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Items: 1 to 20 of 194

1.

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.

2.

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.

3.

Detecting overlapping coding sequences in virus genomes.

Firth AE, Brown CM.

BMC Bioinformatics. 2006 Feb 16;7:75.

4.

Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

Lin Z, Ma H, Nei M.

BMC Evol Biol. 2008 Sep 24;8:260. doi: 10.1186/1471-2148-8-260.

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.

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.

Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C.

Virol J. 2008 Dec 23;5:160. doi: 10.1186/1743-422X-5-160. Review.

7.

Exploration for functional nucleotide sequence candidates within coding regions of mammalian genes.

Suzuki R, Saitou N.

DNA Res. 2011 Jun;18(3):177-87. doi: 10.1093/dnares/dsr010. Epub 2011 May 17.

8.

Synonymous site conservation in the HIV-1 genome.

Mayrose I, Stern A, Burdelova EO, Sabo Y, Laham-Karam N, Zamostiano R, Bacharach E, Pupko T.

BMC Evol Biol. 2013 Aug 4;13:164. doi: 10.1186/1471-2148-13-164.

9.

Overlapping codes within protein-coding sequences.

Itzkovitz S, Hodis E, Segal E.

Genome Res. 2010 Nov;20(11):1582-9. doi: 10.1101/gr.105072.110. Epub 2010 Sep 14.

10.
11.

Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids.

Findeiss S, Engelhardt J, Prohaska SJ, Stadler PF.

Biochimie. 2011 Nov;93(11):2019-23. doi: 10.1016/j.biochi.2011.07.023. Epub 2011 Jul 31.

PMID:
21835221
12.

New tools to analyze overlapping coding regions.

Bayegan AH, Garcia-Martin JA, Clote P.

BMC Bioinformatics. 2016 Dec 13;17(1):530.

13.
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15.

Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

Conceição IC, Long AD, Gruber JD, Beldade P.

PLoS One. 2011;6(8):e23778. doi: 10.1371/journal.pone.0023778. Epub 2011 Aug 31.

16.

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.

17.

A first look at ARFome: dual-coding genes in mammalian genomes.

Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A.

PLoS Comput Biol. 2007 May;3(5):e91.

18.

Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes.

Du J, Dungan SZ, Sabouhanian A, Chang BS.

BMC Evol Biol. 2014 May 3;14:96. doi: 10.1186/1471-2148-14-96.

19.

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. eCollection 2014.

20.

Regions of extreme synonymous codon selection in mammalian genes.

Schattner P, Diekhans M.

Nucleic Acids Res. 2006 Mar 23;34(6):1700-10. Print 2006.

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