Michael S. Waterman

Professor of Mathematics

Professor of Biological Sciences

Professor of Computer Science

University of Southern California

MAIL: 1042W 36th Place, DRB 155, Los Angeles, California 90089-1113

PHONE: (213) 740-2408

FAX: (213) 740-2437

OFFICE: DRB 284

EMAIL: [email protected]

Michael Waterman holds an Endowed Associates Chair at USC. He came to USC in 1982 after positions at Los Alamos National Laboratory and Idaho State University. His bachelors in Mathematics is from Oregon State University, and his PhD in Statistics and Probability is from Michigan State University. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Art and Sciences (1995), and was elected to the National Academy of Sciences (2001). Also he is a Fellow of the American Association for the Advancement of Science and Fellow of the Institute of Mathematical Statistics. He has held visiting positions at the University of Hawaii (1979-80), the University of California at San Francisco (1982), Mt. Sinai Medical School (1988), Chalmers University (2000), and in 2000-2001 he held the Aisenstadt Chair at University of Montreal. He is Professor-at-large at the Keck Graduate Institute of Life Sciences and in fall 2000 he became the first Fellow of Celera Genomics. In 2002 he received a Gairdner Foundation International Award

Professor Waterman works in the area of Computational Biology, concentrating on the creation and application of mathematics, statistics and computer science to molecular biology, particularly to DNA, RNA, and protein sequence data. He is the co-developer of the Smith-Waterman algorithm for sequence comparison and of the Lander-Waterman formula for physical mapping. He is a founding editor of Journal of Computational Biology, is on the editorial board of seven journals, and is author of the text Introduction to Computational Biology: Maps, Sequences and Genomes.

Books and Volumes Edited:

1. Proceedings Third Annual Conference on Computational Molecular Biology (RECOMB 99) S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508991, (April 11-14, 1999) Mathematical Support for Molecular Biology. (1999), M. Faxach-Colton, F.S. Roberts, M. Vingron, and M.S. Waterman, Editors. American Mathematical Society, 288 pages.

2. Proceedings Second Annual Conference on Computational Molecular Biology (RE- COMB 98) S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508981, (Maxch 22-25, 1998)

3. Proceedings First Annual Conference on Computational Molecular Biology (RECOMB 98) M.S. Waterman, S. Istrail and P. Pevzner, Editors. ACM Press, Order Number 508971, (January 19 - 22, 1997)

4. Genetic Mapping and DNA Sequencing (1996), T. Speed and M.S. Waterman, Editors. 81 IMA Volumes in Mathematics and its Applications, Springer-Veriag. 215 pages.

5. Introduction to Computational Biology: Sequences, Maps and Genomes. (1995), M.S. Waterman. Chapman Hall, 431 pages.

6. Calculating the Secrets of Life. (1995) E. Lander and Waterman, M.S. , Editors. National Academy Press, Washington DC. 285 pages.

7. Mathematical Analysis of Molecular Sequences. M.S.Waterman, Guest Editor. Special Issue. Bulletin of Mathematical Biology 51, Issue #1, (1989).

8. Mathematical Methods for DNA Sequences. (1989), M.S. Waterman , Editor. CRC Press. 283 pages.

9. Russian translation of Mathematical Methods for DNA Sequences (1989): Matematicheskie metody dlja analiza posledovatel'noste' DNK pod red. M. Uoterrnena. MIR Publishers (1999).

Papers published (reverse chronological order):

1. Reinert, G., Scabath, S., and Waterman, M.S (2000) Probablistic and statistical properties of words J.Comp. Biol., 7 1-48.

2. Beschler, E.F., Buchsbaum, D.A., Schwartz, J.T., Stanley, R.P., Taylor, B.D., and Waterman, M.S. (2000) Gian-Carlo Rota (1932-1999) Notices of the AMS, February 2000, 47 203-216.

3. Lee, J.K., Dancik, V., and Waterman, M.S. (1997) Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain monte carlo. J. Comp. Biol., 5 505-516.

4. Sun, F., Benson, G., Arnheim, A., and Waterman, M.S. 1997, "Pooling strategies for establishing genome maps using FISH,"J. Comp. Biol, 4 467-486

5. Sun, F. and Waterman, M.S. 1997, "Single chromosome amplification and branching processes," Adv. Appl. Probab, 29 629-668.

6. Komatsoulis, G.A. and Waterman, M.S. 1997, "A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplication from mixed bacterial populations," Appl. and Environ. Microbiology, 63 2338-2346.

7. Xiong, M. and Waterman, M.S. 1997, "A Phase transition for the minimum free energy of secondary structures of a random RNA," Adv. Appl. Math, 18 111-132.

8. Vingron, M. and Waterman, M.S. 1996, "Alignment networks and electrical networks," Discrete Math, 71 297-309.

9. Steel, M., Goldstein, L., and Waterman, M.S. 1996, "A central limit theorem for parsimony length of trees," Appl. Porbab, 28 1051-1071.

10. Arratia, R., Martin, D., Reinert, G., and Waterman, M.S. 1996, "Poisson process approximation for sequence repeats, and sequencing by hybridization," J. Comp. Biol, 3 425-463. 

11. Sun, F., Galas, D., and Waterman, M.S. "A mathematical analysis of in vitro molecular selection-amplification," J. Mol. Biol., 258 650-660 (1996)

12. Sun, F., Arnheim, N., and Waterman, M.S. "Whole genome amplification of single cells: mathematical analysis of PEP and tagged PCR," Nucleic Acids Research, 23 3034-3040.

