Amino acid exchangeabilities vary across the tree of life

Molecular evolution in large steps - Codon substitutions under positive selection

(2019) Qingjian Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary determinants of genome-wide nucleotide composition

(2018) Hongan Long et al.   Nature Ecology & Evolution

Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level

(2017) Siyu Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

(2016) David M. Kristensen et al.   NUCLEIC ACIDS RESEARCH

Prokaryotic Nucleotide Composition Is Shaped by Both Phylogeny and the Environment

(2015) Erin R. Reichenberger et al.   Genome Biology and Evolution

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A selective force favoring increased G+C content in bacterial genes

(2012) R. Raghavan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

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

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

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Evidence That Mutation Is Universally Biased towards AT in Bacteria

(2010) Ruth Hershberg 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

The Universal Trend of Amino Acid Gain–Loss is Caused by CpG Hypermutability

(2008) Kazuharu Misawa et al.   JOURNAL OF MOLECULAR EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION