Martin Tompa

Huei-Hun E. Tseng, Martin Tompa: Algorithms for locating extremely conserved elements in multiple sequence alignments. BMC Bioinformatics 10: 432 (2009)

Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E. Schadt, Jun Zhu: Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases. PLoS Computational Biology 5(12) (2009)

Amol Prakash, Martin Tompa: Assessing the Discordance of Multiple Sequence Alignments. IEEE/ACM Trans. Comput. Biology Bioinform. 6(4): 542-551 (2009)

Adrienne X. Wang, Walter L. Ruzzo, Martin Tompa: How accurately is ncRNA aligned within whole-genome multiple alignments? BMC Bioinformatics 8 (2007)

Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald R. Breaker, Martin Tompa, Walter L. Ruzzo: A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. PLoS Computational Biology 3(7) (2007)

Nan Li, Martin Tompa: Analysis of computational approaches for motif discovery. Algorithms for Molecular Biology 1 (2006)

Shane Neph, Martin Tompa: MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Research 34(Web-Server-Issue): 366-368 (2006)

Amol Prakash, Martin Tompa: Statistics of local multiple alignments. ISMB (Supplement of Bioinformatics) 2005: 344-350

Saurabh Sinha, Mathieu Blanchette, Martin Tompa: PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5: 170 (2004)

Amol Prakash, Mathieu Blanchette, Saurabh Sinha, Martin Tompa: Motif Discovery in Heterogeneous Sequence Data. Pacific Symposium on Biocomputing 2004: 348-359

Saurabh Sinha, Martin Tompa: YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research 31(13): 3586-3588 (2003)

Mathieu Blanchette, Martin Tompa: FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Research 31(13): 3840-3842 (2003)

Mathieu Blanchette, Samson Kwong, Martin Tompa: An Empirical Comparison of Tools for Phylogenetic Footprinting. BIBE 2003: 69-78

Saurabh Sinha, Martin Tompa: Performance Comparison of Algorithms for FindingTranscription Factor Binding Sites. BIBE 2003: 214-

Charles J. Colbourn, Alan C. H. Ling, Martin Tompa: Construction of optimal quality control for oligo arrays. Bioinformatics 18(4): 529-535 (2002)

Rimli Sengupta, Martin Tompa: Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach. Journal of Computational Biology 9(1): 1-22 (2002)

Mathieu Blanchette, Benno Schwikowski, Martin Tompa: Algorithms for Phylogenetic Footprinting. Journal of Computational Biology 9(2): 211-223 (2002)

Jeremy Buhler, Martin Tompa: Finding Motifs Using Random Projections. Journal of Computational Biology 9(2): 225-242 (2002)

Noga Alon, Charles J. Colbourn, Alan C. H. Ling, Martin Tompa: Equireplicate Balanced Binary Codes for Oligo Arrays. SIAM J. Discrete Math. 14(4): 481-497 (2001)

Rimli Sengupta, Martin Tompa: Quality Control in Manufacturing Oligo Arrays: A Combinatorial Design Approach. Pacific Symposium on Biocomputing 2001: 348-359

Jeremy Buhler, Martin Tompa: Finding motifs using random projections. RECOMB 2001: 69-76

Mathieu Blanchette, Benno Schwikowski, Martin Tompa: An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species. ISMB 2000: 37-45

Saurabh Sinha, Martin Tompa: A Statistical Method for Finding Transcription Factor Binding Sites. ISMB 2000: 344-354

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: A Time-Space Tradeoff for Undirected Graph Traversal by Walking Automata. SIAM J. Comput. 28(3): 1051-1072 (1999)

Walter L. Ruzzo, Martin Tompa: A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. ISMB 1999: 234-241

Martin Tompa: An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem. ISMB 1999: 262-271

Emily Rocke, Martin Tompa: An algorithm for finding novel gapped motifs in DNA sequences. RECOMB 1998: 228-233

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata. Inf. Comput. 130(2): 101-129 (1996)

