| 2017 | COMPSAC | Making DNS Servers Resistant to Cyber Attacks: An Empirical Study on Formal Methods and Performance. | Barry S. Fagin, Bradley Klanderman, Martin C. Carlisle |
| 2012 | GLOBECOM | IRONSIDES: DNS with no single-packet denial of service or remote code execution vulnerabilities. | Martin C. Carlisle, Barry S. Fagin |
| 2011 | FIE | Defining, integrating, and assessing a purposeful progression of cross-curricular initiatives into a computer science program. | Steven M. Hadfield, Dino Schweitzer, David Gibson, Barry Fagin, Martin C. Carlisle, Jeff Boleng, David Bibighaus |
| 2010 | SIGCSE | Using You Tube to enhance student class preparation in an introductory Java course. | Martin C. Carlisle |
| 2009 | IJCNN | Partitioned neural networks. | Douglas P. Sutton, Martin C. Carlisle, Traci A. Sarmiento, Leemon C. Baird III |
| 2006 | SIGCSE | Tools for teaching introductory programming: what works? | Kris D. Powers, Paul Gross, Steve Cooper, Myles F. McNally, Kenneth J. Goldman, Viera K. Proulx, Martin C. Carlisle |
| 2006 | SIGITE | Toward a more effective visualization tool to teach novice programmers. | John C. Giordano, Martin C. Carlisle |
| 2005 | SIGCSE | RAPTOR: a visual programming environment for teaching algorithmic problem solving. | Martin C. Carlisle, Terry A. Wilson, Jeffrey W. Humphries, Steven M. Hadfield |
| 1995 | PPoPP | Software Caching and Computation Migration in Olden. | Martin C. Carlisle, Anne Rogers |
| 1991 | ICCI | On the k-Coloring of Intervals. | Martin C. Carlisle, Errol L. Lloyd |