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

IRI-9810537Gaasterland，Theresa gaasterl@cs.uchicago.eduUniversity of Chicago $0 - 18 mos. （与CISE机构基础设施共同资助-总奖金49，998美元）CONACyT：微生物基因组中调控控制元件推理的综合环境这项研究是PI与墨西哥Julio Collado-Vides博士的合作。 目标是通过整合两个不同的研究基因组的平台，使用人工智能技术破译整个细菌基因组中调控元件的保守模式：一种多基因组注释工具，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（已经存在的MAGPIE系统，由Gaasterland开发）和E. coli基因组DNA（Regulon DB，Collado-Vides组装）。要做到这一点，需要开发新的方法来结合不同类型的知识进行预测，并且系统必须能够根据新知识修改先前的预测。 此外，还将深入了解捕获生物体结构和功能的适当知识表示。 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种生物体获得的知识在多大程度上可用于指导新的探索。organism.http://www.cs.uchicago.edu/~gaasterl/

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/