VectorBase: a home for invertebrate vectors of human pathogens. - Daniel Lawson; Peter Arensburger; Peter Atkinson; Nora J. Besansky; Robert V. Bruggner; Ryan Butler; Kathryn S. Campbell; George K. Christophides; Scott Christley; Emmanuel Dialynas; David B. Emmert; Martin Hammond; et al. (Nucleic Acids Res., 2007)

Spatially aware agents: an effective and efficient use of GIS data within an agent-based model. - Ryan C. Kennedy; Kelly E. Lane; Agustín Fuentes; Hope Hollocher; Gregory R. Madey (SpringSim, 2009)

P-SAM: a post-simulation analysis module for agent-based models. - S. M. Niaz Arifin; Ryan C. Kennedy; Kelly E. Lane; Agustín Fuentes; Hope Hollocher; Gregory R. Madey (SummerSim, 2010)

An automated homology-based approach for identifying transposable elements. - Ryan C. Kennedy; Maria F. Unger; Scott Christley; Frank H. Collins; Gregory R. Madey (BMC Bioinform., 2011)

Falsifying an Enzyme Induction Mechanism within a Validated, Multiscale Liver Model. - Glen E. P. Ropella; Ryan C. Kennedy; C. Anthony Hunt (Int. J. Agent Technol. Syst., 2012)

Implementing a cell-centered, agent-based framework with flexible environment granularities using MASON and VTK. - Ryan C. Kennedy; Glen E. P. Ropella; C. Anthony Hunt (SpringSim (ADS), 2016)

Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments. - Andrew K. Smith; Brenden K. Petersen; Glen E. P. Ropella; Ryan C. Kennedy; Neil Kaplowitz; Murad Ookhtens; C. Anthony Hunt (PLoS Comput. Biol., 2016)

Simulation enabled search for explanatory mechanisms of the fracture healing process. - Ryan C. Kennedy; Meir Marmor; Ralph Marcucio; C. Anthony Hunt (PLoS Comput. Biol., 2018)

Contrasting model mechanisms of alanine aminotransferase (ALT) release from damaged and necrotic hepatocytes as an example of general biomarker mechanisms. - Andrew K. Smith; Glen E. P. Ropella; Mitchell R. McGill; Preethi Krishnan; Lopamudra Dutta; Ryan C. Kennedy; Hartmut Jaeschke; C. Anthony Hunt (PLoS Comput. Biol., 2020)