Mathematical Sciences: Improved Algorithms for Functional Analysis of Genomic Information

小行星9407039 需要计算技术来帮助分析基因组信息，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中不同表达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。 需要算法来准确和有效地比较“基因指纹”，以便提供关于差异基因表达的详细定量信息。 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，以及研究在基因组功能分析中出现的其他数学和计算问题。 拟议的奖学金的第一年将是一个DIMACS“特殊的一年”在分子生物学的数学支持。 作为这个特殊年份的一部分，DIMACS将为博士后员工举办为期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，辅导和课程，并参观罗格斯大学的Waksman分子遗传学研究所和华盛顿大学的NSF分子生物技术科学技术中心。 除了博士后培训计划外，特殊的一年还将包括一系列杰出的讲座，一系列研讨会，研讨会和小型研讨会，以及博士后助理，研究生和长期和短期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，但同样有价值，将包括与以下人员的日常接触： CuraGen的分子生物学家和物理科学家，以及无限制地访问生物和仪器实验室。

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.