Michael S. Waterman - Acta Biochimica et Biophysica Sinica

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.