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.

Genome Res. 2010 Jan;20(1):110-21. doi: 10.1101/gr.097857.109. Epub 2009 Oct 26.

7.

Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters.

Hardison R, Miller W.

Mol Biol Evol. 1993 Jan;10(1):73-102. Review.

PMID:
8383794
8.

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.

9.

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

Stone EA, Cooper GM, Sidow A.

Annu Rev Genomics Hum Genet. 2005;6:143-64. Review.

PMID:
16124857
10.

FRESCo: finding regions of excess synonymous constraint in diverse viruses.

Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC.

Genome Biol. 2015 Feb 17;16:38. doi: 10.1186/s13059-015-0603-7.

11.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

12.

Evolutionary constraint in flanking regions of avian genes.

Künstner A, Nabholz B, Ellegren H.

Mol Biol Evol. 2011 Sep;28(9):2481-9. doi: 10.1093/molbev/msr066. Epub 2011 Apr 4.

PMID:
21393603
13.

ABC: software for interactive browsing of genomic multiple sequence alignment data.

Cooper GM, Singaravelu SA, Sidow A.

BMC Bioinformatics. 2004 Dec 8;5:192.

14.
15.

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.

16.

CEGA--a catalog of conserved elements from genomic alignments.

Dousse A, Junier T, Zdobnov EM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D96-100. doi: 10.1093/nar/gkv1163. Epub 2015 Nov 2.

17.

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.

18.

Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes.

Eory L, Halligan DL, Keightley PD.

Mol Biol Evol. 2010 Jan;27(1):177-92. doi: 10.1093/molbev/msp219.

PMID:
19759235
19.

Computation and analysis of genomic multi-sequence alignments.

Blanchette M.

Annu Rev Genomics Hum Genet. 2007;8:193-213. Review.

PMID:
17489682
20.

AuberGene--a sensitive genome alignment tool.

Szklarczyk R, Heringa J.

Bioinformatics. 2006 Jun 15;22(12):1431-6. Epub 2006 Apr 10.

PMID:
16606686

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