Research Papers - Michael Waterman

Papers published (reverse chronological order)

Chen, R.X.F., Reidys, C.M. and Waterman, M.S. (2023) RNA Secondary Structures with Given Motif Specification: Combinatorics and Algorithms. Bull Math Biol 85, 21 (2023).
Waterman, M.S. (2021) The Human Genome Project: the Beginning of the Beginning Quantitative Biology, Vol 9(1) 4-7
Barrett, C., Bura, A.C., He, Q., Huang, F.W., Li, T. J. X., Waterman, M.S., and Reidys, C.M. (2021) Multiscale feedback loops in SARS-CoV-2 viral evolution. J. Comput. Biol., 2021 03; 28(3):248-256
Bonnie Berger; Michael S. Waterman; Yun William Yu (2021) Levenshtein Distance, Sequence Comparison and Biological Database Search IEEE Transactions on Information Theory , vol. 67, no. 6, pp. 3287-3294, June 2021, doi: 10.1109/TIT.2020.2996543, Vol 9(1) 4-7
Zielezinski, A., Girgis, H., Bernard, G., Leimeister, C-A., Tang,K., Dencker, T., Lau, A., Rhling, S., Choi, J., Waterman, M.S., Comin, M., Kim, S-H., Vinga, S., Almeida, J., Chan, C., James, B., Sun, F., Morgenstern, B., and Karlowski. W. (2019) Benchmarking of alignment-free sequence comparison methods BMC Genome Biology, 20 article 144
Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S Waterman, Xuegong Zhang (2019) A new statistic for efficient detection of repetitive sequences Bioinformatics, Volume 35, Issue 22, 15 November 2019, Pages 4596–4606
Y X Rachel Wang, Ke Liu, Elizabeth Theusch, Jerome I Rotter, Marisa W Medina, Michael S Waterman, Haiyan Huang (2018) Generalized correlation measure using count statistics for gene expression data with ordered samples Bioinformatics, Volume 34, Issue 4, 15 February 2018, Pages 617–624
Lu, YY, Tang, K., Ren, J., Fuhrman, J., Waterman, M.S., Sun, F. (2017) CAFE:”aCcelerated Alignment-FrEe sequence analysis NAR -00637-Web-B-2017.R1
Bai,X., Tang, K., Ren, J., Waterman, M.S.and Sun, F. (2017) Optimal choice of word length when comparing two Markov sequences using a chi-square-statistic., BMCGenomics, 18 732 (2017)
Waterman, M.S. (2016) Questions I Was Asked, International Chinese Statistical Association, Bulletin 28(1), 48-51
Wang, R., Waterman, M.S., and Huang, H. (2014) Gene coexpression measures in large heterogenous samples using count statistics., PNAS 46, 16371-16376
Liu CC*, Tseng YT*, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ. (2014). (*Joint 1st author) DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections., Nucleic Acid Research, 2014 June; DOI: 10.1093/nar/gku412
Song, K. , Ren, J., Reinert, G., Deng, M., Waterman, M.S., and Sun, F. (2014) New developments of alignment-free sequence comparison: measures, statistics and next generation sequencing, Brief. Bioinform., 15(3), 343-353
Behnamghader, E., Waterman, M.S., and Smith A.D., (2013) A geometric interpretation for local alignment-free sequence comparison , J. Comput. Biol., 20(7), 471-485
Andersen, J.E., Penner, R.C., Reidys, C.M. and Waterman, M.S., (2013) Topological classification and enumeration of RNA structures by genus , J. Math. Biol., 1261-1278
Zhai, Z., Reinert, G., Song, K., Waterman, M.S., Luan, Y., and Sun, F. (2012) Normal and compound Poisson approximations for pattern occurrences in NGS reads , J. Comput. Biol., 19(6), 839-854
Meng, L., Zhang, X., Sun, F., and Waterman, M.S. (2011) Sequence alignment as hypothesis testing, J. Comput. Biol., 18(5), 677-691.
Liu, X., Wan, L., Li, J., Reinert, G., Waterman, M.S., and Sun, F., (2011) New powerful statistics for alignment-free sequence comparison under a pattern transfer model, J. Theor. Biol., 284 (1), 106-116.
Mehan, MR, Nuñez-Iglesias, J, Dai, C, Waterman, MS, and Zhou, XJ (2010) An integrative modular approach to systematically predict gene-phenotype associations., BMC Bioinformatics, 2010 Jan 18;11 Suppl 1:S62.
