| 2008 | APLAS | Sound and Complete Type Inference for a Systems Programming Language. | Swaroop Sridhar, Jonathan S. Shapiro, Scott F. Smith |
| 2006 | ASPLOS | Type inference for unboxed types and first class mutability. | Swaroop Sridhar, Jonathan S. Shapiro |
| 2004 | CCS | Using build-integrated static checking to preserve correctness invariants. | Hao Chen, Jonathan S. Shapiro |
| 2004 | USENIX | Network Subsystems Reloaded: A High-Performance, Defensible Network Subsystem. | Anshumal Sinha, Sandeep Sarat, Jonathan S. Shapiro |
| 2003 | SP | Vulnerabilities in Synchronous IPC Designs. | Jonathan S. Shapiro |
| 2003 | USENIX | OpenCM: Early Experiences and Lessions Learned. | Jonathan S. Shapiro, John Vanderburgh, Jack Lloyd |
| 2002 | USENIX | Design Evolution of the EROS Single-Level Store. | Jonathan S. Shapiro, Jonathan Adams |
| 2002 | USENIX | CPCMS: A Configuration Management System Based on Cryptographic Names. | Jonathan S. Shapiro, John Vanderburgh |
| 2000 | SP | Verifying the EROS Confinement Mechanism. | Jonathan S. Shapiro, Sam Weber |
| 1999 | SOSP | EROS: a fast capability system. | Jonathan S. Shapiro, Jonathan M. Smith, David J. Farber |