Hannah Verdonk

RhizAeon deconvolves reticulate evolution by analyzing sequence mosaics and detecting recombination breakpoints with high accuracy and efficiency.

This paper introduces B-STILL, a Bayesian framework to detect functional constraints in genomes by analyzing evolutionary stasis, identifying significant clusters of invariant sites in viral and mammalian genomes.

CAPHEINE automates evolutionary analysis of pathogen sequences, performing selection dynamics and positive selection studies.

This paper shows that accounting for global synonymous selection improves the accuracy of detecting episodic positive selection in protein evolution.

The paper develops MSS models to estimate selection on synonymous substitutions, finding significant correlations with covariates of codon usage selection across Drosophila species.

The paper introduces a heuristic method to adaptively select a genetic distance threshold for HIV transmission network inference, demonstrating its utility in identifying clusters with different risk factors.