Li, W., Liu, C-C., Zhang, T., Li, H., Waterman, M.S., and Zhou, X.J., (2010) Integrative analysis of many weighted co-expression networks using tensor computation, PLoS Comput Biol., 7(6): e1001106.
Reinert, G., Chew, D., Sun, F., and Waterman, M.S., (2010) Alignment-free sequence comparison (II): theoretical power of comparison statistics, J Comput Biol., 17 No.11: 1349-1372.
Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churs C, Kidd JM, Kohn S, Runheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, and Schwartz DC, (2010) High-resolution human genome structure by single-molecule analysis, PNAS, 2010.
Zhai, Z., Ku, S-Y, Luan, Y., Reinert, G., Waterman, M.S.and Sun, F. (2010) The power of detecting enriched patterns: an HMM approach, J Comput Biol., 17 581-592.
Schwartz, D.C. and Waterman, M.S., (2010) New generations: sequencing machines and their computational challenges, J. Compt. Sci. and Tech., 25 3-9.
Reinert, G., Chew, D., Sun, F., and Waterman, M.S., (2009) Alignment-free sequence comparison (I): statistics and power, J Comput Biol., 16 1615-1634.
Zhou, S., Fusheng, W., Nguyen, J., Bechner, M., Potamousis, K., Goldstein S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D., Wise, R., Ware, D., Wing, R.A., Waterman, M.S., Livny, M., and Schwartz, D.C. (2009) A single molecule scaffold for the maize genome, PLoS Genetics, 5: e711.
Schnable, P.S. and 157 authors (including Waterman, M.S.), (2009) The B73 maize genome: complexity, diversity and dynamics, Science, 326 (5956), 1112-1115. 39.
Kim JH, Kim W-C, Waterman, M.S., Park, S, and Li LM, (2009) HAOLOWSER: a whole-genome haplotype browser for personal genome and metagenome, Bioinformatics, 25 (18) 2430-2431.
Zhang M.Q., Waterman, M.S., and X. Zhang, (2009) Introduction: The Seventh Asia Pacific Bioinformatics Conference (APBC2009), BMC Bioinformatics, 10(Suppl 1): S1.
Mehan M.R., Nunez-Iglesias J., Kalakrishnan M., Waterman, M.S., and Zhou X., (2008) An integrative network approach to map the transcriptome to the phenome, Lecture Notes in Computer Science , Vol. 4955 232-245.
Huang Yu, Li Haifeng, Hu Haiyan, Yan Xifeng, Waterman, M.S., Huang Hiayan,and Zhou Xianghing, (2007) Systematic discovery of functional modules and context-specific functional annotation of the human genome, Bioinformatics, 23(13): i222-229.
Kim JH,Waterman MS, and Li LM. (2007) Diploid reconstruction of Ciona intestinalis and comparison with Ciona savignyi, Genome research, 11 pages.
Li, H., Valouv, A., Schwartz, D., Waterman, M. and Lei, L.M. (2007) A quantile method for sizing optical maps. J Comput Biol. 14 255-266.
Kim JH, Waterman MS, and Li LM. (2007) Accuracy assessment of diploid consensus sequences. IEEE/ACM Trans Comput Biol Bioinform Jan-Mar;4(1):88-97.
Reinert G, andWaterman MS. (2007) On the length of the longest exact position match in a random sequence. IEEE/ACM Trans Comput Biol Bioinform Jan-Mar;4(1):153-6.
Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, and Zhou XJ. (2006) Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Res. Nov 7
Valouev A, Schwartz DC, Zhou S, andWaterman MS. (2006) An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A [Epub ahead of print]
Valouev A, Zhang Y, Schwartz DC, and Waterman MS. (2006) Refinement of optical map assemblies. Bioinformatics. 22 1217-1224.
Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, and Waterman MS. (2006) Alignment of optical maps. J Comput Biol. 13 442-462.
Zhang, K., Qin, Z., Chen, T., Liu, J., Waterman, M.S. , and Sun, F. (2005) HapBlock: Haplotype Block Partitioning and Tag SNP Selection Software Using a Set of Dynamic Programming Algorithms. Bioinformatics 21 131-134.
