M. Waterman

Most-cited papers

The B73 Maize Genome: Complexity, Diversity, and Dynamics
P. Schnable, D. Ware, R. Fulton, J. Stein +153 more
2009Science3,949 citations
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A dynamic programming algorithm for haplotype block partitioning
Kui Zhang, Minghua Deng, Ting Chen, M. Waterman +1 more
2002Proceedings of the National Academy of Sciences of the United States of America368 citations Open access
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Introduction to Computational Biology: Maps, Sequences and Genomes
M. Waterman
1998353 citations
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Probabilistic and Statistical Properties of Words: An Overview
G. Reinert, S. Schbath, M. Waterman
2000J. Comput. Biol.259 citations
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Alignment-Free Sequence Comparison (I): Statistics and Power
G. Reinert, David S. H. Chew, Feng-Zhu Sun, M. Waterman
2009J. Comput. Biol.216 citations Open access
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Benchmarking of alignment-free sequence comparison methods
A. Zieleziński, Hani Z. Girgis, Guillaume Bernard, Chris-André Leimeister +15 more
2019Genome Biology206 citations Open access
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Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.
Kui Zhang, Z. Qin, Jun S. Liu, Ting Chen +2 more
2004Genome Research199 citations Open access
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Whole-genome shotgun assembly and comparison of human genome assemblies
S. Istrail, G. Sutton, Liliana D. Florea, A. Halpern +32 more
2004Proceedings of the National Academy of Sciences of the United States of America198 citations Open access
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New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing
Kai Song, Jie Jessie Ren, G. Reinert, Minghua Deng +2 more
2014Briefings Bioinform.189 citations Open access
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High-resolution human genome structure by single-molecule analysis
Brian Teague, M. Waterman, Steve Goldstein, Konstantinos D. Potamousis +16 more
2010Proceedings of the National Academy of Sciences of the United States of America179 citations Open access
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Levenshtein Distance, Sequence Comparison and Biological Database Search
B. Berger, M. Waterman, Y. Yu
2020IEEE Transactions on Information Theory145 citations Open access
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A Single Molecule Scaffold for the Maize Genome
Shi-Guo Zhou, Fusheng Wei, John Nguyen, Michael Bechner +13 more
2009PLoS Genetics140 citations Open access
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HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
Kui Zhang, Z. Qin, Ting Chen, Jun S. Liu +2 more
2005Bioinform.127 citations Open access
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An algorithm for assembly of ordered restriction maps from single DNA molecules
Anton Valouev, D. Schwartz, Shi-Guo Zhou, M. Waterman
2006Proceedings of the National Academy of Sciences of the United States of America126 citations Open access
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Alignment-Free Sequence Comparison (II): Theoretical Power of Comparison Statistics
Lin Wan, G. Reinert, Feng-Zhu Sun, M. Waterman
2010J. Comput. Biol.117 citations Open access
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Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation
Wenyuan Li, Chun-Chi Liu, Tong Zhang, Haifeng Li +2 more
2011PLoS Comput. Biol.115 citations Open access
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Estimating the repeat structure and length of DNA sequences using L-tuples.
Xiao-Man Li, M. Waterman
2003Genome Research102 citations Open access
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DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections
Chun-Chi Liu, Yu-Ting Tseng, Wenyuan Li, Chia-Yu Wu +9 more
2014Nucleic Acids Res.101 citations Open access
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Systematic discovery of functional modules and context-specific functional annotation of human genome
Yu S. Huang, Haifeng Li, Hai-Yan Hu, Xi-Feng Yan +3 more
2007ISMB/ECCB97 citations Open access
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Alignment of Optical Maps
Anton Valouev, Lei M. Li, Yu-Chi Liu, D. Schwartz +3 more
2005Annual International Conference on Research in Computational Molecular Biology87 citations
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A graph-based approach to systematically reconstruct human transcriptional regulatory modules
Xi-Feng Yan, M. Mehan, Yu S. Huang, M. Waterman +2 more
2007ISMB/ECCB84 citations Open access
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Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.
Jong Hyun Kim, M. Waterman, Lei M. Li
2007Genome Research77 citations Open access
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CAFE: aCcelerated Alignment-FrEe sequence analysis
Yang Young Lu, Ku-Jin Tang, Jie Jessie Ren, J. Fuhrman +2 more
2017Nucleic Acids Res.74 citations Open access
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A new approach to fragment assembly in DNA sequencing
P. Pevzner, Hai-Xu Tang, M. Waterman
2001Annual International Conference on Research in Computational Molecular Biology72 citations
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Haplotype Reconstruction from SNP Alignment
Lei M. Li, Jong Hyun Kim, M. Waterman
2003Annual International Conference on Research in Computational Molecular Biology57 citations
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Gene Aging Nexus: a web database and data mining platform for microarray data on aging
Fei Pan, C. Chiu, Sudip Pulapura, M. Mehan +6 more
2006Nucleic Acids Res.56 citations Open access
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Zinc Finger Gene Clusters and Tandem Gene Duplication
Meng-Xiang Tang, M. Waterman, S. Yooseph
2001J. Comput. Biol.55 citations
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Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data.
