Mathematical Sciences: Improved Algorithms for Functional Analysis of Genomic Information

9407039 Souvaine需要计算技术来协助分析基因组信息，以确定基因组的结构和功能特性。一个例子是差异基因表达的问题。鉴定在疾病的不同状态下表达不同的基因对于疾病的生物学和临床行为的表征和分类是必不可少的。为了提供基因差异表达的详细定量信息，需要精确高效地比较“基因指纹”的算法。为了设计这样的算法，有必要提供用于表示指纹的有用数据结构和比较算法，以确定两个指纹之间的本质差异和相似性。我建议开发和实现这样的数据结构和算法，以及研究基因组功能分析中出现的其他数学和计算问题。提议奖学金的第一年将是DIMACS分子生物学数学支持的“特殊年”。作为这一特殊年份的一部分，DIMACS将为其博士后开展为期25个月的强化培训计划。该培训计划将包括正在进行的指导生物学研讨会、教程和课程，以及访问罗格斯大学的瓦克斯曼分子遗传学研究所和华盛顿大学的NSF分子生物技术科学与技术中心。除了博士后培训计划，特别年还将包括一个杰出的系列讲座、系列研讨会、讲习班和小型讲习班，以及博士后、研究生和长期和短期访问DIMACS的访问者之间的持续讨论和合作。虽然CuraGen提供的培训不如DIMACS提供的培训有组织，但它同样有价值，并且将包括与CuraGen的分子生物学家和物理科学家的日常接触，以及无限制地访问生物学和仪器实验室。

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.