On some new sequences generalizing the Catalan and Motzkin numbers. - P. R. Stein; Michael S. Waterman (Discret. Math., 1979)

Technical Note - Determining All Optimal and Near-Optimal Solutions when Solving Shortest Path Problems by Dynamic Programming. - Thomas H. Byers; Michael S. Waterman (Oper. Res., 1984)

On the statistical significance of nucleic acid similarities. - David J. Lipman; W. John Wilbur; Temple F. Smith; Michael S. Waterman (Nucleic Acids Res., 1984)

Algorithms for restriction map comparisons. - Michael S. Waterman; Temple F. Smith; H. L. Katcher (Nucleic Acids Res., 1984)

On the number of alignments of k sequences. - Jerrold R. Griggs; Phil Hanlon; Andrew M. Odlyzko; Michael S. Waterman (Graphs Comb., 1990)

Biological information signal processor. - E. T. Chow; Tim Hunkapiller; J. Peterson; Michael S. Waterman (ASAP, 1991)

A systolic array processor for biological information signal processing. - E. T. Chow; John C. Peterson; Michael S. Waterman; Tim Hunkapiller; Barbara A. Zimmermann (ICS, 1991)

Matrix Longest Common Subsequence Problem, Duality and Hibert Bases. - Pavel A. Pevzner; Michael S. Waterman (CPM, 1992)

Dynamic programming algorithms for restriction map comparison. - X. Huang; Michael S. Waterman (Comput. Appl. Biosci., 1992)

A Fast Filtration Algorithm for the Substring Matching Problem. - Pavel A. Pevzner; Michael S. Waterman (CPM, 1993)

Sequence Comparison and Statistical Significance in Molecular Biology (Abstract). - Michael S. Waterman (ESA, 1993)

Linear Trees and RNA Secondary Structure. - William R. Schmitt; Michael S. Waterman (Discret. Appl. Math., 1994)

Approximations to Profile Score Distributions. - Larry Goldstein; Michael S. Waterman (J. Comput. Biol., 1994)

Introduction to computational biology - maps, sequences, and genomes: interdisciplinary statistics. - Michael S. Waterman (CRC Press, 1995)

Open Combinatorial Problems in Computational Molecular Biology. - Pavel A. Pevzner; Michael S. Waterman (ISTCS, 1995)

Multiple Filtration and Approximate Pattern Matching. - Pavel A. Pevzner; Michael S. Waterman (Algorithmica, 1995)

A New Algorithm for DNA Sequence Assembly. - Ramana M. Idury; Michael S. Waterman (J. Comput. Biol., 1995)

Alignment Networks and Electrical Networks. - Martin Vingron; Michael S. Waterman (Discret. Appl. Math., 1996)

Poisson Process Approximation for Sequence Repeats and Sequencing by Hybridization. - Richard Arratia; Daniela Martin; Gesine Reinert; Michael S. Waterman (J. Comput. Biol., 1996)

Chimeric alignment by dynamic programming: algorithm and biological uses. - George A. Komatsoulis; Michael S. Waterman (RECOMB, 1997)

Pooling Strategies for Establishing Physical Genome Maps Using FISH. - Fengzhu Sun; Gary Benson; Norman Arnheim; Michael S. Waterman (J. Comput. Biol., 1997)

Selected Papers from RECOMB'97 - Preface. - Michael S. Waterman; Sorin Istrail; Pavel A. Pevzner (J. Comput. Biol., 1997)

Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo - Jae Kyu Lee; Vlado Dancík; Michael S. Waterman (J. Comput. Biol., 1998)

Probabilistic and Statistical Properties of Words: An Overview. - Gesine Reinert; Sophie Schbath; Michael S. Waterman (J. Comput. Biol., 2000)

A new approach to fragment assembly in DNA sequencing. - Pavel A. Pevzner; Haixu Tang; Michael S. Waterman (RECOMB, 2001)

Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. - Kui Zhang; Ting Chen 006; Michael S. Waterman; Zhaohui S. Qin; Jun S. Liu; Fengzhu Sun (Computational Methods for SNPs and Haplotype Inference, 2002)

Zinc Finger Gene Clusters and Tandem Gene Duplication. - Mengxiang Tang; Michael S. Waterman; Shibu Yooseph (J. Comput. Biol., 2002)

Eulerian Path Methods for Multiple Sequence Alignment. - Michael S. Waterman; Yu Zhang 002 (CSB, 2003)

Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. - Kui Zhang; Fengzhu Sun; Michael S. Waterman; Ting Chen 006 (RECOMB, 2003)

An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences. - Yu Zhang 002; Michael S. Waterman (J. Comput. Biol., 2003)

Haplotype Reconstruction from SNP Alignment. - Lei M. Li; Jong Hyun Kim; Michael S. Waterman (J. Comput. Biol., 2004)

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. - Kui Zhang; Zhaohui S. Qin; Ting Chen 006; Jun S. Liu; Michael S. Waterman; Fengzhu Sun (Bioinform., 2005)

Whole Genome Optical Mapping. - Michael S. Waterman (APBC, 2006)

Stan Ulam and Computational Biology. - Michael S. Waterman (RECOMB, 2006)

Refinement of optical map assemblies. - Anton Valouev; Yu Zhang 002; David C. Schwartz; Michael S. Waterman (Bioinform., 2006)

Integrative missing value estimation for microarray data. - Jianjun Hu; Haifeng Li; Michael S. Waterman; Xianghong Jasmine Zhou (BMC Bioinform., 2006)

Alignment of Optical Maps. - Anton Valouev; Lei Li; Yu-Chi Liu; David C. Schwartz; Yi Yang 047; Yu Zhang 002; Michael S. Waterman (J. Comput. Biol., 2006)

