Rice University
BioSciences at Rice

Matthew Bennett

Associate Professor of BioSciences

My research generally spans the boundary between experimental and theoretical molecular systems biology. I am particularly interested in the dynamics of gene regulation - from small-scale interactions such as transcription and translation, to the large-scale dynamics of gene regulatory networks. I use a hybrid experimental and computational approach to uncover the underlying design principles governing native gene networks and to use these concepts to design novel synthetic circuits. The ultimate goal of synthetic biology is the creation of practical, engineered genetic circuits for medical and industrial applications. Critical to this goal is the elucidation of the fundamental mechanisms that govern gene regulation at all levels. To this end, my work has focused on the kinetic properties of both synthetic networks, such as gene oscillators, and native regulatory networks, such as the galactose utilization pathway in S. cerevisiae.

Currently, my lab uses both bacteria and yeast as model organisms to study genetic signaling networks, which are central to cellular decision-making processes. By detecting and interpreting dynamic cues, these networks enable cells to adapt to their surroundings in a context-dependent manner. We want to know: 1) how information is relayed from one genetic module to the next; 2) how network architecture determines the fidelity of the signal; and 3) how problems arising from network deficiencies or deleterious mutations might be alleviated.

The work in my lab is highly interdisciplinary, combining aspects of synthetic biology, microfluidic engineering, and theoretical physics. Synthetic biology is used to create novel gene circuits as well as perturb naturally occurring gene networks. These networks are then examined at the single-cell level with the aid of microfluidic devices that allow for the precise control over environmental conditions. Finally, mathematical models are used to understand the observed phenomenon and aid in the design of future synthetic gene networks.

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Sadeghpour, Mehdi; Veliz-Cuba, Alan; Orosz, Gábor; Josić, Krešimir; Bennett, Matthew R; Bistability and oscillations in co-repressive synthetic microbial consortia.  Quantitative Biology, 5 2017: 55-66

Winkle, James J; Igoshin, Oleg; Bennett, Matthew R; Josić, Krešimir; Ott, William; Modeling mechanical interactions in growing populations of rod-shaped bacteria.  arXiv preprint arXiv:1702.08091 2017

Dou, Jennifer; Bennett, Matthew R; Synthetic biology and the gut microbiome.  Biotechnology journal 2017

Cheng, Yu-Yu; Hirning, Andrew J; Josić, Krešimir; Bennett, Matthew R; The timing of transcriptional regulation in synthetic gene circuits.  ACS synthetic biology, 6 2017: 1996-2002

Ho, Joanne ML; Mattia, Jacob R; Bennett, Matthew R; Tunable NF-κB Oscillations in Yeast.  Cell systems, 5 2017: 440-442

Sharpee, Tatyana O; Destexhe, Alain; Kawato, Mitsuo; Sekulić, Vladislav; Skinner, Frances K; Wójcik, Daniel K; Chintaluri, Chaitanya; Cserpán, Dorottya; Somogyvári, Zoltán; Kim, Jae Kyoung; 25th Annual Computational Neuroscience Meeting: CNS-2016.  BMC Neuroscience, 17 2016: 54

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). 

Sousa, Filipa L; Parente, Daniel J; Shis, David L; Hessman, Jacob A; Chazelle, Allen; Bennett, Matthew R; Teichmann, Sarah A; Swint-Kruse, Liskin; AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators.  Journal of molecular biology, 428 2016: 671-678

Veliz-Cuba, Alan; Gupta, Chinmaya; Bennett, Matthew R; Josić, Krešimir; Ott, William; Effects of cell cycle noise on excitable gene circuits.  Physical biology, 13 2016: 066007

Gomez, Marcella M; Sadeghpour, Mehdi; Bennett, Matthew R; Orosz, Gábor; Murray, Richard M; Stability of Systems with Stochastic Delays and Applications to Genetic Regulatory Networks.  SIAM Journal on Applied Dynamical Systems, 15 2016: 1844-1873

Gomez, Marcella M; Murray, Richard M; Bennett, Matthew R; The effects of time-varying temperature on delays in genetic networks.  SIAM Journal on Applied Dynamical Systems, 15 2016: 1734-1752

Perez, Anisha M; O'brien, Erin L; Gomez, Marcella M; Bennett, Matthew R; Shamoo, Yousif; A novel in vivo characterization method predicting the physicochemical parameters of an antibiotic efflux pump.  Protein Science, 24 2015: 116-117

Chen Y, Kim JK, Hirning AJ, Josić K & Bennett MR, “Emergent genetic oscillations in a synthetic microbial consortium.” Science 349, 986-989 (2015).

