Abstract
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.
Committee Chair
Michael R Brent
Committee Members
Thomas J Baranski, Jeremy D Buhler, Ron K Cytron, Tamara L Doering, Gary D Stormo
Degree
Doctor of Philosophy (PhD)
Author's Department
Computer Science & Engineering
Document Type
Dissertation
Date of Award
Spring 5-15-2015
Language
English (en)
DOI
https://doi.org/10.7936/K79C6VK2
Recommended Citation
Maier, Ezekiel John, "Strategies for increasing the applicability of biological network inference" (2015). McKelvey School of Engineering Theses & Dissertations. 92.
The definitive version is available at https://doi.org/10.7936/K79C6VK2
Comments
Permanent URL: https://doi.org/10.7936/K79C6VK2