III-CXT:Algorithmic Tools for Determining the Organization and Dynamics of the Cell Nucleus

III-CXT：确定细胞核的组织和动力学的算法工具

• 批准号: 0713489
• 负责人: Jinhui Xu
• 金额: --
• 依托单位: SUNY at Buffalo
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0713489&HistoricalAwards=false
• 关键词: III; CXT; Algorithmic; Tools; Determining

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.

在这个项目中，跨学科团队建议开发一套算法工具来促进对三个重要生物学问题的研究：(A)染色体组织；(B)活细胞核中染色质结构域的动态；(C)功能位点(如复制和转录位点)的移动特性。这个项目的核心是使用计算几何和优化技术来开发有效的算法来解决一系列具有挑战性的计算问题，如集成聚类、中值图、广义最大公共子图、几何拟合、匹配和刚体子结构提取。该项目将为所提出的问题产生一套有效的算法和优化方法。所设计的算法和技术将被用作自动(或半自动)工具，准确可靠地分析核的组织和动力学，并帮助理解基因组表达的协调。这套算法和技术将使用随机生成的数据和真实的生物数据进行实施和测试。来自该项目的算法工具和优化方法将被用于研究活细胞的细胞核。它可能会带来重大的生物学发现，并帮助我们更好地理解癌症的机制及其与染色体组织和动力学的关系。该项目将为研究生和本科生带来研究和教育机会。它将涉及来自计算机科学、工程和生物科学系的几名研究生和本科生。