Chen, Ye; Kim, Jae Kyoung; Hirning, Andrew J; Josić, Krešimir; Bennett, Matthew R; Emergent genetic oscillations in a synthetic microbial consortium.  Science, 349 2015: 986-989

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

Veliz-Cuba, Alan; Hirning, Andrew J; Atanas, Adam A; Hussain, Faiza; Vancia, Flavia; Josić, Krešimir; Bennett, Matthew R; Sources of variability in a synthetic gene oscillator.  PLoS computational biology, 11 2015: e1004674

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

Kim, Jae Kyoung; Josić, Krešimir; Bennett, Matthew R; The relationship between stochastic and deterministic quasi-steady state approximations.  BMC systems biology, 9 2015: 87

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

Nguyen-Huu, Truong D; Gupta, Chinmaya; Ma, Bo; Ott, William; Josić, Krešimir; Bennett, Matthew R; Timing and variability of galactose metabolic gene activation depend on the rate of environmental change.  PLoS computational biology, 11 2015: e1004399

Hussain F, Gupta C, Hirning AJ, Ott W, Matthews KS, Josic K, Bennett MR. Engineered temperature compensation in a synthetic genetic clock.  Proc Natl Acad Sci USA, 111(3) 2014: 972-977

Hussain, Faiza; Gupta, Chinmaya; Hirning, Andrew J; Ott, William; Matthews, Kathleen S; Josić, Krešimir; Bennett, Matthew R; Engineered temperature compensation in a synthetic genetic clock.  Proceedings of the National Academy of Sciences, 111 2014: 972-977

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 2014: 204108

Gupta, Chinmaya; López, José Manuel; Azencott, Robert; Bennett, Matthew R; Josić, Krešimir; Ott, William; Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations.  The Journal of chemical physics, 140 2014: 05B624_1

Shis DL, Hussain F, Meinhardt S, Swint-Kruse L & Bennett MR Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras.  ACS Synthetic Biology, 3 2014: 645-651

Shis, David L; Hussain, Faiza; Meinhardt, Sarah; Swint-Kruse, Liskin; Bennett, Matthew R; Modular, multi-input transcriptional logic gating with orthogonal LacI/GalR family chimeras.  ACS synthetic biology, 3 2014: 645-651

Kim JK, Kilpatrick ZP, Bennett MR & Josic K Molecular mechanisms that regulate the coupled period of the mammalian circadian clock.  Biophys J, 106 2014: 2071-2081

Kim, Jae Kyoung; Kilpatrick, Zachary P; Bennett, Matthew R; Josić, Krešimir; Molecular mechanisms that regulate the coupled period of the mammalian circadian clock.  Biophysical journal, 106 2014: 2071-2081

Shis, David L; Bennett, Matthew R; Synthetic biology: the many facets of T7 RNA polymerase.   2014

Shis DL & Bennett MR The many facets of T7 RNA polymerase.  Mol Syst Biol, 10 2014: 745

Kim JK, Josic K & Bennett MR The validity of quasi-steady-state approximations in discrete stochastic simulations.  Biophys J, 107 2014: 783-793

Kim, Jae Kyoung; Josić, Krešimir; Bennett, Matthew R; The validity of quasi-steady-state approximations in discrete stochastic simulations.  Biophysical journal, 107 2014: 783-793

Shis, D. L. & Bennett M. R. A library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants.  Proc Natl Acad Sci USA, 110 2013: 5028-5033

Gomez, Marcella M; Bennett, Matthew R; Murray, Richard M; Analysis of Delays in Transcriptional Signaling Networks with Time-Varying Temperature-Dependent Rate Coefficients.   2013

Masiello, C. A., Gao, X., Chen, Y., Bennett, M. R., Zygourakis, K., Rudgers, J., Liu, S., Wagner, D. & Silberg, J. J. Biochar and microbial signaling: Production conditions determine effects on microbial communication.  Environmental Science and Technology, 47 2013: 11496-11503