Zhang Y and Waterman MS. (2005) An Eulerian path approach to local multiple alignment for DNA sequences. Proc Natl Acad Sci U S A 102 1285-1290.
Zhang, K., Qin, Z., Chen, T., Waterman, M.S, and Sun, F.(2004), Haplotype block partitioning and tag SNP selection using genotype data and their application to association studies,Genome Research,14 908-916.
Li, L.M., Kim, J.H., and Waterman, M.S, (2004), Haplotype reconstruction from SNP alignment, Journal of Computational Biology,11 505-516.
Zhang, Y., and Waterman, M.S, (2004), DNA sequence assembly and multiple sequence alignment by an Eulerian path approach, Cold spring Harbor Symposium of Qualitative Biology,LXVIII 205-212.
Istrail, S., Sutton, G., Florea, L., Halpern, A., Mobarry, C., Lippert, R., Walenz, B., Shatkay, H., Dew, I., Miller, J., Bolanos, R., Edwards, N., Fasulo, D., Flanigan, M., Halldorsson, B., Hannenhalli, S., Nusskern, D., Shue, B., Zheng, X., Turner, R., Yooseph, S., Delcher, A., Huson , D., Kravitz, S., Mouchard, L., Reinert, K., Remington, K., Clark, A., Waterman, M.S, Adams, M., Myers, E., and Venter J.C. (2003), Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies, Proc. Natl. Acad. Sci. USA,101 1916-1921.
Zhang, K., Sun, F., Waterman, M.S, and Chen, T., (2003), Dynamic programming algorithms for partitioning sequence variation in human chromosomes, HERMIS,4 15-26.
Zhang, Y. and Waterman, M.S (2003), An Eulerian path approach to global multiple alignment for DNA sequences, Journal of Computational Biology,10 803-820.
Li, X., and Waterman, M.S (2003), Estimating the repeat structure and length of DNA sequences using l-tuples, Genome Research,13 1916-1922.
Zhang K, Sun F, Waterman MS, Chen T. (2003), Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data, Am J Hum Genet. 73 63-73
Lippert, R.A., Huang, H., and Waterman, M.S (2002), Distributional regimes for the number of k-word matches between two random sequences, Proc. Natl. Acad. Sci. USA, 99 13980-13989.
Tang, M.,Waterman, M.S, and Yooseph, S. (2002), Zinc finger gene clusters and tandem gene duplication, Journal of Computational Biology, 9 429-446.
Zhang,K., Deng, M., Chen, T., Waterman, M.S , and Sun, F. (2002), A dynamic programming algorithm for haplotype block partitioning, Proc. Natl. Acad. Sci. USA, 99 7335-7339.
Tang M and Waterman, M.S (2001), Local matching of random restriction maps, Journal of Applied Probability, 38 335-356.
Pevzner, P., Tang, H., and Waterman, M.S. (2001), An Eulerian path approach to DNA fragment assembly, Proc. Natl. Acad. Sci. USA, 98 9748-9753.
Waterman, M.S. (2000), Mathematical sciences and the new biology, A chapter in the book Essays on the Future, In Honor of Nick Metropolis, S. Hecker and G.-C. Rota, Eds. 265-276
Reinert, G., Scabath, S., and Waterman, Probablistic and statistical properties of words J.Comp. Biol., 7 1-48.
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.
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.
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
Sun, F. and Waterman, M.S. 1997, “Single chromosome amplification and branching processes,” Adv. Appl. Probab, 29 629-668.
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.
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.
Vingron, M. and Waterman, M.S. 1996,”Alignment networks and electrical networks,” Discrete Math, 71 297-309.
Steel, M., Goldstein, L., and Waterman, M.S. 1996,”A central limit theorem for parsimony length of trees,” Appl. Porbab, 28 1051-1071.
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.
Sun, F., Galas, D., and Waterman, M.S. A mathematical analysis of in vitro molecular selection-amplification,” J. Mol. Biol., 258 650-660 (1996)
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.
Waterman, M.S.”Combinatorics in molecular biology,” Handbook of Combinatorics.
Idury, R. and Waterman, M.S. “A new algorithm for DNA sequence assembly,” Journal of Computational Biology, 2:2, 291-306.
Waterman, M.S., 1995,”Hearing distant echos,” Calculating the Secrets of Life. National Academy Press, E. Lander and Waterman, M.S., Eds. 90-113.
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.
