Publications

When reconstructing a phylogeny from molecular data, it is regarded as best prac- tice to perform relative model selection to determine …

The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as …

HyPhy (Kosakovsky Pond, Frost, and Muse 2005) is a powerful bioinformatics software platform for evolutionary comparative sequence …

We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural …

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced ‘‘laser’’), a tool to infer relative evolutionary rates …

The critical initiation phase of clathrin-mediated endocytosis (CME) determines where and when endocytosis occurs. Heterotetrameric …

The mutation–selection model of coding sequence evolution has received renewed attention for its use in estimating site- specific amino …

Proteins evolve through two primary mechanisms: substitution, where mutations alter a pro- tein’s amino-acid sequence, and insertions …

It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, …

Two broad paradigms exist for inferring dN/dS, the ratio of nonsynonymous to synonymous substitution rates, from coding sequences: i) a …

With the expansion of DNA sequencing technology, quantifying evolution during emerging viral outbreaks has become an important tool for …

Numerous computational methods exist to assess the mode and strength of natural selection in protein-coding sequences, yet how distinct …

We introduce Pyvolve, a flexible Python module for simulating genetic data along a phylog- eny using continuous-time Markov models of …

Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly …

Errors in multiple sequence alignments (MSAs) can reduce accuracy in positive-selection inference. Therefore, it has been suggested to …

The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D …

We have investigated the influence of the plasma membrane environment on the molecular evolution of G protein-coupled receptors …