S. Bonhoeffer

Assessing the role of bacterial innate and adaptive immunity as barriers to conjugative plasmids

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

A network optimisation condition uncovers the role offunctional groups in the feasibility and dynamical stability of microbial model ecosystems.

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

The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution

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

My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages

The paper develops a stochastic model to evaluate CRISPR-Cas plasmid-based anti-phage protection, showing it is robust except under specific parameter conditions where segregation loss enables phage outbreaks.

A Genome-Scale Metabolic Model of Marine Heterotroph Vibrio splendidus sp. 1A01

The paper constructs a genome-scale metabolic model for Vibrio splendidus sp. 1A01 to study its metabolism and addresses challenges in modeling marine microorganisms.

Turnover in life strategies recapitulates microbial succession on synthetic marine particles

The paper identifies two distinct microbial community classes on synthetic marine particles, shaped by environmental selection and facilitation, with distinct metabolic traits.

Constrained optimisation of divisional load in hierarchically-organised tissues during homeostasis

The paper develops a mathematical model to optimise divisional load in hierarchical tissues during homeostasis, finding that binary division trees with non-self-renewing progenitors minimise mutation risk.

Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics

This paper reviews how biological processes of plasmid co-infection are modeled and analyzes their impact on eco-evolutionary outcomes, showing frequency-dependent selection from beneficial and detrimental effects.

Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut

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.

Epidemiological and evolutionary consequences of CRISPR-Cas reactivity

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.

Quantifying the influence of space on social group structure

The paper introduces a method to quantify the relationship between social and spatial structure in animal groups and applies it to both simulated and empirical data.

Evolutionary mechanisms that determine which bacterial genes are carried on plasmids

This paper uses mathematical modeling to show that moderately beneficial bacterial genes are more likely to be on plasmids due to positive frequency-dependent selection and priority effects.

Ecological effects of stress drive bacterial evolvability under sub-inhibitory antibiotic treatments

The paper investigates how stress from sub-inhibitory antibiotic treatments affects bacterial evolvability, finding that ecological factors, not just mutation rates, determine genetic diversity.

Estimating cumulative incidence of SARS-CoV-2 with imperfect serological tests: a cutoff-free approach

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.

Estimating plasmid conjugation rates: a new computational tool and a critical comparison of methods

The paper introduces a new computational tool for estimating plasmid conjugation rates and compares existing methods, showing biases due to population dynamics and growth differences.

Clinical extended-spectrum beta-lactamase antibiotic resistance plasmids have diverse transfer rates and can spread in the absence of antibiotic selection

This study quantifies the conjugative transfer dynamics of ESBL plasmids in vitro and in vivo, showing variation in transfer efficiency and potential for predicting plasmid spread.

Cancer-Induced Immunosuppression can enable Effectiveness of Immunotherapy through Bistability Generation: a mathematical and computational Examination

This paper uses mathematical models to show that cancer-induced immunosuppression can create bistability, which may be exploited for immunotherapy by tipping the system toward a cancer-free state.

Microbial metabolically cohesive consortia and ecosystem functioning

The paper proposes the concept of Metabolically Cohesive Consortia (MeCoCos) to explain stable microbial community structures and their ecological implications.

Stochastic gene expression influences the selection of antibiotic resistance mutations

This study shows stochastic gene expression affects the selection of antibiotic resistance mutations, with regulatory and structural mutations providing different resistance mechanisms.

Antibiotic treatment protocols revisited: The challenges of a conclusive assessment by mathematical modeling

This paper reviews mathematical models of antibiotic treatment protocols and highlights methodological challenges in assessing combination therapy, mixing, and cycling.

Effective polyploidy causes phenotypic delay and influences bacterial evolvability

This study shows antibiotic resistance mutations in E. coli have a 3-4 generation phenotypic delay due to effective polyploidy, impacting mutation rate estimation and evolutionary adaptation.

Death and population dynamics affect mutation rate estimates and evolvability under stress in bacteria

The paper shows that ignoring death during stress reduces mutation rate estimates and evolvability in bacteria, and provides tools to better measure these effects.

Dissecting HIV Virulence: Heritability Of Setpoint Viral Load, CD4+ T Cell Decline And Per-Parasite Pathogenicity

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.