| 2005 | ISMB | Statistics of local multiple alignments. | Amol Prakash, Martin Tompa |
| 2004 | PSB | Motif Discovery in Heterogeneous Sequence Data. | Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa |
| 2003 | BIBE | An Empirical Comparison of Tools for Phylogenetic Footprinting. | Mathieu Blanchette, Samson Kwong, Martin Tompa |
| 2003 | BIBE | Performance Comparison of Algorithms for FindingTranscription Factor Binding Sites. | Saurabh Sinha, Martin Tompa |
| 2001 | PSB | Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach. | Rimli Sengupta, Martin Tompa |
| 2001 | RECOMB | Finding motifs using random projections. | Jeremy Buhler, Martin Tompa |
| 2000 | ISMB | An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. | Mathieu Blanchette, Benno Schwikowski, Martin Tompa |
| 2000 | ISMB | A Statistical Method for Finding Transcription Factor Binding Sites. | Saurabh Sinha, Martin Tompa |
| 1999 | ISMB | A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. | Walter L. Ruzzo, Martin Tompa |
| 1999 | ISMB | An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem. | Martin Tompa |
| 1998 | RECOMB | An algorithm for finding novel gapped motifs in DNA sequences. | Emily Rocke, Martin Tompa |
| 1994 | SPAA | Minimal Adaptive Routing on the Mesh with Bounded Queue Size. | Donald D. Chinn, Frank Thomson Leighton, Martin Tompa |
| 1990 | FOCS | Time-Space Tradeoffs for Undirected Graph Traversal | Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa |
| 1990 | FOCS | Communication-Space Tradeoffs for Unrestricted Protocols | Paul Beame, Martin Tompa, Peiyuan Yan |
| 1989 | STOC | Lower Bounds on the Length of Universal Traversal Sequences (Detailed Abstract) | Allan Borodin, Walter L. Ruzzo, Martin Tompa |
| 1989 | STOC | Tradeoffs Between Communication and Space | Tak Wah Lam, Prasoon Tiwari, Martin Tompa |
| 1988 | TARK | Zero Knowledge Interactive Proofs of Knowledge (A Digest). | Martin Tompa |
| 1987 | FOCS | Parallel Graph Algorithms that Are Efficient on Average | Don Coppersmith, Prabhakar Raghavan, Martin Tompa |
| 1987 | FOCS | Random Self-Reducibility and Zero Knowledge Interactive Proofs of Possession of Information | Martin Tompa, Heather Woll |
| 1986 | CRYPTO | How to Share a Secret with Cheaters. | Martin Tompa, Heather Woll |
| 1986 | FOCS | A New Pebble Game that Characterizes Parallel Complexity Classes | H. Venkateswaran, Martin Tompa |
| 1985 | STOC | The Parallel Complexity of Exponentiating Polynomials over Finite Fields | Faith E. Fich, Martin Tompa |
| 1983 | STOC | Speedups of Deterministic Machines by Synchronous Parallel Machines | Patrick W. Dymond, Martin Tompa |
| 1982 | STOC | Probabilistic, Nondeterministic, and Alternating Decision Trees | Udi Manber, Martin Tompa |
| 1982 | STOC | Space-Bounded Hierarchies and Probabilistic Computations | Walter L. Ruzzo, Janos Simon, Martin Tompa |
| 1981 | FOCS | The Effect of Number of Hamiltonian Paths on the Complexity of a Vertex-Coloring Problem | Udi Manber, Martin Tompa |
| 1980 | STOC | An Optimal Solution to a Wire-Routing Problem (Preliminary Version) | Martin Tompa |
| 1980 | STOC | Two Familiar Transitive Closure Algorithms which Admit No Polynomial Time, Sublinear Space Implementations | Martin Tompa |
| 1979 | FOCS | A Time-Space Tradeoff for Sorting on Non-Oblivious Machines | Allan Borodin, Michael J. Fischer, David G. Kirkpatrick, Nancy A. Lynch, Martin Tompa |
| 1978 | STOC | Time-Space Tradeoffs for Computing Functions, Using Connectivity Properties of their Circuits | Martin Tompa |