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Items: 1 to 20 of 72

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Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates.

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T.

Bioinformatics. 2007 Jul 1;23(13):i319-27.

PMID:
17646313
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.

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins.

Seo TK, Kishino H.

Syst Biol. 2008 Jun;57(3):367-77. doi: 10.1080/10635150802158670.

PMID:
18570032
6.

Lost in translation: implications of HIV-1 codon usage for immune escape and drug resistance.

Kijak GH, Currier JR, Tovanabutra S, Cox JH, Michael NL, Wegner SA, Birx DL, McCutchan FE.

AIDS Rev. 2004 Jan-Mar;6(1):54-60. Review.

PMID:
15168741
7.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

8.

Analysis of discrepancies in the interpretation of antiretroviral drug resistance results in HIV-1 infected patients of Basque Country, Spain.

Muñoz M, Carmona R, Pérez-Alvarez L, Cilla G, Suarez MD, Delgado E, Contreras G, Corral J, de Goicoetxea MJ, Medrano L, Lezaún MJ, Nájera R; Spanish Group for Antiretroviral Resistance Studies in Basque Country.

J Clin Virol. 2005 Jul;33(3):224-9. Epub 2005 Jan 12.

PMID:
15911444
9.

Correlated evolution of nucleotide substitution rates and allelic variation in Mhc-DRB lineages of primates.

Garamszegi LZ, de Groot NG, Bontrop RE.

BMC Evol Biol. 2009 Apr 12;9:73. doi: 10.1186/1471-2148-9-73.

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.

SynPAM-a distance measure based on synonymous codon substitutions.

Schneider A, Gonnet G, Cannarozzi G.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):553-60.

PMID:
17975267
12.

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome.

Song J, Wang M, Burrage K.

J Theor Biol. 2006 Jul 21;241(2):390-401. Epub 2006 Jan 19.

PMID:
16427089
14.

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
16.

ADAPTSITE: detecting natural selection at single amino acid sites.

Suzuki Y, Gojobori T, Nei M.

Bioinformatics. 2001 Jul;17(7):660-1.

PMID:
11448887
17.

Synonymous substitution rates in enterobacteria.

Eyre-Walker A, Bulmer M.

Genetics. 1995 Aug;140(4):1407-12.

18.
19.

Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions.

Tzeng YH, Pan R, Li WH.

Mol Biol Evol. 2004 Dec;21(12):2290-8. Epub 2004 Aug 25.

PMID:
15329386
20.

A codon model of nucleotide substitution with selection on synonymous codon usage.

Kubatko L, Shah P, Herbei R, Gilchrist MA.

Mol Phylogenet Evol. 2016 Jan;94(Pt A):290-7. doi: 10.1016/j.ympev.2015.08.026. Epub 2015 Sep 8.

PMID:
26358614

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