Student Author(s)

Carl Deeg
Shinnosuke Kondo

Faculty Mentor(s)

Dr. Matthew DeJongh

Document Type


Event Date



A metabolic model is a map of the biochemical reactions that take place in an organism. These reactions are catalyzed by enzymes, which are encoded by genes in the organism’s genome. However, there are reactions that are known to exist and needed to complete the metabolic model, but are not associated with any genes. These are called “gap reactions”. Our goal is to find the genes that encode the enzymes that catalyze these gap reactions. We have researched two approaches: a knowledge-driven approach that focuses on finding a small set of good candidates, and a data-driven approach that focuses on scoring all candidates to rank their plausibility. Identifying the genes that are associated with gap reactions produces better predictive models and directs laboratory experimentation.


This research was supported by the National Science Foundation under Award Number DBI-0850546, and by the Department of Energy, subcontract to Argonne National Laboratory.