Publications

2017
Cheng YY, Hirning AJ, Josić K & Bennett MR, “Signaling times in synthetic transcriptional cascades.” Submitted (2017).

Perez AM, Gomez MM, Kalvapalle P, O’Brien-Gilbert E, Bennett MR & Shamoo Y, “Using cellular fitness to map the structure and function of a major facilitator superfaminly effluxer.” Submitted (2017).

Winkle JJ, Igoshin O, Bennett MR, Josić K & Ott W, “Modeling mechanical interactions in growing populations of rod-shaped bacteria.” Submitted (2017).

Chen Y, Gupta C, Long J, Wagner D, Ott W, Josić K & Bennett MR, “Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors.” Submitted (2017).

Bennett MR, “The logic of synthetic biology: turning cells into computers.” Angle Journal (2017).[Article]

Sadeghpour M, Veliz-Cuba A, Orosz G, Josić K & Bennett MR, “Bistability and oscillations in co-repressive microbial consortia.” Quant Biol 5, 55-66 (2017). [PDF]

2016
Gomez MM, Sadeghpour M, Bennett MR, Orosz G & Murray RM, “Stability of systems with stochastic delays and applications to genetic regulatory networks.” SIAM J Appl Dyn Syst 15, 1844-1873 (2016). [PDF]

Veliz-Cuba A, Gupta C, Bennett MR, Josić K & Ott W, “Effects of cell cycle noise on excitable gene circuits.” Phys Biol 13, 066007 (2016). [PDF]

Gomez MM, Murray RM & Bennett MR, “The effects of time-varying temperature on delayed gene networks.” SIAM J Appl Dyn Syst 15, 1734-1752 (2016). [PDF]

Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A, Bennett MR, Teichmann AS & Swint-Kruse L, “AlloRep: a repository of sequence and mutagenesis data for LacI/GalR transcription regulators.” J Mol Biol 428, 671-678 (2016). [PDF]

2015
Veliz-Cuba A, Hirning AJ, Atanas AA, Hussain F, Vancia F, Josic K & Bennett MR, “Sources of noise in a synthetic gene oscillator.” PLoS Comp Biol 11, e1004674 (2015). [PDF]

Kim JK, Josic K & Bennett MR, “The relationship between stochastic and deterministic quasi-steady state approximations.” BMC Syst Biol 9, 87 (2015). [PDF]

Chen Y, Kim JK, Hirning AJ, Josic K & Bennett MR, "Emergent genetic oscillations in a synthetic microbial consortium," Science 349, 986-989 (2015). [PDF]
See also Perspective.

Nguyen-Huu TD, Gupta C, Ma B, Ott W, Josic K & Bennett MR, “Timing and variability of galactose metabolic gene activation depend on the rate of environmental change.” PLoS Comp. Biol. 10, e1004399 (2015). [PDF]

2014
Shis DL, Hussain F, Meinhardt S, Swint-Kruse L & Bennett MR, “Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras,” ACS Synth. Biol. 3, 645-651 (2014). [PDF]

Kim JK, Josic K & Bennett MR, “The validity of quasi-steady-state approximations in discrete stochastic simulations,” Biophys. J. 107, 783-793 (2014). [PDF]

Shis DL & Bennett MR, “The many facets of T7 RNA polymerase,” Mol. Syst. Biol. 10, 745 (2014). [PDF]

Gupta C, Lopez JM, Azencott R, Bennett MR, Josic K & Ott, W, "Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations." J. Chem. Phys. 140, 204108 (2014). [PDF]

Kim JK, Kilpatrick ZP, Bennett MR & Josic K, "Molecular mechanisms that regulate the coupled period of the mammalian circadian clock." Biophys. J. 106, 2071-2081 (2014). [PDF]
See also New and Notable.

Hussain F, Gupta C, Hirning AJ, Ott WR, Matthews KS, Josic K & Bennett MR, “Engineered temperature compensation in a synthetic genetic clock.” Proc. Natl. Acad. Sci. USA 111, 972-977 (2014). [PDF]

2013
Masiello CA, Chen Y, Gao X, Liu S, Cheng HY, Bennett MR, Rudgers JA, Wagner DS, Zygourakis K & Silberg JJ, “Biochar and microbial signaling: Production conditions determine effects on microbial communication.” Environ. Sci. Technol. 47, 11496-11503 (2013). [PDF]

Razinkov IA, Baumgartner BL, Bennett MR, Tsimring LS & Hasty J, “Measuring competitive fitness in dynamic environments.” J. Phys. Chem. 117, 13175-13181 (2013). [PDF]

Gupta C, Lopez JM, Ott WR, Josic K & Bennett MR, “Transcriptional delay stabilizes bistable gene networks.” Phys. Rev. Lett. 111, 058104 (2013). [PDF]

