CSE 440
Areas of interest: 

Computational molecular biology

Comparative assessment of methods for aligning multiple genome sequences

X. Chen, M. TompaNature 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. ZhuPLOS 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-LaraMolecular Microbiology  72 :5 , 2009.

Assessing the Discordance of Multiple Sequence Alignments

A. Prakash, M. TompaIEEE/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. TompaBMC 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. BreakerNucleic Acids Research  35 :14 , 2007.

Measuring the Accuracy of Genome-Size Multiple Alignments

A. Prakash, M. TompaGenome Biology  8 :6 , 2007.

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. RuzzoPLOS 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. BakerJournal of Molecular Biology  362 :5 , 2006.

Analysis of Computational Approaches for Motif Discovery

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

MicroFootPrinter: a Tool for Phylogenetic Footprinting in Prokaryotic Genomes

S. Neph, M. TompaNucleic Acids Research  34 , 2006.

Statistics of Local Multiple Alignments

A. Prakash, M. TompaBioinformatics  21 , 2005.

Discovery of Regulatory Elements in Vertebrates Through Comparative Genomics

A. Prakash, M. TompaNature 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. ZhuNature Biotechnology  23 :1 , 2005.

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

S. Sinha, M. Blanchette, M. TompaBMC 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. WilsonProceedings of the National Academy of Science USA  101 :34 , 2004.

Motif Discovery in Heterogeneous Sequence Data

A. Prakash, M. Blanchette, S. Sinha, M. TompaPacific 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. ShermanMolecular Microbiology  48 :3 , 2003.

Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites

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

FootPrinter: a Program Designed for Phylogenetic Footprinting

M. Blanchette, M. TompaNucleic Acids Research  31 :13 , 2003.

An Empirical Comparison of Tools for Phylogenetic Footprinting

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

Finding Motifs Using Random Projections

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

Quality Control in Manufacturing Oligo Arrays: a Combinatorial Design Approach

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

Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting

M. Blanchette, M. TompaGenome Research  12 :5 , 2002.

Construction of Optimal Quality Control for Oligo Arrays

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

Algorithms for Phylogenetic Footprinting

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

Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation

S. Sinha, M. TompaNucleic Acids Research  30 :24 , 2002.

Identifying Functional Elements by Comparative DNA Sequence Analysis

M. TompaGenome Research  11 :7 , 2001.

Equireplicate Balanced Binary Codes for Oligo Arrays

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

A Statistical Method for Finding Transcription Factor Binding Sites

S. Sinha, M. TompaEighth 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. TompaSeventh International Conference on Intelligent Systems for Molecular Biology , 1999.

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

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

An Algorithm for Finding Novel Gapped Motifs in DNA Sequences

E. Rocke, M. Tompathe 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. TompaJournal of Parallel and Distributed Computing  34 :2 , 1996.

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

J. Buss, M. TompaInformation and Computation  120 :2 , 1995.

Communication-Space Tradeoffs for Unrestricted Protocols

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

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

M. TompaSIAM Journal on Computing  21 :6 , 1992.

Time-Space Tradeoffs for Undirected Graph Traversal

P. Beame, A. Borodin, P. Raghavan, W.L. Ruzzo, M. Tompa31st Annual Symposium on Foundations of Computer Science , 1990.

Zero Knowledge Interactive Proofs of Knowledge (a Digest)

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