The advent of ribosome profiling and other tools to probe mRNA translation has revealed
that codon bias—the uneven use of synonymous codons in the transcriptome—serves as a …

Genome sequence data are now being routinely obtained from many nonmodel organisms.
These data contain a wealth of information about the demographic history of the populations …

Praise for the first edition:… superb, beautifully written and organized work that takes an
engineering approach to systems biology. Alon provides nicely written appendices to …

Most amino acids are encoded by multiple codons, and codon choice has strong effects on
protein expression. Rare codons are enriched at the N terminus of genes in most organisms …

Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at
non-synonymous and synonymous sites. The dN/dS ratio was originally developed for …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

The study of evolution at the molecular level has given the subject of evolutionary biology a
new significance. Phylogenetic'trees' of gene sequences are a powerful tool for recovering …

The genetic code uses 64 codons to represent the 20 standard amino acids and the
translation termination signal. Each codon is recognised by a subset of a cell's transfer …

Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …

The distribution of fitness effects (DFE) has considerable importance in population genetics.
To date, estimates of the DFE come from studies using a small number of individuals. Thus …