J. S. Weitz

Design, optimization, and inference of biphasic decay of infectious virus particles

This paper develops methods to detect and optimize sampling for multiphasic virus decay, applying them to show that 94% of phage ΦD9 decays 16-fold faster than the remaining population.

Accounting for Cellular-Level Variation in Lysis: Implications for Virus-Host Dynamics

This paper shows that one-step growth curves underestimate the mean latent period of bacteriophages due to cellular-level variability in lysis timing, and proposes a computational framework to correct this bias.

Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea

The paper shows that in the phosphorus-limited Sargasso Sea, different microbes uptake phosphorus at different times of day, supporting temporal niche partitioning.

Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection

This study uses a spatially structured metapopulation model and in vivo experiments to evaluate how lung anatomy and immune responses affect the efficacy of phage therapy for Pseudomonas aeruginosa infections.

Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy

This study shows that macrophages reduce bacteriophage density in the lungs, limiting the effectiveness of phage therapy in treating Pseudomonas aeruginosa pneumonia.

Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone

The paper examines how nitrogen availability shapes microbial and viral genome and proteome nitrogen content across spatial scales in a marine oxygen minimum zone.

Time-scales modulate optimal lysis-lysogeny decision switches and near-term phage fitness

This study shows that time-scales influence the optimal lysis-lysogeny decisions of phages, with plastic responses enhancing near-term fitness and being robust to cellular stochasticity.

Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre

The paper develops multitrophic models to investigate top-down and bottom-up drivers of Prochlorococcus population dynamics in the North Pacific Subtropical Gyre, finding grazers are the primary top-down factor despite high viral densities.

Community-scale Synchronization and Temporal Partitioning of Gene Expression, Metabolism, and Lipid Biosynthesis in Oligotrophic Ocean Surface Waters

The paper uses machine learning to analyze time series data from ocean surface waters, revealing synchronized and asynchronous gene expression patterns linked to diel cycles and microbial niche partitioning.

Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations

This study shows that allelic polymorphism in Pseudomonas aeruginosa affects community function and antibiotic tolerance during evolution in biofilms.

When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny

This study investigates when temperate bacteriophage strategies are advantageous by analyzing ecological contexts and fitness outcomes of lytic and lysogenic infection modes.

Topological constraints in early multicellularity favor reproductive division of labor

This study shows reproductive specialization evolves in sparse cellular networks despite saturating returns, highlighting the role of restricted interactions in early multicellularity.

Quantitative Models of Phage-Antibiotics Combination Therapy

This study develops a nonlinear population dynamics model to evaluate phage-antibiotic combination therapy for MDR bacteria, showing improved efficacy with sub-inhibitory antibiotic concentrations and innate immune interactions.

Infect While the Iron is Scarce: Nutrient Explicit Phage-Bacteria Games

The paper models the interaction between phages and bacteria under iron limitation using an evolutionary game theory framework, showing how nutrient dynamics influence host-virus strategies.

Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage

The paper develops a light-driven population model to examine how light-dependent life history traits of Prochlorococcus and cyanophage influence population dynamics, finding that light-dependent adsorption improves model fits but lysis saturation at high virus-to-cell ratios also plays a key role.

Viral Invasion Fitness Across a Continuum from Lysis to Latency

The paper introduces a cell-centric metric to quantify viral invasion fitness, showing that strategies like lysogeny can outperform lytic strategies under certain conditions.

The limitations of correlation-based inference in complex virus-microbe communities

This paper evaluates correlation-based methods for inferring virus-microbe interactions and finds they are inaccurate, suggesting model-based approaches are better.

Information sharing for a coordination game in fluctuating environments

The paper develops a game-theoretic framework to analyze how information sharing affects decision-making in fluctuating environments, identifying Nash equilibria and optimal strategies for coordination.

The effect of strain level diversity on robust inference of virus-induced mortality

The paper examines how strain diversity affects the accuracy of virus-induced lysis rate estimates using the modified dilution method in marine microbial communities.

Disentangling the Relative Strength of Niche Competition from Grazing-Induced Phytoplankton Mortality

The paper shows the dilution method may overestimate zooplankton grazing rates due to niche competition and proposes a modified Z-dilution method to disentangle these effects.

Synergistic elimination of bacteria by phage and the innate immune system

This paper develops a model showing that phage and the innate immune system together can synergistically eliminate bacteria, which neither can achieve alone.

An oscillating tragedy of the commons in replicatordynamics with game-environment feedback

The paper generalizes evolutionary game theory to show oscillatory tragedy of the commons dynamics where environmental states and strategies coevolve, finding cooperation is necessary to avoid system collapse.