Port, E., Sun, F., Martin, D., Waterman, M.S. “Genomic mapping by end-characterized random clones: a mathematical analysis,” Genomics, 26, 84-100, 1995.
Waterman, M.S., 1994,”Genomes, maps and sequences,” Lecture Notes in Biomathematics, 100 28-52.
Benson, G. and Waterman, M.S.,1994, “A method for fast database search for all k-nucleotide repeats,” Nucleic Acids Research, 22 4828-4836.
Waterman, M.S. and Vingron, M.,1994,”Sequence comparison significance and Poisson approximation,” Statistical Sciences, 9 367-381.
Pevzner, P.A. and Waterman, M.S., 1995,”Multiple filtration and approximate pattern matching,” Algorithmica, 13 135-154.
Schmitt, W.R. and Waterman, M.S., 1994,”Linear trees and RNA secondary structure,” Disc. Appl. Math., 51 317-323.
Goldstein, L. and Waterman, M.S., 1994,”Approximations to profile score distributions,” J. Comp. Biol., 1 93-104.
Waterman, M.S., 1994,”Estimating of statistical significance of sequence alignments,” Phil. Trans. R. Soc. London B. 344 383-390.
Waterman, M.S., 1994,”Parametric and ensemble sequence alignment algorithms,” Bull. Math. Biol., 56 743-767.
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.
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.
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.
Waterman, M.S. and von Haeseler, A., 1993, “Designer algorithms for cryptogene searches,” New Zealand J. Bot., 31 269-274.
Penner, R.C. and Waterman, M.S., 1993,”Spaces of RNA secondary structures,” Adv. Math., 101 31-49.
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.
Pevzner, P. and Waterman, M.S., 1993,”Generalized sequence alignment and duality,” Adv. Appl. Math., 14 139-171.
Huang, X. and Waterman, M.S., 1992,”Dynamic programming algorithms for restriction map comparison,” Comp. Appl. Bio. Sci., 8 511-520.
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.
Churchill, G.A. and Waterman, M.S., 1992, “The accuracy of DNA sequences: estimating sequence quality,” Genomics, 14 89-98.
Waterman, M.S., Eggert, M. and Lander, E.S., 1992,”Parametric sequence comparisons,” Proc. Natl. Acad. Sci. USA, 89 6090-6093.
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.
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.
Schoniger, M. and Waterman, M.S., 1992,”A local algorithm for DNA sequence alignment with inversions,” Bull. Math. Biol., 54 521-536.
Smith, T.F. and Waterman, M.S., 1992,”The continuing case of the Florida dentist,” Science, 256 1155-1156.
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.
Waterman, M.S., Joyce, J. and Eggert, M., 1991, Computer alignment of sequences. In Phylogenetic Analysis of DNA Sequences, Oxford University Press, 59-72.
Schmitt, W. and Waterman, M.S., 1991,”Multiple solutions of DNA restriction mapping problems,” Adv. Appl. Math., 12 412-427.
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.
Waterman, M.S., 1990,”Comment on: Poisson approximation and the ChenStein method, by R. Arratia, L. Goldstein and L. Gordon,” Stat. Sci., 5 427429.
Griggs, R.J., Hanlon, P.J., Odlyzko, A.M. and Waterman, M.S., 1990,”On the number of alignments of k sequences,” Graphs and Combinatorics, 6 133-146.
Branscomb, E., Slezak, T., Pae, R., Galas, D., Carrano, A.V. and Waterman, M.S., 1990,”Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries,” Genomics, 8 351-366.
Tang, B. and Waterman, M.S., 1990,”The expected fraction of clonable DNA,” Bull. Math. Biol., 52 455-475.
Arratia, R., Gordon, L. and Waterman, M.S.,1990,”The Erdos-Renyi law in distribution, for coin tossing and sequence matching,” Ann. Stat., 18 539-570.
Waterman, M.S. and Jones, R., 1990,”Consensus methods for DNA and protein sequence alignment,” Meth. Enzym., 183 221-236. Ed. Russell F. Doolittle, Academic Press, Inc.
Waterman, M.S., 1990,”Genomic sequence databases,” Genomics, 6 700-701.
Waterman, M.S. and Gordon, L., 1990,”Multiple hypothesis testing for sequence comparisons,” In Computers and DNA, Addison-Wesley, 127-135.
