Quasispecies Made Simple. - James J. Bull; Lauren Ancel Meyers; Michael Lachmann (PLoS Comput. Biol., 2005)

From Bad to Good: Fitness Reversals and the Ascent of Deleterious Mutations. - Matthew C. Cowperthwaite; James J. Bull; Lauren Ancel Meyers (PLoS Comput. Biol., 2006)

Recombinant vector vaccine evolution. - James J. Bull; Scott L. Nuismer; Rustom Antia (PLoS Comput. Biol., 2019)

Directed attenuation to enhance vaccine immunity. - Rustom Antia; Hasan Ahmed; James J. Bull (PLoS Comput. Biol., 2021)

Interpreting and de-noising genetically engineered barcodes in a DNA virus. - Sylvain Blois; Benjamin M. Goetz; James J. Bull; Christopher S. Sullivan (PLoS Comput. Biol., 2022)