| 2013 | FPGA | Accelerating ncRNA homology search with FPGAs. | Nathaniel McVicar, Walter L. Ruzzo, Scott Hauck |
| 2012 | FCCM | Hardware Acceleration of Short Read Mapping. | Corey B. Olson, Maria Kim, Cooper Clauson, Boris Kogon, Carl Ebeling, Scott Hauck, Walter L. Ruzzo |
| 2008 | APBC | Finding Non-coding RNAs Through Genome-Scale Clustering. | Huei-Hun Elizabeth Tseng, Zasha Weinberg, Jeremy Gore, Ronald R. Breaker, Walter L. Ruzzo |
| 2004 | ISMB | Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. | Zasha Weinberg, Walter L. Ruzzo |
| 2004 | RECOMB | Faster genome annotation of non-coding RNA families without loss of accuracy. | Zasha Weinberg, Walter L. Ruzzo |
| 2003 | PSB | Improved Gene Selection for Classification of Microarrays. | Jochen Jaeger, Rimli Sengupta, Walter L. Ruzzo |
| 2002 | PSB | Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction. | Donald J. Patterson, Ken Yasuhara, Walter L. Ruzzo |
| 2000 | CIAC | Algorithms for a Simple Point Placement Problem. | Joshua Redstone, Walter L. Ruzzo |
| 1999 | ISMB | A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. | Walter L. Ruzzo, Martin Tompa |
| 1991 | STOC | Deterministic Algorithms for Undirected s-t Connectivity Using Polynomial Time and Sublinear Space (Extended Abstract) | Greg Barnes, Walter L. Ruzzo |
| 1990 | FOCS | Time-Space Tradeoffs for Undirected Graph Traversal | Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa |
| 1990 | SPAA | Low Overhead Parallel Schedules for Task Graphs. | Richard J. Anderson, Paul Beame, Walter L. Ruzzo |
| 1989 | STOC | Lower Bounds on the Length of Universal Traversal Sequences (Detailed Abstract) | Allan Borodin, Walter L. Ruzzo, Martin Tompa |
| 1989 | STOC | The Electrical Resistance of a Graph Captures its Commute and Cover Times (Detailed Abstract) | Ashok K. Chandra, Prabhakar Raghavan, Walter L. Ruzzo, Roman Smolensky, Prasoon Tiwari |
| 1989 | SPAA | The Power of Parallel Pointer Manipulation. | Tak Wah Lam, Walter L. Ruzzo |
| 1986 | ICALP | Parallel RAMs with Owned Global Memory and Deterministic Context-Free Language Recognition (Extended Abstract). | Patrick W. Dymond, Walter L. Ruzzo |
| 1982 | STOC | Space-Bounded Hierarchies and Probabilistic Computations | Walter L. Ruzzo, Janos Simon, Martin Tompa |
| 1981 | STOC | Bounds on Minimax Edge Length for Complete Binary Trees (Extended Abstract) | Mike Paterson, Walter L. Ruzzo, Lawrence Snyder |
| 1979 | FOCS | On Uniform Circuit Complexity (Extended Abstract) | Walter L. Ruzzo |
| 1979 | ICALP | On the Complexity of General Context-Free Language Parsing and Recognition (Extended Abstract). | Walter L. Ruzzo |
| 1979 | STOC | Tree-Size Bounded Alternation | Walter L. Ruzzo |
| 1976 | STOC | On Line Context Free Language Recognition in Less than Cubic Time (Extended Abstract) | Susan L. Graham, Michael A. Harrison, Walter L. Ruzzo |
| 1975 | SOSP | On Protection in Operating System. | Michael A. Harrison, Walter L. Ruzzo, Jeffrey D. Ullman |