Automation and integration of components for generalized semantic markup of electronic medical texts. - Jonathan M. Dugan; Daniel C. Berrios; Xiaole Liu; David K. Kim; Herbert Kaizer; Lawrence M. Fagan (AMIA, 1999)

Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances. - Glenn A. Williams; Jonathan M. Dugan; Russ B. Altman (J. Comput. Biol., 2001)

Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). - Matthew J. Gonzales; Jonathan M. Dugan; Robert W. Shafer (Bioinform., 2002)

A multi-disciplinary perspective on emergent and future innovations in peer review. - Jonathan P. Tennant; Jonathan M. Dugan; Daniel Graziotin; Damien C. Jacques; François Waldner; Daniel Mietchen; Yehia Elkhatib; Lauren B. Collister; Christina K. Pikas; Tom Crick; Paola Masuzzo; Anthony Caravaggi; et al. (F1000Research, 2017)