Education:
PhD 1969 Michigan State University
Research Topics: Computational Biology
Research Description
I have been using computational approaches to study molecular sequence data. Currently the sequence databases double in size every two years, and new developments in sequencing technology could accelerate this rate of growth. The importance of computational methods to molecular biology is certainly growing proportionally.
Part of my work has been to develop relevant and rigorous algorithms to compare and analyze nucleic acid and protein sequences. I was the first to introduce multiple gap weights to alignment algorithms and am co-developer of the Smith-Waterman algorithm. I am now studying the effects of different weighting schemes such as the Dayhoff matrix on the resulting optimal alignments. Also I have been studying the expected progress of physical mapping experiments which depends on the cloning vector, the fingerprinting scheme, etc.
Selected Publications
Yan X, Mehan MR, Huang Y, Waterman MS, Yu PS, Zhou XJ. - A graph-based approach to systematically reconstruct human transcriptional regulatory modules. - Bioinformatics [ 2007 ] Jul 1;23(13):i577-i586 . PubMed
Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ. - Systematic discovery of functional modules and context-specific functional annotation of human genome. - Bioinformatics [ 2007 ] Jul 1;23(13):i222-i229 . PubMed
Kim JH, Waterman MS, Li LM. - Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. - Genome Res [ 2007 ] Jul;17(7):1101-10 . PubMed
Li H, Valouev A, Schwartz DC, Waterman MS, Li LM. - A quantile method for sizing optical maps. - J Comput Biol [ 2007 ] Apr;14(3):255-66 . PubMed
Reinert G, Waterman MS. - On the length of the longest exact position match in a random sequence. - IEEE/ACM Trans Comput Biol Bioinform [ 2007 ] Jan-Mar;4(1):153-6 . PubMed
Kim JH, Waterman MS, Li LM. - Accuracy assessment of diploid consensus sequences. - IEEE/ACM Trans Comput Biol Bioinform [ 2007 ] Jan-Mar;4(1):88-97 . PubMed
Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ. - Gene Aging Nexus: a web database and data mining platform for microarray data on aging. - Nucleic Acids Res [ 2007 ] Jan;35(Database issue):D756-9 . PubMed
Valouev A, Schwartz DC, Zhou S, Waterman MS. - An algorithm for assembly of ordered restriction maps from single DNA molecules. - Proc Natl Acad Sci U S A [ 2006 ] Oct 24;103(43):15770-5 . PubMed
Hu J, Li H, Waterman MS, Zhou XJ. - Integrative missing value estimation for microarray data. - BMC Bioinformatics [ 2006 ] Oct 12;7:449 . PubMed
Valouev A, Li L, Liu YC, Schwartz DC, Yang Y, Zhang Y, Waterman MS. - Alignment of optical maps. - J Comput Biol [ 2006 ] Mar;13(2):442-62 . PubMed
