Refereed Publications

Kelly E Lane-deGraaf, Ryan C Kennedy, S M Niaz Arifin, Gregory R Madey, Agustin Fuentes and Hope Hollocher, "A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes", BMC Ecology, Vol 13, Issue 1, September 2013. (pdf) (open access) (additional files)

Lane, K.E., Holley, C., Hollocher, H., and Fuentes, A. 2010. The anthropogenic environment lessens the intensity and prevalence of gastrointestinal parasites in Balinese long-tailed macaques (Macaca fascicularis). Primates 52(2) 117 – 128. DOI 10.1007/ s10329-010-0230-6

Niaz Arifin, S. M., et al. "P-SAM: a post-simulation analysis module for agent-based models." Proceedings of the 2010 Summer Computer Simulation Conference. Society for Computer Simulation International, 2010. (pdf)

Kennedy, R.C., Lane, K.E., Arifin, S. M. Niaz, Fuentes, A., Hollocher, H., Madey, G.R., “A GIS Aware Agent-Based Model of Pathogen Transmission,” International Journal of Intelligent Control and Systems, 14(1): 51-61, March 2009 (invited). (paper)

Kennedy, R.C., Lane, K.E., Arifin, S. M., Hollocher, H., Fuentes, A., Madey, G.R., “Simulation and Analysis of Pathogen Transmission in an Agent- and GIS-based Model,” North American Computational Social and Organization Sciences (NAACSOS 2009), Tempe, AZ, October 2009. (abstract) (slides)

Kennedy, R.C., Lane, K.E., Arifin, S. M., Hollocher, H., Fuentes, A., Madey, G.R., “Effectively Integrating GIS Data into an Agent-based Epidemiological Model,” NICO Complexity Conference, Evanston, IL, September 2009. (poster award winner) (abstract) (poster)

Kennedy, R.C., Lane, K.E., Fuentes, A., Hollocher, H., Madey, G., “Spatially Aware Agents: An effective and efficient use of GIS data with an Agent-based Model,” Agent-Directed Simulation (ADS 2009), Spring Simulation Multiconference 2009, San Diego, CA, March 2009. (paper) (slides)

Non-Refereed Publications

Kennedy, R.C., K.E., Fuentes, A., Hollocher, H., Madey, G.R., “Modeling Pathogen Transmission in Long-tailed Macaques (Macaca fascicularis) on Bali using Agent-based GIS Modeling: Performance Considerations and Enhancements,” SwarmFest 2008, Chicago, IL, May 2008. (abstract) (slides)

Lane, K.E., Neiderwieser, G., Kennedy, R.C., Fuentes, A., Hollocher, H., “Modeling Disease Transmission in Long-tailed Macaques (Macaca fascicularis) on Bali,” SwarmFest 2006, Notre Dame, IN, June 2006. (presented by Lane and Kennedy; best presentation award) (abstract) (slides) (poster)

Arifin, S. N., Kennedy, R. C., Lane, K. E., Fuentes, A., Hollocher, H., & Madey, G. R. P-SAM: A Post-Simulation Analysis Module for Agent-Based Models, Cyberinfrastructure Days, University of Notre Dame, April 29-30, 2010. (poster)

Ph.D. Dissertations

Kennedy, R.C., Identification and Annotation of Transposable Elements and Agent- and GIS-Based Modeling of Pathogen Transmission, PhD Dissertation, Computer Science and Engineering, Notre Dame, IN, 2011. (pdf)

Lane, K. R., Landscape Dynamics: Genetics and Parasitism in Balinese Long-tailed Macaques (Macaca fascicularis), PhD Dissertation, Biological Sciences, Notre Dame, IN, 2011 (pdf)

Arifin, S. M. N., A Spatial Agent-Based Model and a Multi-Dimensional Data Warehouse for Malaria Research, PhD Dissertation, Computer Science and Engineering, Notre Dame, IN, 2013. (See Appendix G, P-Sam: A Post-Simulation Analysis Module) (pdf)


This material is based upon work supported by the National Science Foundation under Grant No. 0639787. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Development of this model was also made possible through partial support from the University of Notre Dame Center for Research Computing and the Leakey Foundation.