Masiello, Caroline A; Chen, Ye; Gao, Xiaodong; Liu, Shirley; Cheng, Hsiao-Ying; Bennett, Matthew R; Rudgers, Jennifer A; Wagner, Daniel S; Zygourakis, Kyriacos; Silberg, Jonathan J; Biochar and microbial signaling: production conditions determine effects on microbial communication.  Environmental science & technology, 47 2013: 11496-11503

Shis, David L; Bennett, Matthew R; Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants.  Proceedings of the National Academy of Sciences, 110 2013: 5028-5033

Razinkov, I. A., Baumgartner, B. L., Bennett, M. R., Tsimring, L. S., & Hasty, J. Measuring competitive fitness in dynamic environments.  Journal of Physical Chemistry B, 117 2013: 13175-13181

Razinkov, Ivan A; Baumgartner, Bridget L; Bennett, Matthew R; Tsimring, Lev S; Hasty, Jeff; Measuring competitive fitness in dynamic environments.  The Journal of Physical Chemistry B, 117 2013: 13175-13181

Gupta, C., Lopez, J. M., Ott, W., Josic, K. & Bennett, M. R. Transcriptional delay stabilizes bistable gene networks.  Physical Review Letters, 111 2013: 058104

Gupta, Chinmaya; López, José Manuel; Ott, William; Josíc, Krešimir; Bennett, Matthew R; Transcriptional delay stabilizes bistable gene networks.  Physical Review Letters, 111 2013: 058104

Nevozhay, D., Adams, R. M., Van Itallie, E., Bennett, M. R. & Balázsi, G. Mapping the environmental fitness landscape of a synthetic gene circuit.  PLoS Comp Biol, 8 2012: e1002480

Nevozhay, Dmitry; Adams, Rhys M; Van Itallie, Elizabeth; Bennett, Matthew R; Balázsi, Gábor; Mapping the environmental fitness landscape of a synthetic gene circuit.  PLoS computational biology, 8 2012: e1002480

O’Brien, E. L., Van Itallie, E., Bennett, M. R. Modeling synthetic gene oscillators.  Math Biosci, 236 2012: 1-15

O’Brien, Erin L; Van Itallie, Elizabeth; Bennett, Matthew R; Modeling synthetic gene oscillators.  Mathematical biosciences, 236 2012: 1-15

Schmidt, C.M., Shis, D. L., Nguyen-Huu, T. D. & Bennett, M. R. Stable maintenance of multiple plasmids in E. coli using a single selective marker.  ACS Synthetic Biology, 1 2012: 445-450

Schmidt, Calvin M; Shis, David L; Nguyen-Huu, Truong D; Bennett, Matthew R; Stable maintenance of multiple plasmids in E. coli using a single selective marker.  ACS Synthetic Biology 2012

Baumgartner, B. L., Bennett, M. R., Ferry, M., Johnson, T., Tsimring, L. S. & Hasty, J. Antagonistic gene transcripts regulate adaptation to new growth environments.  Proc. Natl. Acad. Sci. USA, 108 2011: 21087-21092

Baumgartner, Bridget L; Bennett, Matthew R; Ferry, Michael; Johnson, Tracy L; Tsimring, Lev S; Hasty, Jeff; Antagonistic gene transcripts regulate adaptation to new growth environments.  Proceedings of the National Academy of Sciences, 108 2011: 21087-21092

Nevozhay, Dmitry; Adams, Rhys M; Balázsi, Gábor; Population-level control of gene expression.  Bulletin of the American Physical Society, 56 2011

Josić, K., Lopez, J. M., Ott, W. R., Shiau, L. & Bennett, M. R. Stochastic delay accelerates signaling in gene networks.  PLoS Comp. Biol., 7 2011: e1002264

Josić, Krešimir; López, José Manuel; Ott, William; Shiau, LieJune; Bennett, Matthew R; Stochastic delay accelerates signaling in gene networks.  PLoS computational biology, 7 2011: e1002264

Adams, Rhys; Nevozhay, Dmitry; Van Itallie, Elizabeth; Bennett, Matthew; Balazsi, Gabor; The effects of nongenetic memory on population level sensitivity to stress.  APS Meeting Abstracts 2011

