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Results: 1 to 20 of 99

1.

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
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.

PMID:
15965027
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
4.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

PMID:
19478016
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

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

PMID:
19858363
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Local conservation scores without a priori assumptions on neutral substitution rates.

Dingel J, Hanus P, Leonardi N, Hagenauer J, Zech J, Mueller JC.

BMC Bioinformatics. 2008 Apr 11;9:190. doi: 10.1186/1471-2105-9-190.

PMID:
18405366
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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

Cooper GM, Singaravelu SA, Sidow A.

BMC Bioinformatics. 2004 Dec 8;5:192.

PMID:
15588288
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

PMID:
15804354
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
18166073
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

MotifMap: a human genome-wide map of candidate regulatory motif sites.

Xie X, Rigor P, Baldi P.

Bioinformatics. 2009 Jan 15;25(2):167-74. doi: 10.1093/bioinformatics/btn605. Epub 2008 Nov 18.

PMID:
19017655
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
15590941
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Accurate anchoring alignment of divergent sequences.

Huang W, Umbach DM, Li L.

Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13.

PMID:
16301203
[PubMed - indexed for MEDLINE]
Free Article
15.

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC.

Genome Res. 2005 Aug;15(8):1051-60. Epub 2005 Jul 15.

PMID:
16024817
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

PMID:
15655071
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Genome-wide nucleotide-level mammalian ancestor reconstruction.

Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.

Genome Res. 2008 Nov;18(11):1829-43. doi: 10.1101/gr.076521.108. Epub 2008 Oct 10.

PMID:
18849525
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MuSiC: a tool for multiple sequence alignment with constraints.

Tsai YT, Huang YP, Yu CT, Lu CL.

Bioinformatics. 2004 Sep 22;20(14):2309-11. Epub 2004 Apr 1.

PMID:
15059840
[PubMed - indexed for MEDLINE]
Free Article
19.

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.

Margulies EH, Birney E.

Nat Rev Genet. 2008 Apr;9(4):303-13. doi: 10.1038/nrg2185. Review.

PMID:
18347593
[PubMed - indexed for MEDLINE]
20.

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

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