R. R. Regoes

The paper models how parasite doses interact with host defense tiers, finding that intermediate doses prolong infections by partially overcoming defenses without triggering strong adaptive responses.

This study decomposes virulence into exploitation and per parasite pathogenicity to show how these components relate to bacterial clearance in Drosophila infections.

This study uses stochastic modelling to show that antibiotic treatment failure can result from resistance, persistence, or hyper-mutation, with distinct dependencies on antibiotic concentration and timing.

The paper compares the per-pathogen virulence of HIV-1 subtypes A, C, and D using clinical data and finds subtype C has significantly higher virulence than subtype A.

This study shows that plasmid dissemination in the gut is enhanced by antibiotic degradation in the lumen and cycling between gut and tissue reservoirs in Salmonella Typhimurium.

This study shows that CRISPR-Cas reactivity determines phage extinction or survival during outbreaks and influences host fitness, with optimal reactivity balancing immune efficiency and autoimmunity costs.

The paper investigates how drug resistance evolves through single or multiple mutations and shows that treatment strategies affect resistance development and population diversity.

This study shows that prior exposure to sublethal doses of antimicrobial peptides increases bacterial survival and promotes resistance evolution in E. coli through mechanisms like curli or colanic acid production.

This paper introduces a cutoff-free mixture-model approach to estimate SARS-CoV-2 cumulative incidence using serological tests, showing it reduces bias and improves reliability compared to traditional cutoff-based methods.

The paper examines convergent mutations in HIV-1 env genes during early infection, finding an excess of convergent mutations indicating positive selection and purifying selection on private mutations.

The paper disentangles specific and unspecific transgenerational immune priming effects in Daphnia magna using experiments and mathematical modeling, finding no specificity in transgenerational protection against parasite challenges.

The paper models early HIV infection evolution with selection, finding a mutational fitness effects distribution with a small fraction of beneficial mutations and most mutations neutral or deleterious.

The paper estimates heritability of HIV virulence traits using donor-recipient regression and phylogenetic models, finding moderate heritability for CD4+ T cell decline and per-parasite pathogenicity.