Epistasis not needed to explain low dN/dS

[1]  Michael S. Breen,et al.  Epistasis as the primary factor in molecular evolution , 2012, Nature.

[2]  Richard A. Goldstein,et al.  Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models , 2012, Genetics.

[3]  Dan S. Tawfik,et al.  Initial Mutations Direct Alternative Pathways of Protein Evolution , 2011, PLoS genetics.

[4]  J. Dushoff,et al.  Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins , 2011, PLoS genetics.

[5]  D. Baker,et al.  High Resolution Mapping of Protein Sequence–Function Relationships , 2010, Nature Methods.

[6]  Fyodor A. Kondrashov,et al.  Sequence space and the ongoing expansion of the protein universe , 2010, Nature.

[7]  Hervé Philippe,et al.  Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles , 2010, Proceedings of the National Academy of Sciences.

[8]  A. Kondrashov,et al.  Rate of sequence divergence under constant selection , 2010, Biology Direct.

[9]  R. Nielsen,et al.  Synonymous and nonsynonymous rate variation in nuclear genes of mammals , 1998, Journal of Molecular Evolution.

[10]  J. Thorne,et al.  Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[11]  M. Kimura.  The role of compensatory neutral mutations in molecular evolution , 1985, Journal of Genetics.

[12]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[13]  J. Silva.  Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1. , 2006 .

[14]  Aleksey Y Ogurtsov,et al.  Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. , 2006, Journal of theoretical biology.

[15]  J. Silva.  Site-Specific Amino Acid Frequency, Fitness, and the Mutational Landscape Model of Adaptation in HIV-1 , 2006 .

[16]  M. DePristo,et al.  Missense meanderings in sequence space: a biophysical view of protein evolution , 2005, Nature Reviews Genetics.

[17]  S. Sunyaev,et al.  Dobzhansky–Muller incompatibilities in protein evolution , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  A. Kondrashov,et al.  Multidimensional epistasis and the disadvantage of sex , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[19]  G. Wagner,et al.  Modeling genetic architecture: a multilinear theory of gene interaction. , 2001, Theoretical population biology.

[20]  Gilean McVean,et al.  A population genetic model for the evolution of synonymous codon usage: patterns and predictions , 1999 .

[21]  A. Halpern,et al.  Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. , 1998, Molecular biology and evolution.

[22]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..