Daniel B. Weissman

Within-host antigenic selection of influenza A virus dominates over stochasticity but is limited by fitness tradeoffs and timing of the immune response

This study shows that antigenic selection of influenza virus within hosts is driven by immune pressure timing and fitness tradeoffs, with moderate stochastic effects observed.

Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

The paper shows that bursts of reproduction can create genetic structure in bacterial populations with high recombination rates, even when recombination would otherwise eliminate such structure.

Selection favors context-dependent bias in altruism

The paper shows that context-dependent altruism strategies outperform simple strategies in evolutionary simulations.

Preventing Disease Emergence Following Eradication: Application to Mpox

The paper models factors influencing mpox's evolutionary emergence and finds that increased human-to-human transmissibility has a greater impact on its spread than zoonotic spillovers.

Genetic drift acts strongly on within-host influenza virus populations during acute infection but does not act alone

This study quantifies genetic drift in within-host influenza virus populations using a population genetic model, finding low effective population sizes and evidence against the Wright-Fisher model in swine infections.

The distribution of the time to the most recent pairwise genetic common ancestor of a set of sampled genomes

The paper derives the distribution of the time to the most recent pairwise genetic common ancestor in a recombining population, finding a characteristic scaling with population size.

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years

Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria

This paper models recombination's impact on multi-drug resistance evolution in malaria, showing that most recombinant genotypes arise from multi-clonal infections and that ACT strategies reduce treatment failures and delay resistance.

Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes

The paper develops a coevolution score method to detect coevolving genes in bacterial genomes, finding coordinated gene gain/loss patterns in S. aureus related to antibiotic resistance.