Alignment-free sequence comparison (I): statistics and power von Reinert, Gesine, Chew, David, Sun, Fengzhu, Waterman, Michael S

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An Eulerian Path Approach to DNA Fragment Assembly von Pevzner, Pavel A., Tang, Haixu, Waterman, Michael S.

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Alignment-free sequence comparison (II): theoretical power of comparison statistics von Wan, Lin, Reinert, Gesine, Sun, Fengzhu, Waterman, Michael S

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Topological classification and enumeration of RNA structures by genus von Andersen, J.E., Penner, R.C., Reidys, C.M., Waterman, M.S.

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A Dynamic Programming Algorithm for Haplotype Block Partitioning von Zhang, Kui, Deng, Minghua, Chen, Ting, Waterman, Michael S., Sun, Fengzhu

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

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Estimating the repeat structure and length of DNA sequences using L-tuples von Li, Xiaoman, Waterman, Michael S

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Distributional Regimes for the Number of k-Word Matches between Two Random Sequences von Lippert, Ross A., Huang, Haiyan, Waterman, Michael S.

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Probabilistic and statistical properties of words: an overview von Reinert, G, Schbath, S, Waterman, M S

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Sequence alignment as hypothesis testing von Meng, Lu, Sun, Fengzhu, Zhang, Xuegong, Waterman, Michael S

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Alignment of optical maps von Valouev, Anton, Li, Lei, Liu, Yu-Chi, Schwartz, David C, Yang, Yi, Zhang, Yu, Waterman, Michael S

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An Eulerian Path Approach to Local Multiple Alignment for DNA Sequences von Zhang, Yu, Waterman, Michael S.

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Refinement of optical map assemblies von Valouev, Anton, Zhang, Yu, Schwartz, David C., Waterman, Michael S.

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The power of detecting enriched patterns: an HMM approach von Zhai, Zhiyuan, Ku, Shih-Yen, Luan, Yihui, Reinert, Gesine, Waterman, Michael S, Sun, Fengzhu

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Sequence alignment and penalty choice. Review of concepts, case studies and implications von Vingron, M, Waterman, M.S

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Haplotype Block Partition with Limited Resources and Applications to Human Chromosome 21 Haplotype Data von Zhang, Kui, Sun, Fengzhu, Waterman, Michael S., Chen, Ting

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An integrative network approach to map the transcriptome to the phenome von Mehan, Michael R, Nunez-Iglesias, Juan, Kalakrishnan, Mrinal, Waterman, Michael S, Zhou, Xianghong Jasmine

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Rapid and Accurate Estimates of Statistical Significance for Sequence Data Base Searches von Waterman, Michael S., Vingron, Martin

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On the Length of the Longest Exact Position Match in a Random Sequence von Reinert, G., Waterman, M.S.

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A MULTIPLE-TUBES APPROACH FOR ACCURATE GENOTYPING OF VERY SMALL DNA SAMPLES BY USING PCR - STATISTICAL CONSIDERATIONS von NAVIDI, W, ARNHEIM, N, WATERMAN, MS

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