Churchill, G.A., Daniels, D.L. and Waterman, M.S., 1990,”The distribution of restriction enzyme sites in Ercherichia coli,” Nucleic Acids Research, 18 589-597.
Arratia, R. and Waterman, M.S., 1989,”The Erdos-Renyi strong law for pattern matching with a given proportion of mismatches,” Ann. Prob., 17 1152-1169.
Waterman, M.S., 1989,”Consensus methods for folding single-stranded nucleic acids,” In Mathematical Methods for DNA Sequences. Ed. by M.S. Waterman. CRC Press, 185-224.
Waterman, M.S., 1989,”Consensus patterns in sequences,” In Mathematical Methods for DNA Sequences. Ed. by M.S. Waterman. CRC Press, 93-115.
Waterman, M.S., 1989,”Sequence alignments,” In Mathematical Methods for DNA Sequences. Ed. by M.S. Waterman. CRC Press, 53-92.
Goldstein, L. and Waterman, M.S., 1988,”Neighborhood size in the simulated anealing algorithm,” Amer. J. Math. Manag. Sci. 8 409-424.
Waterman, M.S., 1988,”Computer analysis of nucleic acid sequences,” Meth. Enzym. 164 765-793.
Perlwitz, M.D., Burks, C. and Waterman, M.S., 1988,”Pattern analysis of the genetic code,” Adv. Appl. Math. 9 7-21.
Lander, E.S. and Waterman, M.S., 1988, “Genomic mapping by fingerprinting random clones:a mathematical analysis,” Genomics, 2 231-239.
Arratia, R., Morris, P. and Waterman, M.S., 1988,”Stochastic scrabble: large deviations for sequences with scores,” J. Appl. Prob. 25 106-119.
Waterman, M.S. and Eggert, M., 1987,”A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons,” J. Mol. Biol., 197 723-728.
Goldstein, L. and Waterman, M.S., 1987,”Mapping DNA by stochastic relaxation,” Adv. Appl. Math., 194-207.
Waterman, M.S., Gordon, L. and Arratia, R., 1987,”Phase transitions in sequence matches and nucleic acid structure,” Proc. Natl. Acad. Sci. USA, 84 1239-1243.
Waterman, M.S. and Raymond Jr., R.R., 1987,”The match game:new stratigraphic correlation algorithms,” Math. Geol., 19 194-207.
Waterman, M.S. and Smith, T.F., 1986,”Rapid dynamic programming methods for RNA secondary structure,” Adv. Appl. Math., 7 455-464.
Waterman, M.S., 1986,”Multiple sequence alignment by consensus,” Nucleic Acids Research, 14 9095-9102.
Griggs, J.R., Hanlon, P.J. and Waterman, M.S., 1986,”Sequence alignments with matched sections,” SIAM J. Alg. Disc. Meth., 7 604-608.
Waterman, M.S. and Griggs, J.R., 1986,”Interval graphs and maps of DNA,” Bull. Math. Biol., 48 189-195.
Arratia, R., Gordon, L. and Waterman, M.S., 1986,”An extreme value theory for sequence matching,” Ann. Stat., 14 971-993.
Gordon, L., Schilling, M. and Waterman, M.S., 1986,”An extreme value theory for long head runs,” Prob. Theor. Rel. Fields, 72 279-287.
Darling, R.W.R. and Waterman, M.S., 1986,”Extreme value distribution for the largest cube in a random lattice,” SIAM J. Appl. Math., 46 118-132.
Waterman, M.S., 1986,”Probability distributions for DNA sequence comparisons,” Lect. Life Sci., 17 29-56.
Waterman, M.S., 1985,”Book review: Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison,” Math. Biosci., r6 243-244.
Galas, D.J., Eggert, M. and Waterman, M.S., 1985,”Rigorous pattern recognition methods for DNA sequences: analysis of promoter sequences from E. coli.,” J. Mol. Biol., 186 117-128.
Beyer, W.A., Sellers, P.H. and Waterman, M.S., 1985,”Stanislaw M. Ulam’s contributions to theoretical biology,” Let. Math. Phys., 10 231-242.
Waterman, M.S. and Byers, T.H., 1985,”A dynamic programming algorithm to find all solutions in the neighborhood of the optimum,” Math. Biosci., 77 179-188.
Arratia, R. and Waterman, M.S., 1985,”Critical phenomena in sequence matching,” Ann. Prob., 13 1236-1249.
