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- Parker, Jon, Ophir Frieder, and Gideon Frieder. "Automatic Enhancement and Binarization of Degraded Document Images." In Document Analysis and Recognition (ICDAR), 2013 International Conference on, IEEE, (In Press).
- Parker, Jon, Yifang Wei, Andrew Yates, Ophir Frieder and Nazli Goharian. “A Framework for Detecting Public Health Trends with Twitter” In Proceedings of the International Conference on Advances in Social Networks Analysis and Mining, (In Press).
- Parker, Jon, Andrew Yates, Nazli Goharian, and Wai Gen Yee. "Efficient estimation of aspect weights." In Proceedings of the 35th international ACM SIGIR conference on Research and development in information retrieval, pp. 1057-1058. ACM, 2012.
- Parker, Jon, and Joshua M. Epstein. "A distributed platform for global-scale agent-based models of disease transmission." ACM Transactions on Modeling and Computer Simulation (TOMACS) 22, no. 1 (2011): 2.
- Parker, Jon. “The Inter-Region Epidemic Dynamics Model,” Journal of Homeland Security’s Proceedings of the 2011 DHS Science Conference 5th Annual University Network Summit, focused on Catastrophes and Complex Systems: Transportation, 2011
- Lee, Bruce Y., Sarah M. McGlone, Kim F. Wong, S. Levent Yilmaz, Taliser R. Avery, Yeohan Song, Richard Christie et al. "Modeling the spread of methicillin-resistant Staphylococcus aureus (MRSA) outbreaks throughout the hospitals in Orange County, California." Infection Control and Hospital Epidemiology 32, no. 6 (2011): 562.
- Epstein, Joshua M., Jon Parker, Derek Cummings, and Ross A. Hammond. "Coupled contagion dynamics of fear and disease: mathematical and computational explorations." PLoS One 3, no. 12 (2008): e3955.
- Parker, Jon. "A flexible, large-scale, distributed agent based epidemic model." In Proceedings of the 39th conference on Winter simulation: 40 years! The best is yet to come, pp. 1543-1547. IEEE Press, 2007.
- Burke, Donald S., Joshua M. Epstein, Derek AT Cummings, Jon I. Parker, Kenneth C. Cline, Ramesh M. Singa, and Shubha Chakravarty. "Individual‐based Computational Modeling of Smallpox Epidemic Control Strategies." Academic Emergency Medicine 13, no. 11 (2006): 1142-1149.
- Axtell, Robert L., Joshua M. Epstein, Jeffrey S. Dean, George J. Gumerman, Alan C. Swedlund, Jason Harburger, Shubha Chakravarty, Ross Hammond, Jon Parker, and Miles Parker. "Population growth and collapse in a multiagent model of the Kayenta Anasazi in Long House Valley." Proceedings of the National Academy of Sciences of the United States of America 99, no. Suppl 3 (2002): 7275-7279.
- Parker, Jon, and Hans Engle, “Spoofing a PMF to Reduce Memory Requirement And Speed Up Sampling”
- Parker, Jon, and Chris Wacek, “The Spewy Louie Poker Bot”, The 2012 Computer Poker Symposium
- Parker, Jon, “The Architecture of the Spewy Louie Jr. Poker Bot”, The 2013 Computer Poker Symposium