Michael S. Waterman

Zhiyuan Zhai, Gesine Reinert, Kai Song, Michael S. Waterman, Yihui Luan, Fengzhu Sun: Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads. Journal of Computational Biology 19(6): 839-854 (2012)

Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman: Sequence Alignment as Hypothesis Testing. Journal of Computational Biology 18(5): 677-691 (2011)

Wenyuan Li, Chun-Chi Liu, Tong Zhang, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou: Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation. PLoS Computational Biology 7(6) (2011)

Michael R. Mehan, Juan Nunez-Iglesias, Chao Dai, Michael S. Waterman, Xianghong Jasmine Zhou: An integrative modular approach to systematically predict gene-phenotype associations. BMC Bioinformatics 11(S-1): 62 (2010)

Zhiyuan Zhai, Shih-Yen Ku, Yihui Luan, Gesine Reinert, Michael S. Waterman, Fengzhu Sun: The Power of Detecting Enriched Patterns: An HMM Approach. Journal of Computational Biology 17(4): 581-592 (2010)

Lin Wan, Gesine Reinert, Fengzhu Sun, Michael S. Waterman: Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics. Journal of Computational Biology 17(11): 1467-1490 (2010)

Jong Hyun Kim, Woo-Cheol Kim, Michael S. Waterman, Sanghyun Park, Lei M. Li: HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. Bioinformatics 25(18): 2430-2431 (2009)

Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang: The Seventh Asia Pacific Bioinformatics Conference (APBC2009). BMC Bioinformatics 10(S-1) (2009)

Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou: An Integrative Network Approach to Map the Transcriptome to the Phenome. Journal of Computational Biology 16(8): 1023-1034 (2009)

Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman: Alignment-Free Sequence Comparison (I): Statistics and Power. Journal of Computational Biology 16(12): 1615-1634 (2009)

David C. Schwartz, Michael S. Waterman: New Generations: Sequencing Machines and Their Computational Challenges. J. Comput. Sci. Technol. 25(1): 3-9 (2009)

Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou: An Integrative Network Approach to Map the Transcriptome to the Phenome. RECOMB 2008: 232-245

Haifeng Li, Anton Valouev, David C. Schwartz, Michael S. Waterman, Lei M. Li: A Quantile Method for Sizing Optical Maps. Journal of Computational Biology 14(3): 255-266 (2007)

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: Gene Aging Nexus: a web database and data mining platform for microarray data on aging. Nucleic Acids Research 35(Database-Issue): 756-759 (2007)

Jong Hyun Kim, Michael S. Waterman, Lei M. Li: Accuracy Assessment of Diploid Consensus Sequences. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1): 88-97 (2007)

Gesine Reinert, Michael S. Waterman: On the Length of the Longest Exact Position Match in a Random Sequence. IEEE/ACM Trans. Comput. Biology Bioinform. 4(1): 153-156 (2007)

Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael S. Waterman, Haiyan Huang, Xianghong Jasmine Zhou: Systematic discovery of functional modules and context-specific functional annotation of human genome. ISMB/ECCB (Supplement of Bioinformatics) 2007: 222-229

Xifeng Yan, Michael R. Mehan, Yu Huang, Michael S. Waterman, Philip S. Yu, Xianghong Jasmine Zhou: A graph-based approach to systematically reconstruct human transcriptional regulatory modules. ISMB/ECCB (Supplement of Bioinformatics) 2007: 577-586

Anton Valouev, Yu Zhang, David C. Schwartz, Michael S. Waterman: Refinement of optical map assemblies. Bioinformatics 22(10): 1217-1224 (2006)

Jianjun Hu, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou: Integrative missing value estimation for microarray data. BMC Bioinformatics 7: 449 (2006)

Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman: Alignment of Optical Maps. Journal of Computational Biology 13(2): 442-462 (2006)

Michael S. Waterman: Whole Genome Optical Mapping. APBC 2006: 5

Michael S. Waterman: Stan Ulam and Computational Biology. RECOMB 2006: 159-159

Alberto Apostolico, Concettina Guerra, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman (Eds.): Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006, Venice, Italy, April 2-5, 2006, Proceedings. Lecture Notes in Computer Science 3909, Springer 2006, isbn 3-540-33295-2

Kui Zhang, Zhaohui S. Qin, Ting Chen, Jun S. Liu, Michael S. Waterman, Fengzhu Sun: HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21(1): 131-134 (2005)

Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman: Alignment of Optical Maps. RECOMB 2005: 489-504

Satoru Miyano, Jill P. Mesirov, Simon Kasif, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman (Eds.): Research in Computational Molecular Biology, 9th Annual International Conference, RECOMB 2005, Cambridge, MA, USA, May 14-18, 2005, Proceedings. Lecture Notes in Computer Science 3500, Springer 2005, isbn 3-540-25866-3

Lei M. Li, Jong Hyun Kim, Michael S. Waterman: Haplotype Reconstruction from SNP Alignment. Journal of Computational Biology 11(2/3): 505-516 (2004)

