Sebastian Bonhoeffer

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.

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

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.

misosoup identifies minimal microbial communities through metabolic modeling, revealing cooperative interactions and biotechnological applications.

The paper models how plasmid and chromosomal compensation affect the spread of antimicrobial resistance, finding short-term plasmid-borne compensation dominates but long-term chromosomal or combined compensation leads to multidrug resistance.

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

The paper examines F-like plasmid transfer potential in E. coli from poultry, bovine, and swine environments, finding higher functional completeness in poultry-associated plasmids.

The paper presents a simplified model to study microbial community assembly and stability, showing rich dynamics despite its basic assumptions.

This paper develops a cross-scale model to study how gut microbiota dynamics influence antimicrobial resistance persistence and transmission across hospital and community settings.

This study models how bacterial innate and adaptive immunity affect plasmid spread, finding that immunity suppresses costly plasmids but not beneficial ones.

This study evaluates combination antibiotic therapy to limit resistance evolution by analyzing drug interactions and optimal dosing strategies using a stochastic pharmacodynamic model.

The paper identifies a network optimization condition that reveals how functional groups influence the stability and feasibility of microbial ecosystems.

The paper compares sequencing and assembly methods' impact on plasmid and chromosomal phylogenies and horizontal gene transfer inference in E. coli.

The paper develops a model to study antimicrobial resistance dynamics and competition, finding that competitive release has limited impact once resistance emerges, and effective treatment is key to mitigating spread.