Since the start of the COVID-19 pandemic, numerous variants of SARS-CoV-2 have been
reported worldwide. The advent of variants of concern (VOCs) raises severe concerns amid …

The redundancy of the genetic code implies that most amino acids are encoded by multiple
synonymous codons. In all domains of life, a biased frequency of synonymous codons is …

Quantitative views of cellular functions require precise measures of rates of biomolecule
production, especially proteins—the direct effectors of biological processes. Here, we …

Comparative analyses of natural and mutated sequences have been used to probe
mechanisms of gene expression, but small sample sizes may produce biased outcomes. We …

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical
challenges can confound its analysis. Here, we use improved methods to obtain ribosome …

Despite their name, synonymous mutations have significant consequences for cellular
processes in all taxa. As a result, an understanding of codon bias is central to fields as …

Codon optimization describes gene engineering approaches that use synonymous codon
changes to increase protein production. Applications for codon optimization include …

Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds.
Transient pausing of ribosomes can affect a variety of co-translational processes, including …

Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We
leverage these data to parameterize a computational model of translation, keeping track of …

Synonymous mutations do not alter the encoded protein, but they can influence gene
expression. To investigate how, we engineered a synthetic library of 154 genes that varied …