Evolutionary and dynamic models of infection with internal host structure. - John K. Kelly (Disease Evolution: Models, Concepts, and Data Analyses, 2006)

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing. - Paul M. Magwene; John H. Willis; John K. Kelly (PLoS Comput. Biol., 2011)

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity. - Lex E. Flagel; Benjamin Blackman; Lila Fishman; Patrick J. Monnahan; Andrea Sweigart; John K. Kelly (PLoS Comput. Biol., 2019)