| 2017 | ACISP | Stegogames. | Clark D. Thomborson, Marc Jeanmougin |
| 2016 | PST | Privacy patterns. | Clark D. Thomborson |
| 2015 | ACSAC | Pinpointing and Hiding Surprising Fragments in an Obfuscated Program. | Yuichiro Kanzaki, Clark D. Thomborson, Akito Monden, Christian S. Collberg |
| 2011 | APSEC | Illusions and Perceptions of Transparency in Software Engineering. | Yu-Cheng Tu, Clark D. Thomborson, Ewan D. Tempero |
| 2006 | COMPSAC | Frameworks Built on the Trusted Platform Module. | Matt Barrett, Clark D. Thomborson |
| 2006 | GRC | Obfuscate arrays by homomorphic functions. | William Zhu, Clark D. Thomborson, Fei-Yue Wang |
| 2006 | ICISS | A Survey of Control-Flow Obfuscations. | Anirban Majumdar, Clark D. Thomborson, Stephen Drape |
| 2005 | ISI | On the Use of Opaque Predicates in Mobile Agent Code Obfuscation. | Anirban Majumdar, Clark D. Thomborson |
| 2005 | ISI | On the QP Algorithm in Software Watermarking. | William Zhu, Clark D. Thomborson |
| 2005 | ISI | A Survey of Software Watermarking. | William Zhu, Clark D. Thomborson, Fei-Yue Wang |
| 2005 | KES | Securing Mobile Agents Control Flow Using Opaque Predicates. | Anirban Majumdar, Clark D. Thomborson |
| 2003 | POPL | Folklore confirmed: reducible flow graphs are exponentially larger. | Larry Carter, Jeanne Ferrante, Clark D. Thomborson |
| 2003 | WG | Graph-Based Approaches to Software Watermarking. | Christian S. Collberg, Stephen G. Kobourov, Edward Carter, Clark D. Thomborson |
| 1999 | POPL | Software Watermarking: Models and Dynamic Embeddings. | Christian S. Collberg, Clark D. Thomborson |
| 1998 | ICCD | Data cache parameter measurements. | Enyou Li, Clark D. Thomborson |
| 1998 | POPL | Manufacturing Cheap, Resilient, and Stealthy Opaque Constructs. | Christian S. Collberg, Clark D. Thomborson, Douglas Low |
| 1991 | ARITH | Delay optimization of carry-skip adders and block carry-lookahead adders. | Pak K. Chan, Martine D. F. Schlag, Clark D. Thomborson, Vojin G. Oklobdzija |
| 1990 | FOCS | Asymptotically Tight Bounds for Computing with Faulty Arrays of Processors (Extended Abstract) | Christos Kaklamanis, Anna R. Karlin, Frank Thomson Leighton, Victor Milenkovic, Prabhakar Raghavan, Satish Rao, Clark D. Thomborson, A. Tsantilas |
| 1989 | COMPSAC | Enhancements to Ziv-Lempel data compression. | Clyde Rogers, Clark D. Thomborson |
| 1989 | SPAA | Systolic Implementations of a Move-to-Front Text Compressor. | Clark D. Thomborson, Belle W. Y. Wei |
| 1983 | WG | On the Energy-Time-Area Cost of a Memory Access. | Clark D. Thomborson |