Waterman, Michael S. - Departments of Biological Sciences & Computer Science, University of Southern California

• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 14, Number 3, 2007
• ADVANCES IN APPLIED MATHEMATICS9,7-21 (1988) Pattern Analysis of the Genetic Code
• Applications of Combinatorics to Molecular Michael S. WATERMAN
• A Kuzmiq.~theorem of naznber tbeoretic
• MichaelS. Waterman The authors of this article mention that their inter-
• GEOLOGICAL NOTES 451 N., 1979,Thermaleffectsofridgesubduction: Earth
• MathemaiicalGeology, Vol. 19, No. 2, 1987 The Match Game: New Stratigraphic Correlation
• APPLIEDAND ENVIRONMENTALMICROBIOLOGY,June 1997, p. 2338-2346 Copyright 0 1997, American Society for Microbiology
• TECHNOMETRICS@, VOL. 20, NO. 2, MAY 1978 A Bayesian Model for Determiningthe Optimal Test
• ROCKY MOUNTAIN JOURNAL OF MATHEMATICS
• MATHEMATICS OF COMPUTATION, VOLUME 28, NUMBER 126, APRIL 1974, PAGES 599-604 Error Analysis of a Computation of Euler's Constant*
• ADVANCES IN APPLIED MATHEMATICS 18, 111-132(1997) ARTICLE NO. Ah4960502
• DNA Sequence Assembly and Multiple Sequence Alignment by an Eulerian Path
• Vo1.8. no.5. 1992 Pages 511-520
• An Eulerian path approach to local multiple alignment for DNA sequences
• Proc. Natl. Acad. Sci. USA Biochemistry
• Aequationes Math. 13 (1975), 263-268, University of Waterloo Birkhauser Verlag, Basel F-Expansions of rationals
• ADVANCBS IN APPLIEDMATHEMATICS6,129-134(1985) : Dynamic Programming Algorithms for Picture
• Proc. Natl. Acad. Sci. USA Vol. 91, pp. 4625-4628, May 1994
• ADVANCES IN APPLIED MATHEMATICS 2,482-489 (1981) Comparison of Biosequences
• The Annals of Statistics 1990. Vol. 18,No.2,539-570
• Reprintedfrom the MATI-IehunCsMACWINE Vol. 48, No. 3, May 1975
• Numer. Math. 19,195-205 (1972) 0 by Springer-Verlag 1972
• Moments of Absorption Time for a Conditioned RandomWalk*
• Whole Genome Amplification of Single Cells: Mathematical Analysis of PEP and Fengzhu Sun1'*,Norman Arnheim2and Michael S. Waterman"2
• 4828-4836 Nucleic Acids Research, 1994, Vol. 22, NO. 22 01994 Oxford University Press A method for fast database search for all k-nucleotide
• Distributional regimes for the number of k-word matches between two random sequences
• J. Mol. Bi02. (1985) 186, 117-128 Rigorous Pattern-recognition Methods for
• INT. J. MATH. EDUC. SCI. TECHNOL., 1978, VOL. 9, NO. 2, 127-137 Estimation of probability densities by empirical
• Volume 12 Number 1 1984 NucleicAcids Research Algorithmsfor restriction map comparisons
• Reprintedfrom ADVANCES IN MATHEMATICS AU Rights Reserved by Academic Preas, New York and London
• CANTOR'S SERIES FOR VECTORS M. S.WATERMAN
• Lectureeon Mathematicsin the Life Sciences Volume 17,1986
• Reprinted fromJOURNAL OF M A T A n C A L ANALYSIS AND APPLICATIONSVol. 59,No.Z June 15 1977 All Rights Reserved by Acadermc Press,New York and London Prihtcd in E&um
• JOURNAL OF COMPUTATIONALBIOLOGY Volume 3, Number 3,1996
• Reprinted fromMathl Gaz., 1982,66, 1 -4 SELF-DESCRIPTIVE STRINGS
• RCpflOced frOm AD VAN^^ IN MATHEMATICS AU Rights Rae& by Academic Pres, New York and London
• Nucleic Acids Research, Vol. 18, NO. 3 589 The distribution of restriction enzyme sites in Escherichia
• NATURE VOI w9 IO MAY 1W SClENTlflCCORRESPONOENCE-
• SlAM J. APPL. MATH. Vol. 46. NO.1. February 1986
• ..............................................................*.........................................................................................---23s I92 Mathematical MeIhdsfor DNA Sequences
• Proc.NatLAcad.Sci. USA Vol. 80,pp. 3123-3124, May 1983
• SIAM J. ALO. DISC. METH. Vol. 7. No.4. October 1986
• The A d 01 Probabil&y 1989,Vol. 17. No. 3,1152-1169
