An Integrated Environment for Reasoning about regulatory Control elements in Microbial genomes

IRI-9810537加斯特兰，Theresa Gaasterl@cs.uchicago.edu芝加哥大学，0-18 mos。(与CESE机构基础设施共同资助--总奖金为49,998美元)CONACyT：一个关于微生物基因组中监管控制元素的综合推理环境这项研究是PI与墨西哥Julio Collado-Vdes博士的合作。其目标是利用人工智能技术，通过集成两个不同的基因组研究平台来破译整个细菌基因组中调控元件的保守模式：一个多基因组注释工具，它使用自动推理和合作回答方法将特征与基因组序列相关联(现有的鹊子系统，由Gaasterland开发)，以及一个编码在大肠杆菌基因组DNA中的调控元件、操纵子和相关调控信号的数据库(由Collado-Vdes组装的Regon DB)。要做到这一点，需要开发新的方法，将不同类型的知识结合起来进行预测，该系统必须能够根据新的知识修订先前的预测。此外，还将深入了解适当的知识表示法，这些知识表示法既能捕捉生物的结构，也能捕捉生物体的功能。在生物学方面，该项目开发的基础设施将使人们能够了解从一个生物体获得的知识可以在多大程度上用于指导新organism.http://www.cs.uchicago.edu/~gaasterl/的探索

IRI-9810537Gaasterland, Theresa gaasterl@cs.uchicago.eduUniversity of Chicago$0 - 18 mos. (Jointly funded with the CISE Institutional Infrastructure - Total Award $49,998)CONACyT: An Integrated Environment for Reasoning about Regulatory ControlElements in Microbial GenomesThis research is a collaboration of the PI with Dr. Julio Collado-Vides in Mexico. The goal is to use artificial intelligence techniques in deciphering patterns of conservation of regulatory elements across whole bacterial genomes by integrating two different platforms for investigating genomes: a multi-genome annotation tool that uses automated reasoning and cooperative answering methods to associate features with a genomic sequence (the already existing MAGPIE system, developed by Gaasterland) and a database of regulatory elements, operons, and related regulatory signals encoded in E. coli genomic DNA (Regulon DB, assembled by Collado-Vides). To do this, new methods need to be developed for the combination of different types of knowledge to make predictions, and the system must be able to revise prior predictions based on new knowledge. In addition, there will be insights into appropriate knowledge representations that capture bothstructure and function of living organisms. On the biological side, the infrastructure developed in the project will enable an understanding of the degree to which knowledge gained from one organism can be used to guide the exploration of a new organism.http://www.cs.uchicago.edu/~gaasterl/