In this project, the interdisciplinary team proposes to develop a set of algorithmic tools to facilitate the study of three important biological problems: (a) Chromosome organization; (b) Dynamics of chromatin domains in the nucleus of living cells; (c) Mobility properties of functional sites (such as replication and transcription sites). The core of this project is to use computational geometry and optimization techniques to develop efficient algorithms for solving a set of challenging computational problems, such as ensemble clustering, median graph, generalized maximum common subgraphs, geometric fitting, matching, and rigid substructure extraction. This project will yield a set of efficient algorithms and optimization methods for the proposed problems. The designed algorithms and techniques will be used as automatic (or semi-automatic) tools to accurately and reliably analyze the nucleus organization and dynamics, and help understanding the coordination of genomic expression. The set of algorithms and techniques will be implemented and tested using randomly generated data and real biological data. The algorithmic tools and optimization methods from this project will be used to study the nucleus of living cells. It could potentially lead to significant biological discoveries and help us to better understand the mechanism cancers and their relationship with chromosome organization and dynamics. This project will bring research and educational opportunities to both graduate and undergraduate students. It will involve several graduate students and undergraduate students, from both Computer Science and Engineering and Biological Sciences Departments.