13. Waterman, M.S. "Combinatorics in molecular biology," Handbook of Combinatorics.

14. Idury, R. and Waterman, M.S. "A new algorithm for DNA sequence assembly," Journal of Computational Biology, 2:2, 291-306.

15. Waterman, M.S., 1995, "Hearing distant echos," Calculating the Secrets of Life. National Academy Press, E. Lander and Waterman, M.S., Eds. 90-113.

16. Lander, E., and Waterman, M.S., 1995, "The secrets of life," Calculating the Secrets of Life. National Academy Press, E. Lander and Waterman, M.S., Eds. 1-24.

17. Port, E., Sun, F., Martin, D., Waterman, M.S. "Genomic mapping by end-characterized random clones: a mathematical analysis," Genomics, 26, 84-100, 1995.

18. Waterman, M.S., 1994, "Genomes, maps and sequences," Lecture Notes in Biomathematics, 100 28-52.

19. Benson, G. and Waterman, M.S.,1994, "A method for fast database search for all k-nucleotide repeats," Nucleic Acids Research, 22 4828-4836.

20. Waterman, M.S. and Vingron, M.,1994, "Sequence comparison significance and Poisson approximation," Statistical Sciences, 9 367-381.

21. Pevzner, P.A. and Waterman, M.S., 1995, "Multiple filtration and approximate pattern matching," Algorithmica, 13 135-154.

22. Schmitt, W.R. and Waterman, M.S., 1994, "Linear trees and RNA secondary structure," Disc. Appl. Math., 51 317-323.

23. Goldstein, L. and Waterman, M.S., 1994, "Approximations to profile score distributions," J. Comp. Biol., 1 93-104.

24. Waterman, M.S., 1994, "Estimating of statistical significance of sequence alignments," Phil. Trans. R. Soc. London B. 344 383-390.

25. Waterman, M.S., 1994, "Parametric and ensemble sequence alignment algorithms," Bull. Math. Biol., 56 743-767.

26. Waterman, M.S. and Vingron, M., 1994, "Rapid and accurate estimates of statistical significance for sequence database searches," Proc. Natl. Acad. Sci. USA, 91 46254628.

27. Arratia, R. and Waterman, M.S., 1994, "A phase transition for the score in matching random sequences allowing deletions," Ann. Appl. Prob., 4(1) 200-225.

28. Vingron, M. and Waterman, M.S., 1994, "Sequence alignment and penalty choices: review of concepts, case studies and implications," J. Mol. Bio]., 235 1-12.

29. Waterman, M.S. and von Haeseler, A., 1993, "Designer algorithms for cryptogene searches," New Zealand J. Bot., 31 269-274.

30. Penner, R.C. and Waterman, M.S., 1993, "Spaces of RNA secondary structures," Adv. Math., 101 31-49.

31. Pevzner, P. and Waterman, M.S., 1993, "A fast filtration for the substring matching problem," Lecture Notes in Computer Science. Combinatorial Pattern Matching,Fourth Annual Symposium, 684 197-214.

32. Pevzner, P. and Waterman, M.S., 1993, "Generalized sequence alignment and duality," Adv. Appl. Math., 14 139-171.

33. Huang, X. and Waterman, M.S., 1992, "Dynamic programming algorithms for restriction map comparison," Comp. Appl. Bio. Sci., 8 511-520.

34. Pevzner, P. and Waterman, M.S., 1992, "Matrix longest subsequence problems, duality and Hilbert bases," Lecture Notes in Computer Science. Combinatorial Pattern Matching,Third Annual Symposium, 644 77-87.

35. Churchill, G.A. and Waterman, M.S., 1992, "The accuracy of DNA sequences: estimating sequence quality," Genomics, 14 89-98.

36. Waterman, M.S., Eggert, M. and Lander, E.S., 1992, "Parametric sequence comparisons," Proc. Natl. Acad. Sci. USA, 89 6090-6093.

37. Goldstein, L. and Waterman, M.S., 1992, "Poisson, compound Poisson, and process approximations for testing statistical significance in sequence comparisons," Bull. Math. Biol., 54 785-812.

38. von Haeseler, A., Blum, B., Simpson, L., Strum, N. and Waterman, M.S., 1992, "Computer methods for locating kinetoplastid cryptogenes," Nucleic Acids Research, 20 2717-2724.

39. Schoniger, M. and Waterman, M.S., 1992, "A local algorithm for DNA sequence alignment with inversions," Bull. Math. Biol., 54 521-536.

40. Smith, T.F. and Waterman, M.S., 1992, "The continuing case of the Florida dentist," Science, 256 1155-1156.

41. Navidi, W., Arnheim, N. and Waterman, M.S., 1992, "A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations," Am. J. Hum. Genet., 50 347-359. 

42. Waterman, M.S., Joyce, J. and Eggert, M., 1991, Computer alignment of sequences. In Phylogenetic Analysis of DNA Sequences, Oxford University Press, 59-72.

43. Schmitt, W. and Waterman, M.S., 1991, "Multiple solutions of DNA restriction mapping problems," Adv. Appl. Math., 12 412-427.

44. Arratia, R., Lander, E.S., Tavare, S. and Waterman, M.S., 1991, "Genomic mapping by anchoring random clones: a mathematical analysis," Genomics, 11 806-827.