Donald D. Chinn, Frank Thomson Leighton, Martin Tompa: Minimal Adaptive Routing on the Mesh with Bounded Queue Size. J. Parallel Distrib. Comput. 34(2): 154-170 (1996)

Jonathan F. Buss, Martin Tompa: Lower Bounds on Universal Traversal Sequences Based on Chains of Length Five. Inf. Comput. 120(2): 326-329 (1995)

Prasoon Tiwari, Martin Tompa: A Direct Version of Shamir and Snir's Lower Bounds on Monotone Circuit Depth. Inf. Process. Lett. 49(5): 243-248 (1994)

Paul Beame, Martin Tompa, Peiyuan Yan: Communication-Space Tradeoffs for Unrestricted Protocols. SIAM J. Comput. 23(3): 652-661 (1994)

Donald D. Chinn, Frank Thomson Leighton, Martin Tompa: Minimal Adaptive Routing on the Mesh with Bounded Queue Size. SPAA 1994: 354-363

Allan Borodin, Walter L. Ruzzo, Martin Tompa: Lower Bounds on the Length of Universal Traversal Sequences. J. Comput. Syst. Sci. 45(2): 180-203 (1992)

Tak Wah Lam, Prasoon Tiwari, Martin Tompa: Trade-Offs between Communication and Space. J. Comput. Syst. Sci. 45(3): 296-315 (1992)

Martin Tompa: Lower Bounds on Universal Traversal Sequences for Cycles and Other Low Degree Graphs. SIAM J. Comput. 21(6): 1153-1160 (1992)

Ashok K. Chandra, Martin Tompa: The complexity of short two-person games. Discrete Applied Mathematics 29(1): 21-33 (1990)

Martin Tompa: Figures of merit: the sequel. SIGACT News 21(4): 78-81 (1990)

Paul Beame, Martin Tompa, Peiyuan Yan: Communication-Space Tradeoffs for Unrestricted Protocols. FOCS 1990: 420-428

Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, Martin Tompa: Time-Space Tradeoffs for Undirected Graph Traversal. FOCS 1990: 429-438

Don Coppersmith, Prabhakar Raghavan, Martin Tompa: Parallel Graph Algorithms That Are Efficient on Average. Inf. Comput. 81(3): 318-333 (1989)

H. Venkateswaran, Martin Tompa: A New Pebble Game That Characterizes Parallel Complexity Classes. SIAM J. Comput. 18(3): 533-549 (1989)

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Two Applications of Inductive Counting for Complementation Problems. SIAM J. Comput. 18(3): 559-578 (1989)

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Erratum: Two Applications of Inductive Counting for Complementation Problems. SIAM J. Comput. 18(6): 1283 (1989)

Martin Tompa: Figures of merit. SIGACT News 20(1): 62-71 (1989)

Tak Wah Lam, Prasoon Tiwari, Martin Tompa: Tradeoffs Between Communication and Space. STOC 1989: 217-226

Allan Borodin, Walter L. Ruzzo, Martin Tompa: Lower Bounds on the Length of Universal Traversal Sequences (Detailed Abstract). STOC 1989: 562-573

Faith E. Fich, Martin Tompa: The parallel complexity of exponentiating polynomials over finite fields. J. ACM 35(3): 651-667 (1988)

Martin Tompa, Heather Woll: How to Share a Secret with Cheaters. J. Cryptology 1(2): 133-138 (1988)

Allan Borodin, Stephen A. Cook, Patrick W. Dymond, Walter L. Ruzzo, Martin Tompa: Two applications of complementation via inductive counting. Structure in Complexity Theory Conference 1988: 116-125

Martin Tompa: Zero Knowledge Interactive Proofs of Knowledge (A Digest). TARK 1988: 1-12

Don Coppersmith, Prabhakar Raghavan, Martin Tompa: Parallel Graph Algorithms that Are Efficient on Average. FOCS 1987: 260-269

