Lecture Notes and Articles
Martin Tompa

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• PDF: Use the free Adobe Acrobat viewer.
• PS: Use the free Ghostview/Ghostscript PostScript viewer.

• Here is a video of a lecture on The Role of Mathematics and Computer Science in Molecular Biology Research, intended for undergraduates from any of these disciplines.
• Here is a video of What Can We Do With A Multitude Of Genome Sequences?, presented as a Distinguished Lecture at Georgia Institute of Technology in February 2008.
• Here are slides for a lecture on the RSA Cryptosystem, suitable for motivated high school students.

• Algorithms in Molecular Biology (CSE 527)
  (Updated chapter on Basics of Molecular Biology)
• Message Routing in Parallel Machines (CSE 522)
• Probabilistic Algorithms and Pseudorandom Generators (CSE 522)
• Introduction to Computational Complexity PS PDF (CSE 532)

I have written the definitive book on this strategy, titled Winning Schnapsen.

1. Xiaoyu Chen and Martin Tompa, Comparative assessment of methods for aligning multiple genome sequences. Nature Biotechnology, vol. 28, no. 6, June 2010, 567-572.

2. Huei-Hun Elizabeth Tseng and Martin Tompa, Algorithms for Locating Extremely Conserved Elements in Multiple Sequence Alignments. BMC Bioinformatics, vol. 10, no. 432, 2009.

3. K. Wang, M. Narayanan, H. Zhong, M. Tompa, E. E. Schadt, and J. Zhu, Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases. PLOS Computational Biology, vol. 5, no. 12, 2009, e1000616.

4. Amol Prakash and Martin Tompa, Assessing the Discordance of Multiple Sequence Alignments. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 4, October-December 2009, 542-551.

5. L. Giacani, C. Godornes, M. Puray-Chavez, C. Guerra-Giraldez, M. Tompa, S. A. Lukehart, and A. Centurion-Lara, Tp0262 is a Modulator of Promoter Activity of tpr Subfamily II Genes of Treponema pallidum ssp. pallidum. Molecular Microbiology, vol. 72, no. 5, June 2009, 1087-1099.

6. Adrienne X. Wang, Walter L. Ruzzo, and Martin Tompa, How Accurately Is ncRNA Aligned Within Whole-Genome Multiple Alignments? BMC Bioinformatics, vol. 8, no. 417, October 2007.

7. 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, and R. R. Breaker, Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research, vol. 35, no. 14, July 2007, 4809-4819.

8. Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, and Walter L. Ruzzo, A Computational Pipeline for High-Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes. PLOS Computational Biology, vol. 3, no. 7, July 2007, e126.

9. Amol Prakash and Martin Tompa, Measuring the Accuracy of Genome-Size Multiple Alignments. Genome Biology, vol. 8, issue 6, June 2007, R124.

10. 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, and D. Baker, Mistranslation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution. Journal of Molecular Biology, vol. 362, issue 5, October 6, 2006, 1004-1024.

11. Shane Neph and Martin Tompa, MicroFootPrinter: a Tool for Phylogenetic Footprinting in Prokaryotic Genomes. Nucleic Acids Research, vol. 34, July 2006, W366-W368.

12. Nan Li and Martin Tompa, Analysis of Computational Approaches for Motif Discovery. Algorithms for Molecular Biology, vol. 1, no. 8, May 2006.

13. Amol Prakash and Martin Tompa, Discovery of Regulatory Elements in Vertebrates Through Comparative Genomics. Nature Biotechnology, vol. 23, no. 10, October 2005, 1249 - 1256.

14. Amol Prakash and Martin Tompa, Statistics of Local Multiple Alignments. 13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, MI, June 2005. Bioinformatics, vol. 21, June 2005, i344 - i350.

15. M. Tompa, N. Li, T. L. Bailey , G. M. Church , B. De 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. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu, Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology, vol. 23, no. 1, January 2005, 137 - 144.

16. Saurabh Sinha, Mathieu Blanchette, and Martin Tompa, PhyME: A Probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences. BMC Bioinformatics, vol. 5, 2004, 170.

17. Maria Shnyreva, William M. Weaver, Mathieu Blanchette, Scott L. Taylor, Martin Tompa, David R. Fitzpatrick, and Christopher B. Wilson, Evolutionarily Conserved Sequence Elements that Positively Regulate IFN-γ Expression in T Cells. Proceedings of the National Academy of Science USA, vol. 101, no. 34, August 2004, 12622-12627.

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

19. Mathieu Blanchette and Martin Tompa, FootPrinter: a Program Designed for Phylogenetic Footprinting. Nucleic Acids Research, vol. 31, no. 13, July 2003, 3840-3842.

20. Saurabh Sinha and Martin Tompa, YMF: a Program for Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research, vol. 31, no. 13, July 2003, 3586-3588.

