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Items: 1 to 20 of 94

1.

Estimates of the effect of natural selection on protein-coding content.

Yap VB, Lindsay H, Easteal S, Huttley G.

Mol Biol Evol. 2010 Mar;27(3):726-34. doi: 10.1093/molbev/msp232. Epub 2009 Oct 8.

2.

Codon-substitution models for heterogeneous selection pressure at amino acid sites.

Yang Z, Nielsen R, Goldman N, Pedersen AM.

Genetics. 2000 May;155(1):431-49.

3.

Statistical properties of the branch-site test of positive selection.

Yang Z, dos Reis M.

Mol Biol Evol. 2011 Mar;28(3):1217-28. doi: 10.1093/molbev/msq303. Epub 2010 Nov 18.

PMID:
21087944
4.

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.

5.

Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution.

Bao L, Gu H, Dunn KA, Bielawski JP.

Mol Biol Evol. 2008 Sep;25(9):1995-2007. doi: 10.1093/molbev/msn145. Epub 2008 Jun 26.

PMID:
18586695
6.

The comparative method rules! Codon volatility cannot detect positive Darwinian selection using a single genome sequence.

Dagan T, Graur D.

Mol Biol Evol. 2005 Mar;22(3):496-500. Epub 2004 Nov 3. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1158.

PMID:
15525696
7.

Differential expansion of the merozoite surface protein (msp)-7 gene family in Plasmodium species under a birth-and-death model of evolution.

Garzón-Ospina D, Cadavid LF, Patarroyo MA.

Mol Phylogenet Evol. 2010 May;55(2):399-408. doi: 10.1016/j.ympev.2010.02.017. Epub 2010 Feb 19.

PMID:
20172030
8.

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection.

Rubinstein ND, Doron-Faigenboim A, Mayrose I, Pupko T.

Mol Biol Evol. 2011 Dec;28(12):3297-308. doi: 10.1093/molbev/msr162. Epub 2011 Jun 20.

PMID:
21690564
9.

Selective pressures at a codon-level predict deleterious mutations in human disease genes.

Arbiza L, Duchi S, Montaner D, Burguet J, Pantoja-Uceda D, Pineda-Lucena A, Dopazo J, Dopazo H.

J Mol Biol. 2006 May 19;358(5):1390-404. Epub 2006 Mar 15.

PMID:
16584746
10.

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

Aris-Brosou S, Bielawski JP.

Gene. 2006 Aug 15;378:58-64. Epub 2006 May 22.

PMID:
16797879
11.

Adaptive evolution after duplication of penaeidin antimicrobial peptides.

Padhi A, Verghese B, Otta SK, Varghese B, Ramu K.

Fish Shellfish Immunol. 2007 Sep;23(3):553-66. Epub 2007 Jan 20.

PMID:
17449277
12.

Natural selection on Plasmodium surface proteins.

Hughes MK, Hughes AL.

Mol Biochem Parasitol. 1995 Apr;71(1):99-113.

PMID:
7630387
15.

Positive Darwinian selection at the pantophysin (Pan I) locus in marine gadid fishes.

Pogson GH, Mesa KA.

Mol Biol Evol. 2004 Jan;21(1):65-75. Epub 2003 Aug 29.

PMID:
12949133
16.

Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.

PMID:
15703242
17.

Uncorrected nucleotide bias in mtDNA can mimic the effects of positive Darwinian selection.

Albu M, Min XJ, Hickey D, Golding B.

Mol Biol Evol. 2008 Dec;25(12):2521-4. doi: 10.1093/molbev/msn224. Epub 2008 Oct 8.

18.

The positive correlation between dN/dS and dS in mammals is due to runs of adjacent substitutions.

Stoletzki N, Eyre-Walker A.

Mol Biol Evol. 2011 Apr;28(4):1371-80. doi: 10.1093/molbev/msq320. Epub 2010 Nov 29.

PMID:
21115654
19.

Variation in evolutionary processes at different codon positions.

Bofkin L, Goldman N.

Mol Biol Evol. 2007 Feb;24(2):513-21. Epub 2006 Nov 21.

PMID:
17119011
20.

Accelerated evolution of Fetuin-A (FETUA, also AHSG) is driven by positive Darwinian selection, not GC-biased gene conversion.

Döring Y, Zechner U, Roos C, Rosenkranz D, Zischler H, Herlyn H.

Gene. 2010 Sep 1;463(1-2):49-55. doi: 10.1016/j.gene.2010.04.018. Epub 2010 May 13.

PMID:
20471458

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