Date of Award

Spring 5-15-2015

Author's Department

Computer Science & Engineering

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The manipulation of cellular state has many promising applications, including stem cell biology and regenerative medicine, biofuel production, and stress resistant crop development. The construction of interaction maps promises to enhance our ability to engineer cellular behavior. Within the last 15 years, many methods have been developed to infer the structure of the gene regulatory interaction map from gene abundance snapshots provided by high-throughput experimental data. However, relatively little research has focused on using gene regulatory network models for the prediction and manipulation of cellular behavior. This dissertation examines and applies strategies to utilize the predictive power of gene network models to guide experimentation and engineering efforts. First, we developed methods to improve gene network models by integrating interaction evidence sources, in order to utilize the full predictive power of the models. Next, we explored the power of networks models to guide experimental efforts through inference and analysis of a regulatory network in the pathogenic fungus Cryptococcus neoformans. Finally, we develop a novel, network-guided algorithm to select genetic interventions for engineering transcriptional state. We apply this method to select intervention strains for improving biofuel production in a mixed glucose-xylose environment. The contributions in this dissertation provide the first thorough examination, systematic application, and quantitative evaluation of the utilization of network models for guiding cellular engineering.


English (en)


Michael R Brent

Committee Members

Thomas J Baranski, Jeremy D Buhler, Ron K Cytron, Tamara L Doering, Gary D Stormo


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