David A. Rasmussen

This paper develops a Bayesian framework for inferring mutational and epistatic fitness effects in microbial evolution using multi-feature birth-death models and applies it to Escherichia coli phylogenies.

This study reconstructs the evolutionary history of bat influenza A viruses, finding they diverged 100-200 years ago and show segment-specific selection and host transition dynamics.

The paper investigates factors determining effective reassortment in orthohantaviruses, finding that ecological overlap and molecular compatibility are key for reassortant establishment.

This paper uses Markov decision processes to optimize genomic sampling strategies for demographic and epidemiological inference by maximizing information gain while minimizing costs.

This study investigates how incomplete purifying selection affects viral phylogenies and phylodynamic inference, finding little bias in key epidemiological estimates despite mutation distribution shifts.

This study evaluates the accuracy of recombination breakpoint localization algorithms using simulated data and identifies key factors affecting their performance.

This study quantifies the genomic determinants of fitness in E. coli ST131 using phylodynamic models, finding that fluoroquinolone resistance mutations provide a major fitness advantage.

The paper introduces a model to infer migration history from genealogies with recombination and applies it to fungal lineages to study recombination and migration patterns.

This study uses genomic data from 8746 SARS-CoV-2 genomes across 33 African countries to show that most epidemics were initiated by European importations and later driven by local transmission and mobility, leading to the spread of variants of concern.