J. J. Bull

Modeling the directed evolution of broad host range phages

The paper models how different protocols for exposing phages to novel bacterial strains affect the evolution of generalist versus specialist phages.

Interpreting and de-noising genetically engineered barcodes in a DNA virus

The paper generates and analyzes randomized barcodes in a DNA virus genome, identifies sequencing errors, and develops a method to correct them for accurate interpretation.

Gene drive escape from resistance depends on mechanism and ecology

This study examines how gene drive resistance evolves and shows that multiple drives or ecological effects can reduce resistance risk, but inbreeding can still halt drive spread.

Evading resistance to gene drives

This paper develops models to identify conditions under which gene drives can evade resistance, showing that linkage between resistance and drive loci is critical to resistance evolution.

Vector dynamics influence spatially imperfect genetic interventions against disease

The paper models how human travel affects the persistence of vector-borne diseases in spatially structured populations with imperfect genetic interventions.

Using directed attenuation to enhance vaccine immunity

The paper uses mathematical models to show that directed attenuation of viral immune evasion pathways can reduce viral growth without compromising immunity, potentially enhancing vaccine effectiveness.

Promises and pitfalls of in vivo evolution to improve phage therapy

This study evaluates whether in vivo phage evolution can improve phage therapy outcomes and finds that informed phage selection is more effective than relying on within-host evolution.

Spatial structure undermines parasite suppression by gene drive cargo

The paper shows spatial structure in vector populations can hinder disease eradication by gene drive cargo by facilitating disease agent resistance evolution.

Gene-drive-mediated extinction is thwarted by evolution of sib mating

The paper shows that sib mating can evolve to counteract gene drives, maintaining mean fitness above zero and potentially preventing extinction.

Recombinant vector vaccines and within-host evolution

This paper models within-host evolution of recombinant vector vaccines and finds that vaccine efficacy can be reduced by transgene loss, but this can be mitigated by increasing inoculum size or purity.