• Estimating the Repeat Structure and Length of DNA Sequences Using -Tuples
• 144 PEVZNER AND WATERMAN 3. DUALITYFOR LONGEST< -SEQUENCE PROBLEMS
• Combinatoricsof RNA Hairpinsand Cloverleaves By Michael S.Waterman
• INT. J. MATH. EDUC. SCI. TECHNOL., 1976, VOL. 7, NO. 3, 307-313 The algorithms of Euclid and Jacobit
• J. theor. Biol. (1984) 108,333-337 Efficient Sequence Alignment Algorithms
• RNA Secondary Structure: A Complete Mathematical Analysis
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 2, Number 2, 1995
• TECHNOMETRICSQ, VOL. 16, NO. 1, FEBRUARY 1974 A Restricted Least Squares Problem*
• Volume 10 Number 17 1982 NucleicAcids Research Hiaarchical analysisof influenzaA hemagglutiningene sequences
• Reconstruction of An Account's Past
• New Zealand Journal of Botany, 1993, Vol. 31: 269-274 0028-825X/93/3103-0269 $2.50/0 0 The Royal Society of New Zealand 1993
• 0 1992 Oxjwd University Press Nucleic Acids Research, Vol. 20, No. 11 2717-2724 Computer methods for locating kinetoplastid cryptogenes
• J Mol EVOI(1981) 18:38-46 MolecularMubon
• Adv. Appl. h o b . 29,629-668 (1997) Printed in N. Ireland
• Volume 11 Number 7 1983 NucleicAcids Research J.R.Sadlerl, M.S.Watennanzand T.F.Smith3
• A Dynamic ProgrammingAlgorithm to Find All Solutions in a Neighborhoodof the Optimum
• MathematicalGeology, Vol. 11,No. I,1979 Modeling and Optimizing a Gas-Water Reservoir
• Gene Aging Nexus: a web database and data mining platform for microarray data on aging
• TIw AnnnLs iii I+rhahility 1985, Vol. 13, No. 4, 1236-1249
• the free atmosphere, away from the influ-ences of the earth's surface. From all of
• Monataheftefiir Mathematik 79, 167-163 (1976) 0 by Springer-Verlag1976
• Accuracy Assessment of Diploid Consensus Sequences
• On the Length of the Longest Exact Position Match in a Random Sequence
• TheAIIJI~&of StariStifs 1968,Vol. 14, No.3,871-693
• Am. I. Hum. Genet. 50:347-359, 1992 A Multiple-Tubes Approach for Accurate Genotyping of Very
• Whole-genome shotgun assembly and comparison of human genome assemblies
• J. Mol. Biol. (1987) 197, 723-728 LETTERSTO THE EDITOR
• 10.1101/gr.5894107Access the most recent version at doi: 2007 17: 1101-1110; originally published online Jun 13, 2007;Genome Res.
• Vol. 22 no. 10 2006, pages 12171224 doi:10.1093/bioinformatics/btl063BIOINFORMATICS ORIGINAL PAPER
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 11, Numbers 23, 2004
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 10, Number 6, 2003
• Gian-CarloRota (1932-1 999)
• Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo
• JOURNAL OF COMPUTATIONALBIOLOGY Volume 4, Number 4,1997
• MATHEMATICS Discrete Applied Mathematics 71 (1996) 297-309
• J. Mol. Bid. (1996)258, 650-660 A Mathematical Analysis of in Vitro Molecular
• SEQUENCE COMPARISON SIGNIFICANCE AND POISSON APPROXIMATION MICHAEL S. WATERMAN and MARTIN VINCRON
• Algorithmica(1995) 13: 135-154 Algorithmica
• MATHEMATICS Discrete Applied Mathematics51 (1994) 317-323
• Estimating statistical significance of sequence alignments MICHAEL WATERMAN
• Bwkiin o jMmhemaricatBiolo#y Vol. 56. No. 4. pp. 143-161.1994 ELcviu sdcna Ud
• Reprinted from ADVANCFSIN MATHEMATICS All Rights Rescrved by Academic Press. New York and London
• GENOMES 14,89-98(1992) The Accuracy of DNA Sequences: Estimating Sequence Quality
• . , . .. . , I , I . . . , . I Bullr*rin of Murkemorirul Bioloyy Vol. 54. No.4. pp. 521-536. 1992.
• ADVANCES IN APPLIED MATtlEMATIC3 12, 412-427 (1991) Multiple Solutions of DNA Restriction
• GENOMICS 11.806-827 (1991) Genomic Mapping by Anchoring Random Clones
• GENOMICS 8,351-366 (1990) Optimizing Restriction Fragment Fingerprinting Methods
• .= aJkh o/McuknoaicdBblopy Vol. 52, No. 3. pp. 455415,1990 Rinttd in GrolltBritain.
