Lineage-specific differences in the amino acid substitution process.

[1]  A. Elofsson,et al.  Structure is three to ten times more conserved than sequence—A study of structural response in protein cores , 2009, Proteins.

[2]  Tong Zhou,et al.  Detecting Clusters of Mutations , 2008, PloS one.

[3]  Sergei Maslov,et al.  Constraints imposed by non-functional protein–protein interactions on gene expression and proteome size , 2008, Molecular systems biology.

[4]  Claus O. Wilke,et al.  Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution , 2008, Cell.

[5]  Nicolas Lartillot,et al.  A site- and time-heterogeneous model of amino acid replacement. , 2008, Molecular biology and evolution.

[6]  Timothy Hughes,et al.  The Pattern of Evolution of Smaller-Scale Gene Duplicates in Mammalian Genomes is More Consistent with Neo- than Subfunctionalisation , 2007, Journal of Molecular Evolution.

[7]  Hirohisa Kishino,et al.  Population genetics without intraspecific data. , 2007, Molecular biology and evolution.

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

[9]  Cyrus Chothia,et al.  The selection of acceptable protein mutations , 2007, Proceedings of the National Academy of Sciences.

[10]  Ryan D. Hernandez,et al.  Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques , 2007, Science.

[11]  John Parsch,et al.  INAUGURAL ARTICLE by a Recently Elected Academy Member:Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila , 2007 .

[12]  Wei-Lun Hsu,et al.  Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. , 2007, Molecular biology and evolution.

[13]  Jingchu Luo,et al.  Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. , 2007, Molecular biology and evolution.

[14]  B. Charlesworth,et al.  Background Selection in Single Genes May Explain Patterns of Codon Bias , 2007, Genetics.

[15]  D. Liberles,et al.  A systematic search for positive selection in higher plants (Embryophytes) , 2006, BMC Plant Biology.

[16]  Eugene Shakhnovich,et al.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. , 2006, Chemical reviews.

[17]  C. Wilke,et al.  A single determinant dominates the rate of yeast protein evolution. , 2006, Molecular biology and evolution.

[18]  J. Thorne,et al.  Testing for Spatial Clustering of Amino Acid Replacements Within Protein Tertiary Structure , 2006, Journal of Molecular Evolution.

[19]  Masatoshi Nei,et al.  Selectionism and neutralism in molecular evolution. , 2005, Molecular biology and evolution.

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

[21]  Shamil Sunyaev,et al.  Small fitness effect of mutations in highly conserved non-coding regions. , 2005, Human molecular genetics.

[22]  C. Wilke,et al.  Why highly expressed proteins evolve slowly. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Andreas Wagner,et al.  Energy constraints on the evolution of gene expression. , 2005, Molecular biology and evolution.

[24]  D. Liberles,et al.  Subfunctionalization of duplicated genes as a transition state to neofunctionalization , 2005, BMC Evolutionary Biology.

[25]  Jianzhi Zhang,et al.  Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution , 2005, Genetics.

[26]  Matthew J. Betts,et al.  The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics , 2004, Nucleic Acids Res..

[27]  Emile Zuckerkandl,et al.  Evolutionary processes and evolutionary noise at the molecular level , 1976, Journal of Molecular Evolution.

[28]  Arne Elofsson,et al.  Tertiary Windowing to Detect Positive Diversifying Selection , 2005, Journal of Molecular Evolution.

[29]  Stéphane Guindon,et al.  Modeling the site-specific variation of selection patterns along lineages. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[31]  Hirohisa Kishino,et al.  Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. , 2004, Molecular biology and evolution.

[32]  M. Lynch,et al.  The Origins of Genome Complexity , 2003, Science.

[33]  Ziheng Yang,et al.  Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. , 2003, Molecular biology and evolution.

[34]  Daniel J. Gaffney,et al.  Quantifying the slightly deleterious mutation model of molecular evolution. , 2002, Molecular biology and evolution.

[35]  Bradley P. Carlin,et al.  Bayesian measures of model complexity and fit , 2002 .

[36]  H. Philippe,et al.  Heterotachy, an important process of protein evolution. , 2002, Molecular biology and evolution.

[37]  D. M. Taverna,et al.  Why are proteins marginally stable? , 2002, Proteins.

[38]  M. Hammer,et al.  High levels of Y-chromosome nucleotide diversity in the genus Pan , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[39]  E. Shakhnovich,et al.  Understanding hierarchical protein evolution from first principles. , 2001, Journal of molecular biology.

[40]  X. Gu,et al.  Maximum-likelihood approach for gene family evolution under functional divergence. , 2001, Molecular biology and evolution.

[41]  D. Weinreich.  The Rates of Molecular Evolution in Rodent and Primate Mitochondrial DNA , 2001, Journal of Molecular Evolution.

[42]  Andrew Thomas,et al.  WinBUGS - A Bayesian modelling framework: Concepts, structure, and extensibility , 2000, Stat. Comput..

[43]  C Chothia,et al.  Conservation of folding and stability within a protein family: the tyrosine corner as an evolutionary cul-de-sac. , 2000, Journal of molecular biology.

[44]  L. Duret,et al.  Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. , 2000, Molecular biology and evolution.

[45]  Jianzhi Zhang,et al.  Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes , 2000, Journal of Molecular Evolution.

[46]  M. Nachman.  Y chromosome variation of mice and men. , 1998, Molecular biology and evolution.

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

[48]  M. Levitt,et al.  A structural census of the current population of protein sequences. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[49]  E. Nevo,et al.  Selection versus random drift: long–term polymorphism persistence in small populations (evidence and modelling) , 1997 .

[50]  O. Berg,et al.  Selection intensity for codon bias and the effective population size of Escherichia coli. , 1996, Genetics.

[51]  J. Klein,et al.  Divergence time and population size in the lineage leading to modern humans. , 1995, Theoretical population biology.

[52]  R A Goldstein,et al.  Context-dependent optimal substitution matrices. , 1995, Protein engineering.

[53]  T. Ohta,et al.  Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. , 1995, Journal of molecular evolution.

[54]  S A Benner,et al.  Amino acid substitution during functionally constrained divergent evolution of protein sequences. , 1994, Protein engineering.

[55]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[56]  M. Nei,et al.  Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. , 1990, Molecular biology and evolution.

[57]  R. Grantham.  Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[58]  M. Kimura,et al.  On the probability of fixation of mutant genes in a population. , 1962, Genetics.