Waterman, M.S., 1985, “Dynamic programming algorithms for picture comparison,” Adv. Appl. Math., 6 129-134.
Darling, R.W.R. and Waterman, M.S., 1985, “Matching rectangles in d-dimensions; algorithms and laws of large numbers,” Adv. Math., 55 13-23.
Smith, T.F., Waterman, M.S. and Burks, C., 1985, “The statistical distribution of nucleic acid similarities,” Nucleic Acids Research, 13 645-656.
Breen, S., Waterman, M.S. and Zhang, N., 1985, “Renewal theory for several patterns,” J. Appl. Prob. 22 228-234.
Arratia, R. and Waterman, M.S., 1985, “An Erdos-Renyi law with shifts,” Adv. Math., 55 13-23.
Byers, T. and Waterman, M.S., 1984, “Determining all optimal and nearoptimal solutions when solving shortest path problems by dynamic programming,” Oper. Res., 32 1381-1384.
Waterman, M.S. and Perlwitz, M.D., 1984, “Line geometries for sequence comparisons,” Bull. Math. Biol., 46 567-577.
Waterman, M.S., Arratia, R. and Galas, D.J., 1984, “Pattern recognition in several sequences; consensus and alignment,” Bull. Math. Biol., 46 515-527.
Waterman, M.S., 1984, “General methods of sequence comparison,” Bull. Math. Biol., 46 473-500.
Waterman, M.S., 1984, “Efficient sequence alignment algorithms,” J. Theor. Biol., 108 333-337.
Waterman, M.S., 1984, “How do you spell DNA?” Nature, 309 118.
Waterman, M.S., 1984, “Some applications of information theory to cellular automata,” Physica D 45-51.
Waterman, M.S., Smith, T.F. and Katcher, H., 1984, “Algorithms for restriction map comparisons,” Nucleic Acids Research, 12 237-242.
Lipman, D.J., Wilbur, W.J., Smith, T.F. and Waterman, M.S., 1984, “On the statistical significance of nucleic acid similarities,” Nucleic Acids Research, 12 215-226.
Waterman, M.S., 1983, “Frequencies of restriction sites,” Nucleic Acids Research, 11 8951-8956.
Waterman, M.S., l983, “Sequence alignments in the neighborhood of the optimum with general application to dynamic programming,” Proc. Natl. Acad. Sci. USA 80 3123-3124.
Sadler, J.R., Waterman, M.S. and Smith, T.F., 1983, “Regulatory pattern identification in nucleic acid sequences,” Nucleic Acids Research, 11 22212231.
Smith, T.F., Waterman, M.S. and Sadler, J.R., 1983, “Statistical characterization of nucleic acid sequence functional domains,” Nucleic Acids Research, 11 2205-2220.
Lipman, D.J., Smith, T.F., Beckman, R.J. and Waterman, M.S., 1982, “Hierarchical analysis of influenza A hemagglutinin gene sequences,” Nucleic Acids Research, 10 5375-5389.
McKay, M.D. and Waterman, M.S., 1982, “Self-descriptive strings,” Math. Gaz., 66 1-4.
Smith, T.F. and Waterman, M.S., 1981, “Identification of common molecular subsequences,” J. Mol. Biol., 147 195-197.
Smith, T.F. and Waterman, M.S., 1981, “Overlapping genes and information theory,” J. Theor. Biol., 91 379-380.
Smith, T.F. and Waterman, M.S., 1981, “Comparison of biosequences,” Adv. Appl. Math., 2 482-489.
Smith, T.F., Waterman, M.S. and Fitch, W.M., 1981, “Comparative biosequence metrics,” J. Mol. Evol., 18 38-46.
Smith, T.F. and Waterman, M.S., 1980, “How alike are two trees?” Math. Month., 87, 552-553.
Howell, J.A., Smith, T.F. and Waterman, M.S., 1980, “Computation of generating functions for biological molecules,” SIAM J. Appl. Math, 39 119133.
Smith, T.F. and Waterman, M.S., 1980, “New stratigraphic correlation techniques,” J. Geol., 88 451-457.
Smith, T.F. and Waterman, M.S., 1980, “Protein constraints induced by multiframe encoding,” Math. Biosci., 49 17-26.
