| 2022 | WACV | Auditing saliency cropping algorithms. | Abeba Birhane, Vinay Uday Prabhu, John Whaley |
| 2021 | AAAI | Rotation-Invariant Gait Identification with Quaternion Convolutional Neural Networks (Student Abstract). | Bowen Jing, Vinay Uday Prabhu, Angela Gu, John Whaley |
| 2008 | PEPM | Securing web applications with static and dynamic information flow tracking. | Monica S. Lam, Michael C. Martin, V. Benjamin Livshits, John Whaley |
| 2006 | PLDI | Effective static race detection for Java. | Mayur Naik, Alex Aiken, John Whaley |
| 2005 | APLAS | Reflection Analysis for Java. | V. Benjamin Livshits, John Whaley, Monica S. Lam |
| 2005 | APLAS | Using Datalog with Binary Decision Diagrams for Program Analysis. | John Whaley, Dzintars Avots, Michael Carbin, Monica S. Lam |
| 2005 | ICPP | Heuristics for Profile-Driven Method-Level Speculative Parallelization. | John Whaley, Christos Kozyrakis |
| 2005 | PODS | Context-sensitive program analysis as database queries. | Monica S. Lam, John Whaley, V. Benjamin Livshits, Michael C. Martin, Dzintars Avots, Michael Carbin, Christopher Unkel |
| 2004 | PLDI | Cloning-based context-sensitive pointer alias analysis using binary decision diagrams. | John Whaley, Monica S. Lam |
| 2002 | ISSTA | Automatic extraction of object-oriented component interfaces. | John Whaley, Michael C. Martin, Monica S. Lam |
| 2002 | SAS | An Efficient Inclusion-Based Points-To Analysis for Strictly-Typed Languages. | John Whaley, Monica S. Lam |
| 2001 | OOPSLA | Partial Method Compilation using Dynamic Profile Information. | John Whaley |
| 1999 | OOPSLA | Compositional Pointer and Escape Analysis for Java Programs. | John Whaley, Martin C. Rinard |