Roland R. Regoes

Parallel evolution of full-length genomes in a long-term evolution experiment with phage ΦX174

The paper tracks parallel evolution of full-length genomes in bacteriophage populations over 412 generations, showing non-neutral evolutionary dynamics and biases in phylodynamic analysis.

Antimicrobial Combination Effects at Sub-inhibitory Doses do not Reliably Predict Effects at Inhibitory Concentrations

The paper evaluates how well sub-inhibitory drug combination effects predict inhibitory effects, finding that interaction labels depend on concentration and mixing ratio.

High-Throughput Quantification of Population Dynamics using Luminescence

This study compares luminescence and CFU assays for quantifying bacterial population decline at super-MIC concentrations, finding they differ due to physiological effects and the quantity of interest.

The danger hypothesis of virulence evolution

The paper develops a mathematical model based on danger theory to show that cost-based immune activation favors avirulence in microbes, proposing the danger hypothesis of virulence evolution.

The role of the innate immune system in shaping the dynamics of antimicrobial treatment

This study shows that the innate immune system, not antibiotic type or bacterial resistance, determines treatment success in infections using Galleria mellonella and Staphylococcus aureus.

Evolution of ivermectin resistance in the nematode model Caenorhabditis elegans: critical influence of population size and unexpected cross-resistance to emodepside

This study shows that large population size accelerates ivermectin resistance in C. elegans, with unexpected cross-resistance to emodepside and sexual recombination playing a role.

Dissecting multi-gene virulence phenotypes with base editing requires consideration of target-independent mutagenesis

The paper develops a base-editing pipeline for multi-gene knockouts in Salmonella Typhimurium, showing reduced virulence but also off-target mutations affecting fitness.

Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection

This study shows that phylodynamic migration rate estimates for HIV-1 within hosts are overestimated under selection using common models like BEAST2.

Substantial Deceleration of Adaptation of HIV-1 Within 1,500 Generations in an Experimental Evolution: A Genomic Perspective

This study tracks HIV-1 adaptation over 1,500 generations in human T-cell lines, finding a substantial deceleration in adaptive mutation fixation rates and fitness gains.

Investigating the consequences of the mating system for drug resistance evolution in C. elegans

This study uses a population genetic model to show that androdioecious C. elegans populations adapt rapidly to drug selection and exhibit high genetic diversity.

The role of innate immunity, antibiotics, and bacteriophages in the course of bacterial infections and their treatment

This study uses Galleria mellonella larvae to test hypotheses about innate immunity's role in bacterial infections and shows bacteriostatic drugs and phages are as effective as bactericidal antibiotics.

The pharmacodynamic inoculum effect from the perspective of bacterial population modeling

The paper models the inoculum effect in bacterial populations using a multi-hit framework, showing its impact on antimicrobial efficacy and population dynamics.

The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is severely constrained by random peptide mixtures

This study shows that random antimicrobial peptide mixtures reduce resistance evolution in Pseudomonas aeruginosa compared to single peptides, preventing cross-resistance and maintaining drug sensitivity.