D. A. Rasmussen

Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects

This paper conducts a meta-analysis of viral mutation fitness effects across hosts, finding positive pleiotropy is common and fitness effects are positively correlated between hosts.

Plasmodium falciparum genetic diversity in coincident human and mosquito hosts

The paper assesses genetic diversity of Plasmodium falciparum in human and mosquito hosts, finding higher diversity in mosquitoes than humans.

Espalier: Efficient tree reconciliation and ARG reconstruction using maximum agreement forests

This paper introduces a method to reconcile discordant phylogenetic trees and reconstruct ancestral recombination graphs (ARGs) using maximum agreement forests, demonstrating its accuracy and efficiency in analyzing viral genomes.

Decomposing the sources of SARS-CoV-2 fitness variation in the United States

This study decomposes SARS-CoV-2 fitness variation in the US by analyzing genetic and non-genetic factors using phylodynamic models.

Evolutionary dynamics of Tomato spotted wilt virus within and between alternate plant hosts and thrips

This study tracks the evolutionary dynamics of Tomato spotted wilt virus across alternate plant hosts and thrips, finding high genetic diversity and positive pleiotropy drive adaptation.

Coupling adaptive molecular evolution to phylodynamics using fitness-dependent birth-death models

The paper introduces a new birth-death model that links molecular evolution to phylodynamics by estimating lineage fitness and mutation effects from phylogenetic branching patterns.

The Structured Coalescent and its Approximations

The paper presents an exact solution to the structured coalescent and improves approximations for phylogeographic analysis without inferring ancestral migration histories.

MASCOT: Parameter and state inference under the marginal structured coalescent approximation

The paper introduces MASCOT, an algorithm that improves parameter and state inference under the structured coalescent approximation, enabling analysis of larger datasets with more states.