Martin Tompa, Heather Woll: Random Self-Reducibility and Zero Knowledge Interactive Proofs of Possession of Information. FOCS 1987: 472-482

Martin Tompa, Heather Woll: How to Share a Secret with Cheaters. CRYPTO 1986: 261-265

H. Venkateswaran, Martin Tompa: A New Pebble Game that Characterizes Parallel Complexity Classes. FOCS 1986: 348-360

Udi Manber, Martin Tompa: The Complexity of Problems on Probabilistic Nondeterministic, and Alternating Decision Trees. J. ACM 32(3): 720-732 (1985)

Patrick W. Dymond, Martin Tompa: Speedups of Deterministic Machines by Synchronous Parallel Machines. J. Comput. Syst. Sci. 30(2): 149-161 (1985)

Allan Borodin, Ronald Fagin, John E. Hopcroft, Martin Tompa: Decreasing the Nesting Depth of Expressions Involving Square Roots. J. Symb. Comput. 1(2): 169-188 (1985)

Faith E. Fich, Martin Tompa: The Parallel Complexity of Exponentiating Polynomials over Finite Fields. STOC 1985: 38-47

Walter L. Ruzzo, Janos Simon, Martin Tompa: Space-Bounded Hierarchies and Probabilistic Computations. J. Comput. Syst. Sci. 28(2): 216-230 (1984)

Udi Manber, Martin Tompa: The Effect of Number of Hamiltonian Paths on the Complexity of a Vertex-Coloring Problem. SIAM J. Comput. 13(1): 109-115 (1984)

Patrick W. Dymond, Martin Tompa: Speedups of Deterministic Machines by Synchronous Parallel Machines. STOC 1983: 336-343

Martin Tompa: Two Familiar Transitive Closure Algorithms Which Admit No Polynomial Time, Sublinear Space Implementations. SIAM J. Comput. 11(1): 130-137 (1982)

Walter L. Ruzzo, Janos Simon, Martin Tompa: Space-Bounded Hierarchies and Probabilistic Computations. STOC 1982: 215-223

Udi Manber, Martin Tompa: Probabilistic, Nondeterministic, and Alternating Decision Trees. STOC 1982: 234-244

Martin Tompa: An Extension of Savitch's Theorem to Small Space Bounds. Inf. Process. Lett. 12(2): 106-108 (1981)

Allan Borodin, Michael J. Fischer, David G. Kirkpatrick, Nancy A. Lynch, Martin Tompa: A Time-Space Tradeoff for Sorting on Non-Oblivious Machines. J. Comput. Syst. Sci. 22(3): 351-364 (1981)

Martin Tompa: Corrigendum: Time-Space Tradeoffs for Computing Functions, Using Connectivity Properties of Their Circuits. J. Comput. Syst. Sci. 23(1): 106 (1981)

Martin Tompa: An Optimal Solution to a Wire-Routing Problem. J. Comput. Syst. Sci. 23(2): 127-150 (1981)

Udi Manber, Martin Tompa: The Effect of Number of Hamiltonian Paths on the Complexity of a Vertex-Coloring Problem. FOCS 1981: 220-227

Martin Tompa: Time-Space Tradeoffs for Computing Functions, Using Connectivity Properties of Their Circuits. J. Comput. Syst. Sci. 20(2): 118-132 (1980)

Martin Tompa: An Optimal Solution to a Wire-Routing Problem (Preliminary Version). STOC 1980: 161-176

Martin Tompa: Two Familiar Transitive Closure Algorithms which Admit No Polynomial Time, Sublinear Space Implementations. STOC 1980: 333-338

Allan Borodin, Michael J. Fischer, David G. Kirkpatrick, Nancy A. Lynch, Martin Tompa: A Time-Space Tradeoff for Sorting on Non-Oblivious Machines. FOCS 1979: 319-327

Martin Tompa: Time-Space Tradeoffs for Computing Functions, Using Connectivity Properties of their Circuits. STOC 1978: 196-204