Sorin Istrail, Michael S. Waterman, Andrew G. Clark (Eds.): Computational Methods for SNPs and Haplotype Inference, DIMACS/RECOMB Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002, Revised Papers. Lecture Notes in Computer Science 2983, Springer 2004, isbn 3-540-21249-3

Yu Zhang, Michael S. Waterman: An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences. Journal of Computational Biology 10(6): 803-819 (2003)

Michael S. Waterman, Yu Zhang: Eulerian Path Methods for Multiple Sequence Alignment. CSB 2003: 29

Lei M. Li, Jong Hyun Kim, Michael S. Waterman: Haplotype reconstruction from SNP alignment. RECOMB 2003: 207-216

Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen: Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. RECOMB 2003: 332-340

Mengxiang Tang, Michael S. Waterman, Shibu Yooseph: Zinc Finger Gene Clusters and Tandem Gene Duplication. Journal of Computational Biology 9(2): 429-446 (2002)

Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun: Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. Computational Methods for SNPs and Haplotype Inference 2002: 96-112

Pavel A. Pevzner, Haixu Tang, Michael S. Waterman: A new approach to fragment assembly in DNA sequencing. RECOMB 2001: 256-267

Mengxiang Tang, Michael S. Waterman, Shibu Yooseph: Zinc finger gene clusters and tandem gene duplication. RECOMB 2001: 297-304

Gesine Reinert, Sophie Schbath, Michael S. Waterman: Probabilistic and Statistical Properties of Words: An Overview. Journal of Computational Biology 7(1-2): 1-46 (2000)

Jae Kyu Lee, Vlado Dancík, Michael S. Waterman: Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo. Journal of Computational Biology 5(3): 505-515 (1998)

Jae Kyu Lee, Vlado Dancík, Michael S. Waterman: Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo. RECOMB 1998: 147-152

Michael S. Waterman, Sorin Istrail, Pavel A. Pevzner: Selected Papers from RECOMB'97 - Preface. Journal of Computational Biology 4(3): 215-216 (1997)

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling Strategies for Establishing Physical Genome Maps Using FISH. Journal of Computational Biology 4(4): 467-486 (1997)

George A. Komatsoulis, Michael S. Waterman: Chimeric alignment by dynamic programming: algorithm and biological uses. RECOMB 1997: 174-180

Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman: Pooling strategies for establishing physical genome maps using FISH. RECOMB 1997: 294-299

Martin Vingron, Michael S. Waterman: Alignment Networks and Electrical Networks. Discrete Applied Mathematics 71(1-3): 297-309 (1996)

Richard Arratia, D. Martin, Gesine Reinert, Michael S. Waterman: Poisson Process Approximation for Sequence Repeats and Sequencing by Hybridization. Journal of Computational Biology 3(3): 425-463 (1996)

Michael S. Waterman: Introduction to computational biology - maps, sequences, and genomes: interdisciplinary statistics. CRC Press 1995, isbn 978-0-412-99391-6, pp. I-XV, 1-431

Pavel A. Pevzner, Michael S. Waterman: Multiple Filtration and Approximate Pattern Matching. Algorithmica 13(1/2): 135-154 (1995)

Ramana M. Idury, Michael S. Waterman: A New Algorithm for DNA Sequence Assembly. Journal of Computational Biology 2(2): 291-306 (1995)

Pavel A. Pevzner, Michael S. Waterman: Open Combinatorial Problems in Computational Molecular Biology. ISTCS 1995: 158-173

William R. Schmitt, Michael S. Waterman: Linear Trees and RNA Secondary Structure. Discrete Applied Mathematics 51(3): 317-323 (1994)

Larry Goldstein, Michael S. Waterman: Approximations to Profile Score Distributions. Journal of Computational Biology 1(2): 93-104 (1994)

Pavel A. Pevzner, Michael S. Waterman: A Fast Filtration Algorithm for the Substring Matching Problem. CPM 1993: 197-214

Michael S. Waterman: Sequence Comparison and Statistical Significance in Molecular Biology (Abstract). ESA 1993: 396

X. Huang, Michael S. Waterman: Dynamic programming algorithms for restriction map comparison. Computer Applications in the Biosciences 8(5): 511-520 (1992)

Pavel A. Pevzner, Michael S. Waterman: Matrix Longest Common Subsequence Problem, Duality and Hibert Bases. CPM 1992: 79-89

E. T. Chow, J. C. Peterson, Michael S. Waterman, Tim Hunkapiller, B. A. Zimmermann: A systolic array processor for biological information signal processing. ICS 1991: 216-223

Jerrold R. Griggs, Phil Hanlon, Andrew M. Odlyzko, Michael S. Waterman: On the number of alignments of k sequences. Graphs and Combinatorics 6(2): 133-146 (1990)

David J. Lipman, W. John Wilbur, Temple F. Smith, Michael S. Waterman: On the statistical significance of nucleic acid similarities. Nucleic Acids Research 12(1): 215-226 (1984)

Michael S. Waterman, Temple F. Smith, H. L. Katcher: Algorithms for restriction map comparisons. Nucleic Acids Research 12(1): 237-242 (1984)