| 2011 | IJCAI | Active Graph Reachability Reduction for Network Security and Software Engineering. | Alice X. Zheng, John Dunagan, Ashish Kapoor |
| 2010 | NSDI | Centrifuge: Integrated Lease Management and Partitioning for Cloud Services. | Atul Adya, John Dunagan, Alec Wolman |
| 2010 | NSDI | Volley: Automated Data Placement for Geo-Distributed Cloud Services. | Sharad Agarwal, John Dunagan, Navendu Jain, Stefan Saroiu, Alec Wolman |
| 2010 | USENIX | Stout: An Adaptive Interface to Scalable Cloud Storage. | John McCullough, John Dunagan, Alec Wolman, Alex C. Snoeren |
| 2009 | SOSP | Heat-ray: combating identity snowball attacks using machinelearning, combinatorial optimization and attack graphs. | John Dunagan, Alice X. Zheng, Daniel R. Simon |
| 2008 | NSDI | Characterizing Botnets from Email Spam Records. | Li Zhuang, John Dunagan, Daniel R. Simon, Helen J. Wang, Ivan Osipkov, J. Doug Tygar |
| 2007 | NDSS | Generic Application-Level Protocol Analyzer and its Language. | Nikita Borisov, David Brumley, Helen J. Wang, John Dunagan, Pallavi Joshi, Chuanxiong Guo |
| 2007 | STOC | Iteratively constructing preconditioners via the conjugate gradient method. | John Dunagan, Nicholas J. A. Harvey |
| 2006 | IMC | Finding diversity in remote code injection exploits. | Justin Ma, John Dunagan, Helen J. Wang, Stefan Savage, Geoffrey M. Voelker |
| 2006 | OSDI | BrowserShield: Vulnerability-Driven Filtering of Dynamic HTML. | Charles Reis, John Dunagan, Helen J. Wang, Opher Dubrovsky, Saher Esmeir |
| 2005 | NDSS | A Black-Box Tracing Technique to Identify Causes of Least-Privilege Incompatibilities. | Shuo Chen, John Dunagan, Chad Verbowski, Yi-Min Wang |
| 2004 | MOBICOM | SSCH: slotted seeded channel hopping for capacity improvement in IEEE 802.11 ad-hoc wireless networks. | Paramvir Bahl, Ranveer Chandra, John Dunagan |
| 2004 | OSDI | FUSE: Lightweight Guaranteed Distributed Failure Notification. | John Dunagan, Nicholas J. A. Harvey, Michael B. Jones, Dejan Kostic, Marvin Theimer, Alec Wolman |
| 2004 | STOC | A simple polynomial-time rescaling algorithm for solving linear programs. | John Dunagan, Santosh S. Vempala |
| 2002 | SODA | Smoothed analysis of the perceptron algorithm for linear programming. | Avrim Blum, John Dunagan |
| 2001 | STOC | Optimal outlier removal in high-dimensional. | John Dunagan, Santosh S. Vempala |