By formalizing the relationship between genotype or phenotype and fitness, fitness
landscapes harbor information on molecular and evolutionary constraints. The shape of the …

With the molecular revolution in Biology, a mechanistic understanding of the genotype–
phenotype relationship became possible. Recently, advances in DNA synthesis and …

The fitness effects of synonymous mutations, nucleotide changes that do not alter the
encoded amino acid, have often been assumed to be neutral, but a growing body of …

Variation in synonymous codon usage is abundant across multiple levels of organization:
between codons of an amino acid, between genes in a genome, and between genomes of …

Gene-environment interactions have long been theorized to influence molecular evolution.
However, the environmental dependence of most mutations remains unknown. Using deep …

A protein's genetic architecture–the set of causal rules by which its sequence produces its
functions–also determines its possible evolutionary trajectories. Prior research has …

Medical discoveries mainly depend on the capability to process and analyze biological
datasets, which inundate the scientific community and are still expanding as the cost of next …

Viruses like influenza are infamous for their ability to adapt to new hosts. Retrospective
studies of natural zoonoses and passaging in the lab have identified a modest number of …

Deep mutational scanning studies suggest that synonymous mutations are typically silent
and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that …

Transposable elements (TEs) are ubiquitous in the eukaryote genomes, but their
evolutionary and functional significance remains largely obscure and contentious. Here, we …