The Relationship between dN/dS and Scaled Selection Coefficients

A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data

(2014) Asif U. Tamuri et al.   GENETICS

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

(2014) Slavica Dimitrieva et al.   PLoS One

Precise estimates of mutation rate and spectrum in yeast

(2014) Y. O. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

(2013) N. Rodrigue et al.   BIOINFORMATICS

On the Need for Mechanistic Models in Computational Genomics and Metagenomics

(2013) David A. Liberles et al.   Genome Biology and Evolution

Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution

(2013) F. Zanini et al.   JOURNAL OF VIROLOGY

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

(2013) A. G. Meyer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

Modeling coding-sequence evolution within the context of residue solvent accessibility

(2012) Michael P Scherrer et al.   BMC EVOLUTIONARY BIOLOGY

Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants

(2012) Wanjun Gu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Expression Levels Are Correlated with Synonymous Codon Usage, Amino Acid Composition, and Gene Architecture in the Red Flour Beetle, Tribolium castaneum

(2012) Anna Williford et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

(2012) Austin G. Meyer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme

(2012) Deepa Agashe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses

(2011) Tong Zhou et al.   BMC EVOLUTIONARY BIOLOGY

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Evolutionary Models Accounting for Layers of Selection in Protein-Coding Genes and their Impact on the Inference of Positive Selection

(2011) N. D. Rubinstein et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

(2011) José M. Cuevas et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus

(2011) Samir Bhatt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm

(2010) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Detecting positive selection within genomes: the problem of biased gene conversion

(2010) A. Ratnakumar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

(2010) Sergei Kosakovsky Pond et al.   PLoS One

Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

(2010) N. Rodrigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

(2010) Wanjun Gu et al.   PLoS Computational Biology

Estimates of the Effect of Natural Selection on Protein-Coding Content

(2009) V. B. Yap et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computational Methods for Evaluating Phylogenetic Models of Coding Sequence Evolution with Dependence between Codons

(2009) N. Rodrigue et al.   MOLECULAR BIOLOGY AND EVOLUTION

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation

(2009) Ville Mustonen et al.   TRENDS IN GENETICS

Selection on Codon Bias

(2008) Ruth Hershberg et al.   Annual Review of Genetics

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Bayesian Comparisons of Codon Substitution Models

(2008) Nicolas Rodrigue et al.   GENETICS

Spatial and Temporal Heterogeneity in Nucleotide Sequence Evolution

(2008) S. Whelan   MOLECULAR BIOLOGY AND EVOLUTION

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

(2008) M. T Holder et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics