| 2016 | FOCS | Zero-Knowledge Proof Systems for QMA. | Anne Broadbent, Zhengfeng Ji, Fang Song, John Watrous |
| 2010 | STOC | QIP = PSPACE. | Rahul Jain, Zhengfeng Ji, Sarvagya Upadhyay, John Watrous |
| 2009 | FOCS | Two-Message Quantum Interactive Proofs Are in PSPACE. | Rahul Jain, Sarvagya Upadhyay, John Watrous |
| 2007 | STOC | Toward a general theory of quantum games. | Gus Gutoski, John Watrous |
| 2006 | STOC | Zero-knowledge against quantum attacks. | John Watrous |
| 2005 | STACS | Quantum Interactive Proofs with Competing Provers. | Gus Gutoski, John Watrous |
| 2002 | FOCS | imits on the Power of Quantum Statistical Zero-Knowledge. | John Watrous |
| 2001 | STOC | One-dimensional quantum walks. | Andris Ambainis, Eric Bach, Ashwin Nayak, Ashvin Vishwanath, John Watrous |
| 2001 | STOC | Quantum algorithms for solvable groups. | John Watrous |
| 2000 | FOCS | Fast parallel circuits for the quantum Fourier transform. | Richard Cleve, John Watrous |
| 2000 | FOCS | Succinct quantum proofs for properties of finite groups. | John Watrous |
| 2000 | STOC | Parallelization, amplification, and exponential time simulation of quantum interactive proof systems. | Alexei Y. Kitaev, John Watrous |
| 1999 | FOCS | PSPACE Has Constant-Round Quantum Interactive Proof Systems. | John Watrous |
| 1999 | FOCS | On Quantum and Classical Space-bounded Processes with Algebraic Transition Amplitudes. | John Watrous |
| 1997 | FOCS | On the Power of Quantum Finite State Automata. | Attila Kondacs, John Watrous |
| 1995 | FOCS | On One-Dimensional Quantum Cellular Automata. | John Watrous |