The Dynamics of Cellular Motility (M. Murase). - Joseph M. Mahaffy (SIAM Rev., 1994)

PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. - Florent E. Angly; Beltran Rodriguez-Brito; David Bangor; Pat McNairnie; Mya Breitbart; Peter Salamon; Ben Felts; James Nulton; Joseph Mahaffy; Forest Rohwer (BMC Bioinform., 2005)

Membrane Remodeling and Diffusion of Cytochrome C from a Geometrically Idealized Mitochondrial Crista. - John Manor; Peter Salamon; James Nulton; Joseph Mahaffy; Arlette Baljon; Terrence Frey (BIOCOMP, 2006)

Modeling Cyclic Waves of Circulating T Cells in Autoimmune Diabetes. - Joseph M. Mahaffy; Leah Edelstein-Keshet (SIAM J. Appl. Math., 2007)

Geometry of Basins of Attraction and Heteroclinic Connections in Coupled Bistable Systems. - Daniel Lyons; Joseph M. Mahaffy; Sara Wang; Antonio Palacios; Visarath In (Int. J. Bifurc. Chaos, 2014)

An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation. - Jerry S. Chen; Abygail M. Gumbayan; Robert W. Zeller; Joseph M. Mahaffy (PLoS Comput. Biol., 2014)