21. Heui-Dong Park, Kristi M. Guinn, Maria I. Harrell, Reiling Liao, Martin I. Voskull, Martin Tompa, Gary K. Schoolnik and David R. Sherman, Rv3133c/dosR is a Transcription Factor that Mediates the Hypoxic Response of Mycobacterium tuberculosis. Molecular Microbiology, vol. 48, issue 3, May 2003, 833-843.

22. Mathieu Blanchette, Samson Kwong, and Martin Tompa, An Empirical Comparison of Tools for Phylogenetic Footprinting. Third IEEE Symposium on Bioinformatics and Bioengineering, Washington, D.C., March 2003, 69-78.

23. Saurabh Sinha and Martin Tompa, Performance Comparison of Algorithms for Finding Transcription Factor Binding Sites. Third IEEE Symposium on Bioinformatics and Bioengineering, Washington, D.C., March 2003, 214-220.

24. Saurabh Sinha and Martin Tompa, Discovery of Novel Transcription Factor Binding Sites by Statistical Overrepresentation. Nucleic Acids Research, vol. 30, no. 24, December 2002, 5549-5560.

25. Mathieu Blanchette and Martin Tompa, Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting. Genome Research, vol. 12, no. 5, May 2002, 739-748.

26. Mathieu Blanchette, Benno Schwikowski, and Martin Tompa, Algorithms for Phylogenetic Footprinting. Journal of Computational Biology, vol. 9, no. 2, 2002, 211-223.

27. Jeremy Buhler and Martin Tompa, Finding Motifs Using Random Projections. Journal of Computational Biology, vol. 9, no. 2, 2002, 225-242. Awarded the RECOMB 2013 Test of Time Award.

28. Charles J. Colbourn, Alan C. H. Ling, and Martin Tompa, Construction of Optimal Quality Control for Oligo Arrays. Bioinformatics, vol. 18, no. 4, April 2002, 529-535.

29. Rimli Sengupta and Martin Tompa, Quality Control in Manufacturing Oligo Arrays: a Combinatorial Design Approach. Journal of Computational Biology, vol. 9, no. 1, 2002, 1-22.

30. Martin Tompa, Identifying Functional Elements by Comparative DNA Sequence Analysis. Invited Insight/Outlook commentary, Genome Research, vol. 11, no. 7, July 2001, 1143-1144.

31. Noga Alon, Charles J. Colbourn, Alan C. H. Ling, and Martin Tompa, Equireplicate Balanced Binary Codes for Oligo Arrays. SIAM Journal on Discrete Mathematics, vol. 14, 2001, 481-497.

32. Saurabh Sinha and Martin Tompa, A Statistical Method for Finding Transcription Factor Binding Sites. Eighth International Conference on Intelligent Systems for Molecular Biology, San Diego, CA, August 2000, 344-354.

33. Martin Tompa, An Exact Method for Finding Short Motifs in Sequences, with Application to the Ribosome Binding Site Problem. Seventh International Conference on Intelligent Systems for Molecular Biology, Heidelberg, Germany, August 1999, 262-271.

34. Walter L. Ruzzo and Martin Tompa, A Linear Time Algorithm for Finding All Maximal Scoring Subsequences. Seventh International Conference on Intelligent Systems for Molecular Biology, Heidelberg, Germany, August 1999, 234-241.

35. Emily Rocke and Martin Tompa, An Algorithm for Finding Novel Gapped Motifs in DNA Sequences. RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology, New York, NY, March 1998, 228-233.

36. Donald D. Chinn, Tom Leighton, and Martin Tompa, Minimal Adaptive Routing on the Mesh with Bounded Queue Size. Journal of Parallel and Distributed Computing, vol. 34, no. 2, May 1, 1996, 154-170.

37. Jonathan Buss and Martin Tompa, Lower Bounds on Universal Traversal Sequences Based on Chains of Length Five. Information and Computation, vol. 120, no. 2, August 1995, 326-329.

38. Paul Beame, Penyuan Yan, and Martin Tompa, Communication-Space Tradeoffs for Unrestricted Protocols. SIAM Journal on Computing, vol. 23, no. 3, June 1994, 652-661.

39. Martin Tompa, Lower Bounds on Universal Traversal Sequences for Cycles and Other Low Degree Graphs. SIAM Journal on Computing, vol. 21, no. 6, December 1992, 1153-1160.

40. Paul Beame, Allan Borodin, Prabhakar Raghavan, Walter L. Ruzzo, and Martin Tompa, Time-Space Tradeoffs for Undirected Graph Traversal. 31st Annual Symposium on Foundations of Computer Science, St. Louis, Missouri, October 1990, 429-438.

41. Martin Tompa, Zero Knowledge Interactive Proofs of Knowledge (a Digest). Proceedings of the Second Conference on Theoretical Aspects of Reasoning about Knowledge, Monterey, California, March 1988, 1-12 (invited address).

42. Martin Tompa, Figures of Merit. SIGACT News, vol. 20, no. 1, Winter 1989, 62-71.

43. Martin Tompa, Figures of Merit: The Sequel. SIGACT News, vol. 21, no. 4, Fall 1990, 78-81.