Claus O Wilke

A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation

This paper compares one-rate and two-rate frameworks for estimating dN/dS in coding sequences under model misspecification, finding one-rate methods more accurate for moderate-to-weak purifying selection.

Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza H3N2 hemagglutinin

This study shows that passaging influenza H3N2 isolates in cell culture introduces spurious adaptation signals in hemagglutinin sequences, which can mislead evolutionary analyses.

Pyvolve: a flexible Python module for simulating sequences along phylogenies

Pyvolve simulates genetic sequences along phylogenies using customizable Markov models and offers features for developing new evolutionary models.

Dissecting the roles of local packing density and longer-range effects in protein sequence evolution

The paper investigates the structural factors influencing protein sequence evolution, showing that local packing density and solvent accessibility both contribute to site-specific evolutionary rates, with additional variation explained by longer-range effects.

Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

This paper shows that geometric proximity to the receptor-binding region, not immune epitopes, primarily drives the evolution of influenza H3 hemagglutinin.

Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli

The paper predicts growth conditions of E. coli from metabolic fluxes using regularized multinomial regression and finds that metabolic end products and a small number of reactions are sufficient for accurate prediction.

Intermediate Migration Yields Optimal Adaptation in Structured, Asexual Populations

This study shows that intermediate migration rates in structured asexual populations enhance adaptive success by enabling optimal exploration of multiple fitness peaks through leapfrogging.