Dunlop Lab

Journal Papers

J. Garcia-Bernardo, M. J. Dunlop. "Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops." PLoS Computational Biology, 9(9), 2013.
(PDF) (Supplementary)

M. E. Harrison, M. J. Dunlop. "Synthetic Feedback Loop Model for Increasing Microbial Biofuel Production Using a Biosensor." Frontiers in Microbiology 3:360, 2012.
(PDF)

R. S. Koh, M. J. Dunlop. "Modeling Suggests that Gene Circuit Architecture Controls Phenotypic Variability in a Bacterial Persistence Network." BMC Systems Biology 6:47, 2012.
(PDF)

M. J. Dunlop. "Engineering Microbes for Tolerance to Next-Generation Biofuels." Biotechnology for Biofuels 4:32, 2011.
(PDF)

M. J. Dunlop, Z. Y. Dossani, H. L. Szmidt, H. C. Chu, T. S. Lee, J. D. Keasling, M. Hadi, A. Mukhopadhyay. "Engineering Microbial Biofuel Tolerance and Export Using Efflux Pumps." Molecular Systems Biology 7:487, 2011.
(PDF) (Supplementary)
 
M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay. "A Model for Improving Microbial Biofuel Production Using a Synthetic Feedback Loop." Systems and Synthetic Biology DOI 10.1007/s11693-010-9052-5, 2010.
(PDF)
 
R. S. Cox, M. J. Dunlop, M. B. Elowitz. "A Synthetic Three-Color Reporter Framework for Monitoring Genetic Regulation and Noise." Journal of Biological Engineering 4:10, 2010.
(PDF)
 
M. J. Dunlop, R. S. Cox, J. H. Levine, R. M. Murray, M. B. Elowitz. "Regulation Revealed by Dynamic Correlations In Gene Expression Noise." Nature Genetics 40:1493-1498, 2008.
(PDF) (Supplementary) (Movie1) (Movie2)
 
M. E. Wall, M. J. Dunlop, W. S. Hlavacek. "Multiple Functions of a Feed-Forward Loop Gene Circuit." Journal of Molecular Biology 349:501-514, 2005.
(PDF)

Ph.D. Thesis

M. J. Dunlop. "Dynamics and Correlated Noise in Gene Regulation." California Institute of Technology, 2008. (PDF)

Patents

M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay. "Identification of Efflux Pumps to Improve Tolerance to Toxic or Inhibitory Biofuel, Biochemical Metabolites, or Compounds from Deconstructed Ligno-cellulosic Biomass." Provisional patent filed May 25, 2010.

Conference Papers

M. J. Dunlop, E. Franco, R. M. Murray. "A Multi-Model Approach to Identification of Biosynthetic Pathways." In Proceedings of the 26th American Control Conference 2007.
(PDF)
 
J. Ugander, M. J. Dunlop, R. M. Murray. "Analysis of a Digital Clock for Molecular Computing." In Proceedings of the 26th American Control Conference 2007.
(PDF)
 
M. J. Dunlop, M. E. Wall. "Robustness in Gene Circuits: Clustering of Functional Responses." In Proceedings of the 24th American Control Conference 2005.
(PDF)
 
M. B. Reiser, J. S. Humbert, M. J. Dunlop, D. Del Vecchio, R. M. Murray, M. H. Dickinson. "Vision as a Compensatory Mechanism for Disturbance Rejection in Upwind Flight." In Proceedings of the 23rd American Control Conference 2004.
(PDF)
 
T. Colonius, M. J. Dunlop, R. Reba, S. Narayanan. "A Study of the Role of Organized Structures in Jet Noise Generation." AIAA Paper 2003-3314, 2003.
(PDF)