University of Minnesota
University Relations

Minnesota Supercomputing Institute

Log out of MyMSI

Research Abstracts Online
January 2008 - March 2009

University of Minnesota Twin Cities
College of Biological Sciences
BioTechnology Institute

PI: Friedrich Srienc, Associate Fellow

Elementary Mode Analysis for Biochemical Networks

Evolution has developed the metabolism of organisms with a highly coupled network of hundreds of enzyme-catalyzed reactions. Advances in molecular biological techniques, such as PCR, have provided means of rapidly altering the topography of these reaction networks. Analysis of native and recombinant metabolic networks has been simplified by a number of theoretical tools. One such method is elementary mode analysis. An elementary mode is the simplest balanced combination of substrates, products, and intracellular reactions operating at steady state.

Projects this group has worked on during this period include: developing and analyzing a metabolic model of Escherichia coli; constructing a relational database of an E. coli metabolic network that is employed to map the function of gene products on their corresponding metabolic network; developing an efficient algorithm to compute the elementary modes of genome-scale metabolic networks; and developing and analyzing Saccharomyces cerevisiae and Shewanella oneidensis metabolic models for biofuel production.

Group Members

Christopher M. Flynn, Graduate Student
Alan Gilbert, Graduate Student
Johnathan Gorke, Graduate Student
Greg W. Sitton, Graduate Student
Cong T. Trinh, Graduate Student
Pornkamol (Apple) Unrean, Graduate Student