2024
de Freitas Magalhães, Bárbara, Gaoyang Fan, Eduardo Sontag, Krešimir Josić, and Matthew R. Bennett. "Pattern formation and bistability in a synthetic intercellular genetic toggle." ACS Synthetic Biology (2024).
Zinke, Aasha, Neethu Pottackal, Farhan Zahin, Mohammed Intishar Nur, Faravi Ahmed, Yue Ji, Zaheeruddin Mohammed et al. "Preserving Fresh Eggs via Egg‐Derived Bionanocomposite Coating." Advanced Functional Materials(2024): 2310091.
2023
Zong, David M., Mehdi Sadeghpour, Sara Molinari, Razan N. Alnahhas, Andrew J. Hirning, Charilaos Giannitsis, William Ott, Krešimir Josić, and Matthew R. Bennett. "Tunable Dynamics in a Multistrain Transcriptional Pulse Generator." ACS Synthetic Biology 12, no. 12 (2023): 3531-3543.
Liu, Baiyang, Christian Cuba Samaniego, Matthew R. Bennett, Elisa Franco, and James Chappell. "A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria." Nature Communications 14, no. 1 (2023): 5268.
Winkle, James J., Soutick Saha, Joseph Essman, Matthew R. Bennett, William Ott, Krešimir Josić, and Andrew Mugler. "Signaling in microbial communities with open boundaries." Biophysical Journal 122, no. 13 (2023): 2808-2817.
Ganiga Prabhakar, Ramya, Gaoyang Fan, Razan N. Alnahhas, Andrew J. Hirning, Matthew R. Bennett, and Yousif Shamoo. "Indirect enrichment of desirable, but less fit phenotypes, from a synthetic microbial community using microdroplet confinement." ACS Synthetic Biology 12, no. 4 (2023): 1239-1251.
2022
Liu, Baiyang, Christian Cuba Samaniego, Matthew Bennett, James Chappell, and Elisa Franco. "RNA compensation: a positive feedback insulation strategy for RNA-based transcription networks." PACS Synthetic Biology 11, no. 3 (2022): 1240-1250.
Picard HR, Schwingen KS, Green LM, Shis DL, Egan SM, Bennett MR & Swint-Kruse L, “Allosteric regulation within the highly interconnected structural scaffold of AraC/XylS homologs tolerates a wide range of amino acid changes,” PROTEINS 90, 186-199 (2022).
Miller CA, Ho JML & Bennett MR, “Strategies for improving small-molecule biosensors in bacteria,” Biosensors 12, 64 (2022).
Sarmadi, Sorena, James J. Winkle, Razan N. Alnahhas, Matthew R. Bennett, Krešimir Josić, Andreas Mang, and Robert Azencott. "Stochastic neural networks for automatic cell tracking in microscopy image sequences of bacterial colonies." Mathematical and Computational Applications 27, no. 2 (2022): 22.
2021
Miller CA, Ho JML, Parks S & Bennett MR, “Macrolide biosensor optimization through cellular substrate sequestration.”ACS Synth Biol 10, 258-264 (2021).
Ho JML, Miller CA, Mattia JR & Bennett MR, “Improved pyrrolysine biosynthesis through continuous directed evolution of the complete pathway.” Nat Comm 12, 3914 (2021).
Grandel NE, Reyes Gamas K & Bennett MR, “Control of synthetic microbial consortia in time, space, and composition,” Trends in Microbiology 29, 1095-1105 (2021).
Winkle JJ, Karamched BR, Bennett MR, Ott W & Josić K, “Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia,” PLOS Comp Biol 9, e1009381 (2021).
2020
Choi B, Cheng Y-Y, Cinar S, Ott W, Bennett MR, Josić K & Kim JK, “Bayesian inference of distributed time delay in transcriptional and translational regulation.” Bioinformatics 36, 586-593 (2020).[PDF]
Jung S et al. “Sustainable bio-nanocomposite coatings for perishable fruit“ Advanced Materials 12, 1908291 (2020).[PDF]
Alnahhas RN, Sadeghpour M, Chen Y, Frey A, Ott W, Josić J & Bennett MR, “Majority sensing in synthetic microbial consortia.”Nature Comm 11, 3659 (2020).[PDF]
Ho JML, Miller CA, Parks S, Mattia J & Bennett MR, “A suppressor tRNA-mediated feedforward loop eliminates leaky gene expression in bacteria.” Nucl Acids Res (2020) [PDF]
2019
Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Jośic K & Bennett MR, “Spatiotemporal dynamics of synthetic microbial consortia in microfluidic devices.” ACS Synth Biol 8, 2051-2058 (2019).[PDF]
Kim JK, Chen Y, Hirning AJ, Josić K & Bennett MR, “Temporal coordination of gene expression in spatially extended synthetic microbial consortia.” Nat Chem Biol 15, 1102-1109 (2019).[PDF]
Molinari M, Shis DL, Chappell J, Igoshin OA & Bennett MR, “A synthetic system for asymmetric cell division in Escherichia coli.” Nat Chem Biol 15, 917-924 (2019).[PDF]
Miller C, Ho JML & Bennett MR, “Bacterial killers engineered to exterminate pathogenic microbes.” Molec Cell 75, 5-6 (2019).
[PDF]
Karamched BR, Ott W, Timofeyev I, Alnahhas RN, Bennett MR & Josić K, “Moran model of spatial alignment in microbial colonies.” Physica D 7, 1834-1843 (2019).[PDF]
2018
Zong DM, Cinar S, Shis DL, Josić K, Ott W & Bennett MR, “Predicting transcriptional output of synthetic multi-input promoters.” ACS Synth Biol 7, 1834-1843 (2018).[PDF]
Dou J & Bennett MR, “Synthetic biology and the gut microbiome.” Biotech J 13, 1700158 (2018).[PDF]
Shis DL, Bennett MR & Igoshin OA, “Dynamics of bacterial gene regulatory networks.” Annu Rev Biophys 47, 21.1-21.21 (2018).[PDF]
Ho JML & Bennett MR, “Improved memory devices for synthetic cells.” Science 350, 150-151 (2018).[PDF]
Chen Y, Ho JML, Shis DL, 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.” Nature Comm 9, 64 (2018).[PDF]
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 superfamily effluxer.” Mol Syst Biol 13, 964 (2017).[PDF]
Ho JML, Mattia JR & Bennett MR, “Tunable NF-kappaB oscillations in yeast.” Cell Systems 5, 440-442 (2017).[PDF]
Cheng YY, Hirning AJ, Josić K & Bennett MR, “Signaling times in synthetic transcriptional cascades.” ACS Synth Biol 6, 1996-2002 (2017).[PDF]
Winkle JJ, Igoshin O, Bennett MR, Josić K & Ott W, “Modeling mechanical interactions in growing populations of rod-shaped bacteria.” Phys Biol 14, 055001 (2017).[PDF]
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]