| 2008 | RECOMB | 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 |
| 2007 | ISMB | Systematic discovery of functional modules and context-specific functional annotation of human genome. | Yu Huang, Haifeng Li, Haiyan Hu, Xifeng Yan, Michael S. Waterman, Haiyan Huang, Xianghong Jasmine Zhou |
| 2007 | ISMB | A graph-based approach to systematically reconstruct human transcriptional regulatory modules. | Xifeng Yan, Michael R. Mehan, Yu Huang, Michael S. Waterman, Philip S. Yu, Xianghong Jasmine Zhou |
| 2006 | APBC | Whole Genome Optical Mapping. | Michael S. Waterman |
| 2006 | RECOMB | Stan Ulam and Computational Biology. | Michael S. Waterman |
| 2005 | RECOMB | Alignment of Optical Maps. | Anton Valouev, Lei Li, Yu-Chi Liu, David C. Schwartz, Yi Yang, Yu Zhang, Michael S. Waterman |
| 2003 | RECOMB | Haplotype reconstruction from SNP alignment. | Lei M. Li, Jong Hyun Kim, Michael S. Waterman |
| 2003 | RECOMB | Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data. | Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen |
| 2002 | RECOMB | Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. | Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun |
| 2001 | RECOMB | A new approach to fragment assembly in DNA sequencing. | Pavel A. Pevzner, Haixu Tang, Michael S. Waterman |
| 2001 | RECOMB | Zinc finger gene clusters and tandem gene duplication. | Mengxiang Tang, Michael S. Waterman, Shibu Yooseph |
| 1998 | RECOMB | Estimation for restriction sites observed by optical mapping using reversible-jump Markov chain Monte Carlo. | Jae Kyu Lee, Vlado Danck, Michael S. Waterman |
| 1997 | RECOMB | Chimeric alignment by dynamic programming: algorithm and biological uses. | George A. Komatsoulis, Michael S. Waterman |
| 1997 | RECOMB | Pooling strategies for establishing physical genome maps using FISH. | Fengzhu Sun, Gary Benson, Norman Arnheim, Michael S. Waterman |
| 1993 | CPM | A Fast Filtration Algorithm for the Substring Matching Problem. | Pavel A. Pevzner, Michael S. Waterman |
| 1993 | ESA | Sequence Comparison and Statistical Significance in Molecular Biology (Abstract). | Michael S. Waterman |
| 1992 | CPM | Matrix Longest Common Subsequence Problem, Duality and Hibert Bases. | Pavel A. Pevzner, Michael S. Waterman |
| 1991 | ICS | A systolic array processor for biological information signal processing. | E. T. Chow, John C. Peterson, Michael S. Waterman, Tim Hunkapiller, Barbara A. Zimmermann |