Gaasterland, Theresa
CONACyT: An Integrated Environment for Reasoning about Regulatory Control Elements in Microbial Genomes
This 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 both structure 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.