Systematic discovery of functional modules and context-specific functional annotation of human genome. - Yu Huang 003; Haifeng Li; Haiyan Hu; Xifeng Yan; Michael S. Waterman; Haiyan Huang; Xianghong Jasmine Zhou (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A graph-based approach to systematically reconstruct human transcriptional regulatory modules. - Xifeng Yan; Michael R. Mehan; Yu Huang 003; Michael S. Waterman; Philip S. Yu; Xianghong Jasmine Zhou (ISMB/ECCB (Supplement of Bioinformatics), 2007)

A Quantile Method for Sizing Optical Maps. - Haifeng Li; Anton Valouev; David C. Schwartz; Michael S. Waterman; Lei M. Li (J. Comput. Biol., 2007)

Gene Aging Nexus: a web database and data mining platform for microarray data on aging. - Fei Pan; Chi-Hsien Chiu; Sudip Pulapura; Michael R. Mehan; Juan Nunez-Iglesias; Kangyu Zhang; Kiran Kamath; Michael S. Waterman; Caleb E. Finch; Xianghong Jasmine Zhou (Nucleic Acids Res., 2007)

Accuracy Assessment of Diploid Consensus Sequences. - Jong Hyun Kim; Michael S. Waterman; Lei M. Li (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

On the Length of the Longest Exact Position Match in a Random Sequence. - Gesine Reinert; Michael S. Waterman (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. - Jong Hyun Kim; Woo-Cheol Kim; Michael S. Waterman; Sanghyun Park 003; Lei M. Li (Bioinform., 2009)

The Seventh Asia Pacific Bioinformatics Conference (APBC2009). - Michael Q. Zhang; Michael S. Waterman; Xuegong Zhang (BMC Bioinform., 2009)

An Integrative Network Approach to Map the Transcriptome to the Phenome. - Michael R. Mehan; Juan Nunez-Iglesias; Mrinal Kalakrishnan; Michael S. Waterman; Xianghong Jasmine Zhou (J. Comput. Biol., 2009)

Alignment-Free Sequence Comparison (I): Statistics and Power. - Gesine Reinert; David Chew; Fengzhu Sun; Michael S. Waterman (J. Comput. Biol., 2009)

New Generations: Sequencing Machines and Their Computational Challenges. - David C. Schwartz; Michael S. Waterman (J. Comput. Sci. Technol., 2009)

An integrative modular approach to systematically predict gene-phenotype associations. - Michael R. Mehan; Juan Nunez-Iglesias; Chao Dai; Michael S. Waterman; Xianghong Jasmine Zhou (BMC Bioinform., 2010)

Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. - Lin Wan; Gesine Reinert; Fengzhu Sun; Michael S. Waterman (J. Comput. Biol., 2010)

The Power of Detecting Enriched Patterns: An HMM Approach. - Zhiyuan Zhai; Shih-Yen Ku; Yihui Luan; Gesine Reinert; Michael S. Waterman; Fengzhu Sun (J. Comput. Biol., 2010)

Sequence Alignment as Hypothesis Testing. - Lu Meng; Fengzhu Sun; Xuegong Zhang; Michael S. Waterman (J. Comput. Biol., 2011)

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation. - Wenyuan Li 006; Chun-Chi Liu; Tong Zhang 001; Haifeng Li; Michael S. Waterman; Xianghong Jasmine Zhou (PLoS Comput. Biol., 2011)

Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. - Zhiyuan Zhai; Gesine Reinert; Kai Song; Michael S. Waterman; Yihui Luan; Fengzhu Sun (J. Comput. Biol., 2012)

A Geometric Interpretation for Local Alignment-Free Sequence Comparison. - Ehsan Behnam; Michael S. Waterman; Andrew D. Smith (J. Comput. Biol., 2013)

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. - Kai Song; Jie Ren 006; Gesine Reinert; Minghua Deng; Michael S. Waterman; Fengzhu Sun (Briefings Bioinform., 2014)

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. - Chun-Chi Liu; Yu-Ting Tseng; Wenyuan Li 006; Chia-Yu Wu; Ilya Mayzus; Andrey Rzhetsky; Fengzhu Sun; Michael S. Waterman; Jeremy J. W. Chen; Preet M. Chaudhary; Joseph Loscalzo; Edward Crandall; et al. (Nucleic Acids Res., 2014)

CAFE: aCcelerated Alignment-FrEe sequence analysis. - Yang Young Lu; Kujin Tang; Jie Ren 006; Jed A. Fuhrman; Michael S. Waterman; Fengzhu Sun (Nucleic Acids Res., 2017)

Generalized correlation measure using count statistics for gene expression data with ordered samples. - Y. X. Rachel Wang; Ke Liu; Elizabeth Theusch; Jerome I. Rotter; Marisa W. Medina; Michael S. Waterman; Haiyan Huang (Bioinform., 2018)

A new statistic for efficient detection of repetitive sequences. - Sijie Chen; Yixin Chen; Fengzhu Sun; Michael S. Waterman; Xuegong Zhang (Bioinform., 2019)

Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution. - Christopher L. Barrett; Andrei C. Bura; Qijun He; Fenix W. D. Huang; Thomas J. X. Li; Michael S. Waterman; Christian M. Reidys (J. Comput. Biol., 2021)

The Human Genome Project: the Beginning of the Beginning. - Michael S. Waterman (Quant. Biol., 2021)

Levenshtein Distance, Sequence Comparison and Biological Database Search. - Bonnie Berger; Michael S. Waterman; Yun William Yu (IEEE Trans. Inf. Theory, 2021)