• [14] Consensus Methods for DNA and Protein Sequence By MICHAELS. WATERMANand ROBERTJONES
• SEQUENCE ALIGNMENTS Mkhacl S. Waterman
• 1521 COMPUTER ANALYSIS OF NUCLEIC ACID SEQUENCES 765 [52]Computer Analysis of Nucleic Acid Sequences
• J: Appl. Prob. 25, 106-1 19 (I 988) Printed in Israel
• Proc. Nail. Acad. Sci. USA Vol. 84, pp. 1239-1243, March 1987
• Bulletin ofMothematicalBiology Vol. 48, No. 2, pp. 189-195.1986. Printed in Great Britain.
• Probab. Th. Rel. Fields 72, 279-287 (1986) probability 0Springer-Verlag1986
• Letters in Mathenlatical Physics 10 (1985) 231-242. 0 1985 by D. Reidel Publishing Company.
• ADVANCES IN MATHEMATICS 55, 1-12 (1985) Matching Rectangles in d-Dimensions
• Volumo 13 Number 2 1966 NucleicAcids Research Temple F.Smith1, MichaelS.Watennanzand Christian BurksJ
• 568 M. S. WATERMAN AND M. D. PERLWITZ p(C, G,C , G, C , G, C ) = d(xi,C ) = 3.
• Bulletin ofMafhematicalBiology Vol. 46, No.4, pp. 515-527, 1984. Printed in Great Britain
• Physica 10D (1984) 45-51 North-Holland, Amsterdam
• Volume 12 Number 1 1984 Nucleic Acids Research On the statistical significanceof nucleic acid similarities
• Volume 11 Number 24 1983 NucleicAcids Research Frequenciesof restriction sites
• Volume 11 Number 7 1983 Nucleic Acids Research Statistical characterizationof nucleic acid sequence functional domains
• SlAM 1. APPL MATH Vol. 39. So 1. Aupua 1980
• Rotein Constraints Induced by Multiframe Encoding TEMPLE F.SMITH*
• J. theor. Biol. (1978) 73, 789-800 On the Similarity of Dendrograms
• STUDIES IN FOUNDATIONS A N D COMBINATORICS ADVANCES IN MATHEMATICS SUPPLEMENTARY STUDIES, VOL. 1
• J. theor. Biol. (1977) 69, 561-562 LETTERTO THB EDITOR
• D J.L. KOVNER f factorial moments and using
• Mathematical Geology, Vol. 9, No. I , 1977 Locating Maximum Variance Segments
• I J. theor. Biol. (1977) 64, 199-213 AdditiveEvolutionaryTreest
• MULTIDIMENSIONAL GREATEST COMMON DIVISOR AND LEHMER ALGORITHMS
• The Annals of 1971,Vol.42,
• Z. Wahrscheinlichkeitstheorie verw. Geb. 16,77-103 (1970) 0by Springer-Verlag1970
• 7I.AppL Rob. 22,228-234 (198s) Printed in I s r ~ /
• TlreAnnala of Applied Probability 1994,Vol. 4, No.1,200-225
• JOURNAL OF COMPUTATIONAL BIOLOGY Volume 13, Number 2, 2006
• Graphs and Combinatorics6,133-146 (1990) CombCnatoricS
• An algorithm for assembly of ordered restriction maps from single DNA molecules
• .I. Mol. Bid. (1994) 235, 1-12 RCVIEU' ARTICLE
• ADVANCES IN APPLIED MATHEMATICS7,455-464 Rapid Dynamic Programming Algorithms for RNA
• SPECIAL FEATURES Genomic Sequence Databases
• J. theor. Biol. (1981)91,379-380 LETTERSTO THE EDITOR
• A Fast Filtration Algorithm for the Substring Matching Problem *
• Reprinted from lhe American Mathematicel Monthly, Vol. 87, No. 7, Aug. -Sept. 1980. Let r,, be the set of binary trees with the same n labeled terminal vertices. (Such trees are
• Caralan and Morzkin numbers 263 This recurrence rule generates the sequence 1, 1, 2, 4, 9, 21,
• BOOK REVIEW David Sankoff and Joseph B. Kruskal, Editors, Time Warps, String Edits,
• 10.1101/gr.1837404Access the most recent version at doi: 2004 14: 908-916; originally published online Apr 12, 2004;Genome Res.
• Volume 14 Number 22 1986 NucleicAcids Research Multiple sequence alignment by consensus
• Reprinted from JOURNALOF NUMB~RTHEORY All Rights Reservedby AcademicPress, New York and London
• AMERICANJOURNAL OF MATHEMATICALAND MANAGEMENT SCIENCES CopyllgMQISM by American SclonurPmr, Inc.
• SYMMETRIES FOR CONDITIONED RUIN PROBLEMS W. A. BEYER AND M. S. WATERMAN
• r GENERAL METHODS OF SEQUENCE h41cli.s~~S. W A T E R M A N *
• DeterminingAll Optimal and Near-Optimal Solutions when Solving Shortest Path Problems