Mathematical Sciences: Improved Algorithms for Functional Analysis of Genomic Information

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9407039 Souvaine Computational techniques are needed to assist in the analysis of genomic information to determine structural and functional properties of the genome. An example is the problem of differential gene expression. The identification of genes expressed differently in different states of a disease is essential for the characterization and classification of the biological and clinical behavior of the disease. Algorithms are needed to accurately and efficiently compare "gene fingerprints" in order to provide detailed quantitative information on differential gene expression. To devise such algorithms, it will be necessary to provide both useful data structures for representing fingerprints and comparison algorithms to determine the essential differences and similarities between two fingerprints. I propose to develop and implement such data structures and algorithms, as well as investigate other mathematical and computational problems that arise in the analysis of genomic function. The first year of the proposed fellowship will be a DIMACS "special year" in Mathematical Support for Molecular Biology. As part of this special year, DIMACS will be holding a 25-month intensive training plan for its postdoctoral associates. This training plan will include ongoing mentoring biology seminars, tutorials and courses, and visits to the Waksman Institute of Molecular Genetics at Rutgers and the NSF Science and Technology Center for Molecular Biotechnology at the University of Washington. In addition to the postdoctoral training plan, the special year will involve a distinguished lecture series, a seminar series, workshops and mini-workshops, and ongoing discussion and collaboration between the postdoctoral associates, graduate students, and long- and short- term visitors to DIMACS. While the training provided by CuraGen will be less organized than the training provided by DIMACS, it will be equally valuable, and will consist of day-to-day contact with CuraGen's molecular biologists and physical scientists, as well as unlimited access to the biology and instrumentation laboratories.