Johnson, M.E., Monash, E.A. and Waterman, M.S., 1979, “Modeling and optimizing a gas-water reservoir I: Enhanced recovery with waterflooding,” J. Int. Assoc. Math. Geol., 11 63-74.
Waterman, M.S., 1979, “Combinatorics of RNA hairpins and cloverleaves,” Stud. Appl. Math., 60 91-96.
Beyer, W.A. and Waterman, M.S., 1979, “Moments of absorption time for a conditioned random walk,” Stud. Appl. Math., 60 83-90.
Stein, P.R. and Waterman, M.S., 1978, “On some new sequences generalizing the Catalan and Motzkin numbers,” Discrete Math., 26 261-272.
Smith, T.F. and Waterman, M.S., 1978, “RNA secondary structure,” Math. Biosci., 42 257-266.
Waterman, M.S. and Smith, T.F., 1978, “On the similarity of dendrograms,” J. Theor. Biol., 73 789-800.
Martz Jr., H.F. and Waterman, M.S., 1978, “A Bayesian model for determining the optimal test stress for a single test unit,” Technometrics, 20 179-185.
Kahaner, D. and Waterman, M.S., 1978, “Asymptotics for gamma and beta percentiles,” J. Stat. Comp. Sim., 6 315-316.
Waterman, M.S., 1978, “Secondary structure of single stranded nucleic acids,” Adv. Math. Suppl. Stud., I 167-212.
Waterman, M.S. and Whiteman, D.E., 1978, “Estimation of probability densities by empirical density functions,” Int. J. Math. Educ. Sci. Tech., 9 127-137.
Waterman, M.S. and Lowe, V.W., 1977-1978, “Reconstruction of an account’s past,” J. Inst. of Nuc. Mat. Mgmt., VI 55-57.
Beckman, R.J. and Waterman, M.S., 1977, “On the random distribution of nucleoli in metabolic cells,” J. Theor. Biol., 69 561-562.
Waterman, M.S., 1977, “Least squares with non-negative regression coefficients,” J. Statist. Comput. Simul., 6 67-70.
Wailer, R.A. and Waterman, M.S., 1977, “Percentiles for the gamma distribution,” SIAM Review, 19 146.
Beyer, W.A. and Waterman, M.S., 1977, “Symmetries for conditioned ruin problems,” Math. Mag., 50 42-45.
Bement, T.R. and Waterman, M.S., 1977, “Locating maximum variance segments in sequential data,” J. Int. Assoc. Math. Geol.,9 55-61.
Waterman, M.S., Smith, T.F., Singh, M. and Beyer, W.A., 1977, “Additive evolutionary trees,” J. Theor. Biol., 64 199-213.
Waterman, M.S., 1977, “Multidimensional greatest common divisor and Lehmer algorithms,” BIT, 17 465-478.
Waterman, M.S., 1977, “A Jacobi algorithm and metric theory for greatest common divisors,” J. Math. Anal. Appl., 59 288-300.
Lowe, V.W. and Waterman, M.S., 1976, “On the variance of a product with application to uranium estimation,” J. Inst. Nuc. Mat. Manag., V 36-41.
Waterman, M.S., Smith, T.F. and Beyer, W.A., 1976, “Some biological sequence metrics,” Adv. Math., 20 367-387.
Johnson, R.W. and Waterman, M.S., 1976, “The algorithms of Eulid and Jacobi,” Int. J. Math. Educ. Sci. and Technol., 7 307-313.
Waterman, M.S., 1976, “On the approximation of invariant measures for continued fractions,” Rocky Mountain J. Math., 6 181-189.
Waterman, M.S., 1975, “F-expansions of rationals,” Ae~uationes Math., 13 263-268.
Waterman, M.S., 1975, “On Jacobi’s solution of linear Diophantine equations,” Math. Mag., 48 159-163.
Waterman, M.S., 1975, “Cantor series for vectors,” Math. Month., 82 622-625.
Waterman, M.S., 1975, “Remarks on invariant measures for number theoretic transformations,” Monatsh. Math., 79157-163.
Beyer, W.A. and Waterman, M.S., 1974, “Error analysis of a computation of Euler’s constant,” Math. Comp., 28 599-604.
Waterman, M.S., 1974, “A restricted least squares problem,” Technometrics, 16 135.
Schweiger, F. and Waterman, M.S., 1973, “Some remarks on Kuzmin’s theorem for F-expansions,” J. Nllmber Theory, 5 123-131.