Shis DL & Bennett MR, “A library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants.” Proc. Natl. Acad. Sci. USA 110, 5028-5033 (2013). [PDF]

2012
Schmidt CM, Shis DL, Nguyen-Huu TD & Bennett MR, “Stable maintenance of multiple plasmids in E. coli using a single selective marker.” ACS Synth. Biol. 1, 445-450 (2012). [PDF]

Nevozhay D, Adams RM, Van Itallie E, Bennett MR & Balázsi G, “Mapping the environmental fitness landscape of a synthetic gene circuit,” PLoS Comp. Biol. 8, e1002480 (2012). [PDF]

O’Brien EL, Van Itallie E & Bennett MR, “Modeling synthetic gene oscillators,” Math. Biosci. 236, 1-15 (2012). [PDF]

2011
Baumgartner BL, Bennett MR, Ferry M, Johnson T, Tsimring LS & Hasty J, “Antagonistic gene transcripts regulate adaptation to new growth environments,” Proc. Natl. Acad. Sci. USA 108, 21087-21092 (2011). [PDF]

Josic K, López JM, Ott W, Shiau L & Bennett MR, “Stochastic delay accelerates signaling in gene networks,” PLoS Comp. Biol. 7, e1002264 (2011). [PDF]

2010
Pena MI, Davlieva M, Bennett MR, Olson JS & Shamoo Y, “Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection,” Mol. Syst. Biol. 6, 387 (2010). [PDF]

Pena MI, Van Itallie E, Bennett MR & Shamoo Y, “Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness,” CHAOS 20, 026107 (2010). [PDF]

2009
Bennett MR & Hasty J, “Microfluidic devices for measuring gene network dynamics in single cells,” Nat. Rev. Gen. 10, 628-638 (2009). [PDF]

Bennett MR & Hasty J, “Overpowering the component problem,” Nat. Biotech. 27, 450-451 (2009). [PDF]

Mather W, Bennett MR, Hasty J & Tsimring LS, “Delay-induced degrade-and-fire oscillations in small genetic circuits,” Phys. Rev. Lett. 102, 068105 (2009). [PDF]

2008
Handel A & Bennett MR, “Surviving the bottleneck: Transmission mutants and the evolution of microbial populations,” Genetics 180, 2193-2200 (2008). [PDF]

Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS & Hasty J, “A fast, robust and tunable synthetic gene oscillator,” Nature 456, 516-519 (2008). [PDF]

Bennett MR, Pang WL, Ostroff NA, Baumgartner BL, Nayak S, Tsimring LS & Hasty J, “Metabolic gene regulation in a dynamically changing environment,” Nature 454, 1119-1122 (2008). [PDF]

Bennett MR & Hasty J, “Genome rewired,” Nature 452, 824-825 (2008). [PDF]

2007
Lu T, Shen T, Bennett MR, Wolynes PG & Hasty J, “Phenotypic variability of growing cellular populations,” Proc. Natl. Acad. Sci. USA 104, 18982-18987 (2007). [PDF]

Grilly C, Stricker J, Pang WL, Bennett MR & Hasty J, “A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae,” Mol. Syst. Biol. 3, 127 (2007). [PDF]

Bennett MR, Volfson D, Tsimring L & Hasty J, “Transient dynamics of genetic regulatory networks,” Biophys. J. 92, 3501-3512 (2007). [PDF]

Bennett MR and Hasty J, “A DNA methylation-based switch generates bistable gene expression,” Nat. Gen. 39, 146-147 (2007). [PDF]

2006
Bennett MR & Wiesenfeld K, “Towards a unified rate theory of stochastic resonance,” Fluct. Noise Lett. 6, L405-L413 (2006). [PDF]

Bennett MR, “Synchronization and Signal Enhancement in Nonlinear and Stochastic Systems,” Ph.D. Dissertation, Georgia Tech (2006). [PDF]

Lindner JF, Bennett M & Wiesenfeld K, “Potential energy landscape and finite-state models of array-enhanced stochastic resonance,” Phys. Rev. E 73, 031107 (2006). [PDF]

2005
Lindner JF, Bennett M & Wiesenfeld K, “Stochastic resonance in the mechanoelectrical transduction of hair cells,” Phys. Rev. E 72, 051911 (2005). [PDF]

2004
Bennett M, Wiesenfeld K & Jaramillo F, “Stochastic resonance in hair cells,” Fluct. Noise Lett. 4, L1-L10 (2004). [PDF]

Bennett M & Wiesenfeld K, “Averaged equations for distributed Josephson junction arrays,” Physica D 192, 196-214 (2004). [PDF]

2002
Bennett M, Schatz MF, Rockwood H & Wiesenfeld K, “Huygens’ clocks,” Proc. Roy. Soc. London A 458, 563-579 (2002). [PDF]