Kui Zhang, Feng-Zhu Sun, M. Waterman, Ting Chen
2003American Journal of Human Genetics52 citations Open access
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New Powerful Statistics for Alignment-free Sequence Comparison Under a Pattern Transfer Model
Xue-Mei Liu, Lin Wan, Jing Li, G. Reinert +2 more
2011Journal of Theoretical Biology45 citations Open access
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An Eulerian path approach to local multiple alignment for DNA sequences.
Yu Zhang, M. Waterman
2005Proceedings of the National Academy of Sciences of the United States of America44 citations Open access
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An Eulerian Path Approach to Global Multiple Alignment for DNA Sequences
Yu Zhang, M. Waterman
2003J. Comput. Biol.44 citations
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Computational Methods for SNPs and Haplotype Inference
S. Istrail, M. Waterman, A. Clark
2002Lecture Notes in Computer Science43 citations Open access
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Integrative missing value estimation for microarray data
Jianjun Hu, Haifeng Li, M. Waterman, X. Zhou
2006BMC Bioinformatics40 citations Open access
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Gene coexpression measures in large heterogeneous samples using count statistics
Y. X. Rachel Wang, M. Waterman, Haiyan Huang
2014Proceedings of the National Academy of Sciences of the United States of America36 citations Open access
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Refinement of optical map assemblies
Anton Valouev, Yu Zhang, D. Schwartz, M. Waterman
2006Bioinform.33 citations Open access
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Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data
Kui Zhang, Feng-Zhu Sun, M. Waterman, Ting Chen
2003Annual International Conference on Research in Computational Molecular Biology33 citations
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New Generations: Sequencing Machines and Their Computational Challenges
D. Schwartz, M. Waterman
2010Journal of Computational Science and Technology20 citations Open access
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Proceedings of the Sixth Annual International Conference on Computational Biology, RECOMB 2002, Washington, DC, USA, April 18-21, 2002
G. Myers, S. Hannenhalli, D. Sankoff, S. Istrail +2 more
2002Annual International Conference on Research in Computational Molecular Biology19 citations
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Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump Markov Chain Monte Carlo
Jae Kyu Lee, Vlado Dancík, M. Waterman
1998Annual International Conference on Research in Computational Molecular Biology18 citations Open access
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An Integrative Network Approach to Map the Transcriptome to the Phenome
M. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, M. Waterman +1 more
2008Annual International Conference on Research in Computational Molecular Biology16 citations Open access
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An integrative modular approach to systematically predict gene-phenotype associations
M. Mehan, Juan Nunez-Iglesias, Chao Dai, M. Waterman +1 more
2010BMC Bioinformatics15 citations Open access
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Proceedings of the seventh annual international conference on Research in computational molecular biology
M. Vingron, S. Istrail, P. Pevzner, M. Waterman +1 more
2003Annual International Conference on Research in Computational Molecular Biology14 citations
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The Power of Detecting Enriched Patterns: An HMM Approach
Zhi-Yuan Zhai, S. Ku, Y. Luan, G. Reinert +2 more
2010J. Comput. Biol.12 citations Open access
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A Geometric Interpretation for Local Alignment-Free Sequence Comparison
E. Behnam, M. Waterman, Andrew D. Smith
2013J. Comput. Biol.11 citations Open access
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Accuracy Assessment of Diploid Consensus Sequences
Jong Hyun Kim, M. Waterman, Lei M. Li
2007IEEE/ACM Transactions on Computational Biology & Bioinformatics11 citations
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Shotgun optical mapping: a comprehensive statistical and computational analysis
M. Waterman, Anton Valouev
200611 citations
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Generalized correlation measure using count statistics for gene expression data with ordered samples
Y. X. Rachel Wang, Ke Liu, E. Theusch, J. Rotter +3 more
2018Bioinform.10 citations Open access
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Sequence Alignment as Hypothesis Testing
Lu Meng, Feng-Zhu Sun, Xue-Gong Zhang, M. Waterman
2011J. Comput. Biol.10 citations Open access
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Mathematical Support for Molecular Biology
Martín Farach-Colton, F. Roberts, M. Vingron, M. Waterman
199910 citations
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A new statistic for efficient detection of repetitive sequences
Sijie Chen, Feng-Zhu Sun, M. Waterman, Xue-Gong Zhang
2018bioRxiv8 citations Open access
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