Beyer, W.A. and Waterman, M.S., 1972, “Ergodic computations with continued fractions and Jacobi’s algorithm,” Numer. Math., 19 195-205. (1973) Errata,20430.
Waterman, M.S., 1971, “A note on the reparametrization of an exponential family,” Ann. Math. Statist., 42 752-754.
Waterman, M.S., 1971, “A Kuzmin theorem for a class of number theoretic endomorphisms,” Acta Arith., 19 31-41.
Waterman, M.S., 1970, “Some ergodic properties of multi-dimensional F-expansions,” Z. Wahrscheinlichkeitstheorie verw. Geb., 16 77-103.

Books and Volumes Edited (reverse chronological order)

Proceedings Tenth Annual Conference on Computational Molecular Biology (RECOMB 2006) A. Apostolico, C. Guerra, S. Istrail, and M. Waterman, Editors. Lecture Notes in Bioinformatics (LNBI 3909), Springer (2006).
Computational Genome Analysis, An Introduction R. Deonier, S, Tavare, and M.S. Waterman, Springer, 2005.
Proceedings Ninth Annual Conference on Computational Molecular Biology (RECOMB 2005)
S. Miyano, J. Meserov, S. Kasif, S. Istrail, P. Pevzner and M.S. Waterman, Editors. Lecture Notes in Bioinformatics (LNBI 3500), Springer (2005).
Mathematics and 21st Century Biology, member of Editorial Committee, National Research Council, National Academies Press (2005).
Computational Methods for SNPs and Haplotype Inference: DIMACS/RECOMB Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002. Revised Papers
S. Istrail, Waterman, M.S. , and A. Clark, Editors, Lecture Notes in Computer Science, (LNCS 2983), Springer (2004).
Proceedings Eighth Annual Conference on Computational Molecular Biology (RECOMB 2004) D. Gusfield, P. Bourne, S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508041, (March 27-31, 2004)
Computational Methods for SNPs and Haplotype Inference, Istrail, S., Waterman, M.S., and Clark A., Editors, LNBI 2983, Springer (2004).
Proceedings Seventh Annual Conference on Computational Molecular Biology (RECOMB 2003) T. Lengauer, W. Miller, S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508031, (April 10-13, 2003)
Proceedings Sixth Annual Conference on Computational Molecular Biology (RECOMB 2002) T. Lengauer, E. Meyers , S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number , (April 18-21, 2002)
Proceedings Fifth Annual Conference on Computational Molecular Biology (RECOMB 2001) T. Lengauer, D. Sanko®, S. Istrail, P. Pevzner and M.S.Waterman, Editors. ACM Press, Order Number 508011, (April 22-25, 2001)
Proceedings Fourth Annual Conference on Computational Molecular Biology (RECOMB 2000) R. Shamir, S. Miyano, S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508001, (April 8-11, 2000)
Russian translation of Mathematical Methods for DNA Sequences (1989): Matematicheskie metody dlja analiza posledovatel’noste’ DNK pod red. M. Uoterrnena. MIR Publishers (1999).
Proceedings Third Annual Conference on Computational Molecular Biology (RECOMB 1999) 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. Farach-Colton, F.S. Roberts, M. Vingron, and M.S. Waterman, Editors. American Mathematical Society, 288 pages.
Proceedings Second Annual Conference on Computational Molecular Biology (RECOMB 1998) S. Istrail, P. Pevzner and M.S. Waterman, Editors. ACM Press, Order Number 508981, (March 22-25, 1998)
Proceedings First Annual Conference on Computational Molecular Biology (RECOMB 1997) M.S. Waterman, S. Istrail and P. Pevzner, Editors. ACM Press, Order Number 508971, (January 19 – 22, 1997)
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.
Introduction to Computational Biology: Sequences, Maps and Genomes. (1995),M.S. Waterman. Chapman Hall, 431 pages.
Calculating the Secrets of Life. (1995) E. Lander and Waterman, M.S. , Editors. National Academy Press, Washington DC. 285 pages.
Mathematical Analysis of Molecular Sequences. M.S.Waterman, Guest Editor. Special Issue. Bulletin of Mathematical Biology 51, Issue #1, (1989).
Mathematical Methods for DNA Sequences. (1989), M.S. Waterman, Editor. CRC Press. 283 pages.