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A Computational Framework for Interpreting Metabolomics Data—Genomatica, Inc., 5405 Morehouse Drive, Suite 210, San Diego, CA 92121-4722; 858-824-1771, www.genomatica.com
Dr. Stephen James Van Die, Principal Investigator, svandien@genomatica.com
Dr. Christophe Heinz Schilling, Business Official, cschilling@genomatica.com
DOE Grant No. DE-FG02-06ER84416
Amount: $99,870
Advances in bioinformatics and genome research have generated a rapid expansion in the availability of information at all levels of biological investigation. One of the goals of the of the DOE’s Genomes-to-Life Program is the development of a computational systems-biology infrastructure, in order to interpret this information at the whole cell level and to predict the behavior of these complex systems in response to their environment. This project will develop a combined experimental/in-silico simulation platform to improve the predictive capabilities of models that use metabolite profile (metabolomics) data. The approach will include a methodology for interpreting metabolomics data within the context of genome-scale metabolic models. Phase I will create a database containing intracellular metabolite concentrations of three organisms under various conditions. The database will be used first to improve existing in silico models by elucidating new metabolic pathways, and second to characterize, compare, and contrast metabolic phenotypes under the different conditions studied.
Commercial Applications And Other Benefits as described by the awardee: The technology should leverage metabolite concentration data to expand in silico models of metabolism and improve the predictive capability of these models. In addition, a general methodology for extracting useful biological information from metabolomics data would be established. The technology would advance basic biological research, drive metabolic engineering efforts for the production of chemicals from renewable feedstocks, and assist in developing strains to sequester greenhouse gases.