Contact

Martin Tompa
CSE 440
206-543-9263
tompacs.washington.edu
Areas of interest: 

Computational molecular biology

Comparative assessment of methods for aligning multiple genome sequences

X. Chen, M. Tompa, Nature Biotechnology 28:6, 2010.

Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases

K. Wang, M. Narayanan, H. Zhong, M. Tompa, E.E. Schadt, J. Zhu, PLOS Computational Biology 5:12, 2009.

Tp0262 is a Modulator of Promoter Activity of tpr Subfamily II Genes of Treponema pallidum ssp. pallidum

L. Giacani, C. Godornes, M. Puray-Chavez, C. Guerra-Giraldez, M. Tompa, S.A. Lukehart, A. Centurion-Lara, Molecular Microbiology 72:5, 2009.

Assessing the Discordance of Multiple Sequence Alignments

A. Prakash, M. Tompa, IEEE/ACM Transactions on Computational Biology and Bioinformatics 6:4, 2009.

Algorithms for Locating Extremely Conserved Elements in Multiple Sequence Alignments

H.H.E. Tseng, M. Tompa, BMC Bioinformatics 10:432, 2009.

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research

Z. Weinberg, J.E. Barrick, Z. Yao, A. Roth, J.N. Kim, J. Gore, J.X. Wang, E.R. Lee, K.F. Block, N. Sudarsan, S. Neph, M. Tompa, W.L. Ruzzo, R.R. Breaker, Nucleic Acids Research 35:14, 2007.

Measuring the Accuracy of Genome-Size Multiple Alignments

A. Prakash, M. Tompa, Genome Biology 8:6, 2007.

How accurately is ncRNA aligned within whole-genome multiple alignments?

A.X. Wang, W.L. Ruzzo, M. Tompa, BMC bioinformatics 8, 2007.
http://www.ncbi.nlm.nih.gov/pubmed/17963514?dopt=Abstract Abstract

A Computational Pipeline for High-Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Z. Yao, J. Barrick, Z. Weinberg, S. Neph, R. Breaker, M. Tompa, W.L. Ruzzo, PLOS Computational Biology 3:7, 2007.

Mistranslation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution

G. Dantas, A.L. Watters, B.M. Lunde, Z.M. Eletr, N.G. Isern, T. Roseman, J. Lipfert, S. Doniach, M. Tompa, B. Kuhlman, B.L. Stoddard, G. Varani, D. Baker, Journal of Molecular Biology 362:5, 2006.

Analysis of Computational Approaches for Motif Discovery

N. Li, M. Tompa, Algorithms for Molecular Biology 1:8, 2006.

MicroFootPrinter: a Tool for Phylogenetic Footprinting in Prokaryotic Genomes

S. Neph, M. Tompa, Nucleic Acids Research 34, 2006.

Statistics of Local Multiple Alignments

A. Prakash, M. Tompa, Bioinformatics 21, 2005.

Discovery of Regulatory Elements in Vertebrates Through Comparative Genomics

A. Prakash, M. Tompa, Nature Biotechnology 23:10, 2005.

Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites

M. Tompa, N. Li, T.L. Bailey, G.M. Church, D.B. Moor, E. Eskin, A.V. Favorov, M.C. Frith, Y. Fu, W.J. Kent, V.J. Makeev, A.A. Mironov, W.S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, Z. Zhu, Nature Biotechnology 23:1, 2005.

PhyME: A Probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences

S. Sinha, M. Blanchette, M. Tompa, BMC Bioinformatics 5, 2004.

Evolutionarily Conserved Sequence Elements that Positively Regulate IFN-γ Expression in T Cells

M. Shnyreva, W.M. Weaver, M. Blanchette, S.L. Taylor, M. Tompa, D.R. Fitzpatrick, C.B. Wilson, Proceedings of the National Academy of Science USA 101:34, 2004.

Motif Discovery in Heterogeneous Sequence Data

A. Prakash, M. Blanchette, S. Sinha, M. Tompa, Pacific Symposium on Biocomputing, 2004.

Rv3133c/dosR is a Transcription Factor that Mediates the Hypoxic Response of Mycobacterium tuberculosis

H.D. Park, K.M. Guinn, M.I. Harrell, R. Liao, M.I. Voskull, M. Tompa, G.K. Schoolnik, D.R. Sherman, Molecular Microbiology 48:3, 2003.

YMF: a Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation

S. Sinha, M. Tompa, Nucleic Acids Research 31:13, 2003.

Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites

S. Sinha, M. Tompa, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003.

FootPrinter: a Program Designed for Phylogenetic Footprinting

M. Blanchette, M. Tompa, Nucleic Acids Research 31:13, 2003.

An Empirical Comparison of Tools for Phylogenetic Footprinting

M. Blanchette, S. Kwong, M. Tompa, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003.

Finding Motifs Using Random Projections

J. Buhler, M. Tompa, Journal of Computational Biology 9:2, 2002.

Quality Control in Manufacturing Oligo Arrays: a Combinatorial Design Approach

R. Sengupta, M. Tompa, Journal of Computational Biology 9:1, 2002.

Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting

M. Blanchette, M. Tompa, Genome Research 12:5, 2002.

Construction of Optimal Quality Control for Oligo Arrays

C.J. Colbourn, A.C.H. Ling, M. Tompa, Bioinformatics 18:4, 2002.

Algorithms for Phylogenetic Footprinting

M. Blanchette, B. Schwikowski, M. Tompa, Journal of Computational Biology 9:2, 2002.

Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation

S. Sinha, M. Tompa, Nucleic Acids Research 30:24, 2002.

Identifying Functional Elements by Comparative DNA Sequence Analysis

M. Tompa, Genome Research 11:7, 2001.

Equireplicate Balanced Binary Codes for Oligo Arrays

N. Alon, C.J. Colbourn, A.C.H. Ling, M. Tompa, SIAM Journal on Discrete Mathematics 14, 2001.

A Statistical Method for Finding Transcription Factor Binding Sites

S. Sinha, M. Tompa, Eighth International Conference on Intelligent Systems for Molecular Biology, 2000.

An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem

M. Tompa, Seventh International Conference on Intelligent Systems for Molecular Biology, 1999.

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

W.L. Ruzzo, M. Tompa, Seventh International Conference on Intelligent Systems for Molecular Biology, 1999.

An Algorithm for Finding Novel Gapped Motifs in DNA Sequences

E. Rocke, M. Tompa, the Second Annual International Conference on Computational Molecular Biology, 1998.

Minimal Adaptive Routing on the Mesh with Bounded Queue Size

D.D. Chinn, T. Leighton, M. Tompa, Journal of Parallel and Distributed Computing 34:2, 1996.

Lower Bounds on Universal Traversal Sequences Based on Chains of Length Five

J. Buss, M. Tompa, Information and Computation 120:2, 1995.

Communication-Space Tradeoffs for Unrestricted Protocols

P. Beame, P. Yan, M. Tompa, SIAM Journal on Computing 23:3, 1994.

Lower Bounds on Universal Traversal Sequences for Cycles and Other Low Degree Graphs

M. Tompa, SIAM Journal on Computing 21:6, 1992.

Time-Space Tradeoffs for Undirected Graph Traversal

P. Beame, A. Borodin, P. Raghavan, W.L. Ruzzo, M. Tompa, 31st Annual Symposium on Foundations of Computer Science, 1990.

Zero Knowledge Interactive Proofs of Knowledge (a Digest)

M. Tompa, Second Conference on Theoretical Aspects of Reasoning about Knowledge, 1988.