Date of Award

Spring 5-15-2015

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Cell Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The control of cellular state has many promising applications, including stem cell biology and

regenerative medicine, biofuel production, and gene therapy. This dissertation demonstrates a

comprehensive approach to cellular state control at the transcriptional level. We introduce a

novel algorithm, NetSurgeon, which utilizes genome-wide gene regulatory networks to identify

interventions that will force a cell toward a desired expression state. Following extensive in

silico validation, we applied NetSurgeon to S. cerevisiae biofuel production, generating

interventions designed to promote a fermentative state during xylose catabolism. Our selected

interventions successfully promoted a fermentative transcriptional state and generated strains

with higher xylose import rates, improved xylose integration and increased ethanol production

rates. We then step down to a single gene level and exhibit a cis-engineering strategy that

enables precise expression control. We demonstrate that synthetic promoters can be functionally

decomposed into individual components that can be characterized in isolation and used to train a

composite model capable of predicting the action of the full system. These findings represent

significant progress towards the insertion of orthogonal control circuits into the cell for the

control of gene expression. Taken together, this dissertation represents an integrative process of

quantitative measurement, modeling, and intervention that comprehensively examines methods

for cellular state control at the genome-wide and gene levels.


English (en)

Chair and Committee

Michael R Brent

Committee Members

Thomas Baranski, Barak Cohen, Gautam Dantas, James Havranek, Joseph Jez


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