Effective population size does not predict codon usage bias in mammals

Evidence that Natural Selection on Codon Usage in Drosophila pseudoobscura Varies Across Codons

(2014) Richard M. Kliman   G3-Genes Genomes Genetics

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding

(2014) Jian-Rong Yang et al.   PLOS BIOLOGY

Stabilizing Selection, Purifying Selection, and Mutational Bias in Finite Populations

(2013) Brian Charlesworth   GENETICS

Faster-X Adaptive Protein Evolution in House Mice

(2013) Athanasios Kousathanas et al.   GENETICS

Evolution of Codon Usage in the Smallest Photosynthetic Eukaryotes and Their Giant Viruses

(2013) Stephanie Michely et al.   Genome Biology and Evolution

Translational Selection Frequently Overcomes Genetic Drift in Shaping Synonymous Codon Usage Patterns in Vertebrates

(2013) Aoife Doherty et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

(2013) S. A. Shabalina et al.   NUCLEIC ACIDS RESEARCH

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus

(2013) Kord M. Kober et al.   G3-Genes Genomes Genetics

Strong Purifying Selection at Synonymous Sites in D. melanogaster

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

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

(2012) Susanta K. Behura et al.   BIOLOGICAL REVIEWS

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

(2012) Zhang Zhang et al.   BMC BIOINFORMATICS

The Effect of Variation in the Effective Population Size on the Rate of Adaptive Molecular Evolution in Eukaryotes

(2012) Toni I. Gossmann et al.   Genome Biology and Evolution

Adaptive Evolution and Effective Population Size in Wild House Mice

(2012) M. Phifer-Rixey et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved Implementation of Effective Number of Codons (Nc)

(2012) X. Sun 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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Contributions of Speed and Accuracy to Translational Selection in Bacteria

(2012) Wenqi Ran et al.   PLoS One

Speeding with control: codon usage, tRNAs, and ribosomes

(2012) Eva Maria Novoa et al.   TRENDS IN GENETICS

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast

(2011) Nina Stoletzki   BMC EVOLUTIONARY BIOLOGY

Mutation Bias is the Driving Force of Codon Usage in the Gallus gallus genome

(2011) Y. Rao et al.   DNA RESEARCH

Selection for Translation Efficiency on Synonymous Polymorphisms in Recent Human Evolution

(2011) Yedael Y. Waldman et al.   Genome Biology and Evolution

Characterizing the Influence of Effective Population Size on the Rate of Adaptation: Gillespie’s Darwin Domain

(2011) Jeffrey D. Jensen et al.   Genome Biology and Evolution

Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species

(2011) Suo Qiu et al.   Genome Biology and Evolution

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

(2011) M. F. Lin et al.   GENOME RESEARCH

Higher differentiation among subspecies of the house mouse (Mus musculus) in genomic regions with low recombination

(2011) A. GERALDES et al.   MOLECULAR ECOLOGY

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

(2011) P. Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Estimating the Parameters of Selection on Nonsynonymous Mutations in Drosophila pseudoobscura and D. miranda

(2010) P. R. Haddrill et al.   GENETICS

Evolution of the Genomic Recombination Rate in Murid Rodents

(2010) B. L. Dumont et al.   GENETICS

Effective Population Size and the Efficacy of Selection on the X Chromosomes of Two Closely Related Drosophila Species

(2010) Peter Andolfatto et al.   Genome Biology and Evolution

Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps

(2010) B. L. Dumont et al.   GENOME RESEARCH

Coadaptation of isoacceptor tRNA genes and codon usage bias for translation efficiency in Aedes aegypti and Anopheles gambiae

(2010) S. K. Behura et al.   INSECT MOLECULAR BIOLOGY

Patterns of Codon Usage Bias in Silene latifolia

(2010) S. Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of Synonymous and Nonsynonymous Variability in Three Species of Drosophila

(2010) Penelope R. Haddrill et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria

(2010) W. Ran et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

(2010) Michael F Hammer et al.   NATURE GENETICS

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

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

Forces that influence the evolution of codon bias

(2010) P. M. Sharp et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A General Model of Codon Bias Due to GC Mutational Bias

(2010) Gareth A. Palidwor et al.   PLoS One

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

(2010) Wanjun Gu et al.   PLoS Computational Biology

Molecular evolution of synonymous codon usage in Populus

(2009) Pär K Ingvarsson   BMC EVOLUTIONARY BIOLOGY

Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity

(2009) W. Hense et al.   GENETICS

Estimating Selection Intensity on Synonymous Codon Usage in a Nonequilibrium Population

(2009) K. Zeng et al.   GENETICS

A New Standard Genetic Map for the Laboratory Mouse

(2009) Allison Cox et al.   GENETICS

Studying Patterns of Recent Evolution at Synonymous Sites and Intronic Sites in Drosophila melanogaster

(2009) Kai Zeng et al.   JOURNAL OF MOLECULAR EVOLUTION

Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula

(2009) P. K. Ingvarsson   MOLECULAR BIOLOGY AND EVOLUTION

Distributions of Selectively Constrained Sites and Deleterious Mutation Rates in the Hominid and Murid Genomes

(2009) L. Eory et al.   MOLECULAR BIOLOGY AND EVOLUTION

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Fine-Scale Phylogenetic Discordance across the House Mouse Genome

(2009) Michael A. White et al.   PLoS Genetics

Clustering of Codons with Rare Cognate tRNAs in Human Genes Suggests an Extra Level of Expression Regulation

(2009) Joanna L. Parmley et al.   PLoS Genetics

General Rules for Optimal Codon Choice

(2009) Ruth Hershberg et al.   PLoS Genetics

Selection on Codon Bias

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

Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

(2008) M. Carneiro et al.   GENETICS

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

Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes

(2008) ARMANDO GERALDES et al.   MOLECULAR ECOLOGY

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

(2008) Michael F. Hammer et al.   PLoS Genetics