| 2012 | DSN | Design and implementation of a hardware checkpoint/restart core. | Ashwin A. Mendon, Ron Sass, Zachary K. Baker, Justin L. Tripp |
| 2009 | FCCM | In-situ FPGA Debug Driven by On-Board Microcontroller. | Zachary K. Baker, Joshua S. Monson |
| 2007 | FCCM | On the Acceleration of Shortest Path Calculations in Transportation Networks. | Zachary K. Baker, Maya B. Gokhale |
| 2007 | FCCM | Matched Filter Computation on FPGA, Cell and GPU. | Zachary K. Baker, Maya B. Gokhale, Justin L. Tripp |
| 2006 | FCCM | An Architecture for Efficient Hardware Data Mining using Reconfigurable Computing Systems. | Zachary K. Baker, Viktor K. Prasanna |
| 2006 | FPL | Regular Expression Software Deceleration for Intrusion Detection Systems. | Zachary K. Baker, Viktor K. Prasanna, Hong-Jip Jung |
| 2005 | FCCM | Efficient Hardware Data Mining with the Apriori Algorithm on FPGAs. | Zachary K. Baker, Viktor K. Prasanna |
| 2004 | FCCM | A Methodology for Synthesis of Efficient Intrusion Detection Systems on FPGAs. | Zachary K. Baker, Viktor K. Prasanna |
| 2004 | FPGA | Time and area efficient pattern matching on FPGAs. | Zachary K. Baker, Viktor K. Prasanna |
| 2004 | FPL | Efficient FPGA-Based Security Kernels. | Zachary K. Baker |
| 2004 | FPL | Automatic Synthesis of Efficient Intrusion Detection Systems on FPGAs. | Zachary K. Baker, Viktor K. Prasanna |
| 2002 | EuroPar | Performance Modeling and Interpretive Simulation of PIM Architectures and Applications (Research Note). | Zachary K. Baker, Viktor K. Prasanna |