Pena, M., Van Itallie, E., Bennett, M.R., & Shamoo, Y. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness.  CHAOS, 20 2010: 026107

Peña, Matthew I; Van Itallie, Elizabeth; Bennett, Matthew R; Shamoo, Yousif; Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness.  Chaos: An Interdisciplinary Journal of Nonlinear Science, 20 2010: 026107

Pena, M., Davlieva, M., Bennett, M.R., Olson, J., and Shamoo, Y. Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection.  Mol Syst Biol, 6 2010: 387

Peña, Matthew I; Davlieva, Milya; Bennett, Matthew R; Olson, John S; Shamoo, Yousif; Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection.  Molecular systems biology, 6 2010: 387

Mather, W., Bennett, M.R., Hasty, J., and Tsimring, L.S. Delay-induced degrade-and-fire oscillations in small genetic circuits.  Phys Rev Lett, 102 2009: 068105

Mather, William; Bennett, Matthew R; Hasty, Jeff; Tsimring, Lev S; Delay-induced degrade-and-fire oscillations in small genetic circuits.  Physical review letters, 102 2009: 068105

Bennett, M.R. and Hasty, J. Microfluidic devices for measuring gene network dynamics in single cells.  Nature Reviews Genetics, 10 2009: 628-638

Bennett, Matthew R; Hasty, Jeff; Microfluidic devices for measuring gene network dynamics in single cells.  Nature Reviews Genetics, 10 2009: 628-638

Bennett, M.R. and Hasty, J. Overpowering the component problem.  Nat Biotech, 27 2009: 450-451

Bennett, Matthew R; Hasty, Jeff; Overpowering the component problem.  Nature biotechnology, 27 2009: 450-451

Stricker, J., Cookson, S., Bennett, M.R., Mather, W.H., Tsimring, L.S., and Hasty, J. A fast, robust and tunable synthetic gene oscillator.  Nature, 456 2008: 516-519

Stricker, Jesse; Cookson, Scott; Bennett, Matthew R; Mather, William H; Tsimring, Lev S; Hasty, Jeff; A fast, robust and tunable synthetic gene oscillator.  Nature, 456 2008: 516-519

Bennett, M.R. and Hasty, J. Genome rewired.  Nature, 452 2008: 824-825

Bennett, M.R., Pang, W.L., Ostroff, N.A., Baumgartner, B.L., Nayak, S., Tsimring L.S., and Hasty, J. Metabolic gene regulation in a dynamically changing environment.  Nature, 454 2008: 1119-1122

Bennett, Matthew R; Pang, Wyming Lee; Ostroff, Natalie A; Baumgartner, Bridget L; Nayak, Sujata; Tsimring, Lev S; Hasty, Jeff; Metabolic gene regulation in a dynamically changing environment.  Nature, 454 2008: 1119-1122

Handel, A. and Bennett, M.R. Surviving the bottleneck: Transmission mutants and the evolution of microbial populations.  Genetics, 180 2008: 2193-2200

Handel, Andreas; Bennett, Matthew R; Surviving the bottleneck: transmission mutants and the evolution of microbial populations.  Genetics, 180 2008: 2193-2200

Bennett, Matthew R; Hasty, Jeff; Systems biology: genome rewired.  Nature, 452 2008: 824-825

Bennett, M.R. and Hasty, J. A DNA methylation-based switch generates bistable gene expression.  Nat Genet, 39 2007: 146-147

Bennett, Matthew R; Hasty, Jeff; A DNA methylation–based switch generates bistable gene expression.  Nature genetics, 39 2007: 146-147

Grilly, C., Stricker, J., Pang, W.L., Bennett, M.R., and Hasty, J. A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae.  Mol Sys Bio, 3 2007: 127

Grilly, Chris; Stricker, Jesse; Pang, Wyming Lee; Bennett, Matthew R; Hasty, Jeff; A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae.  Molecular systems biology, 3 2007: 127

Lu, T., Shen, T., Bennett, M.R., Wolynes, P.G., and Hasty, J. Phenotypic variability of growing cellular populations.  Proc Natl Acad Sci USA, 104 2007: 18982-18987

Lu, Ting; Shen, Tongye; Bennett, Matthew R; Wolynes, Peter G; Hasty, Jeff; Phenotypic variability of growing cellular populations.  Proceedings of the National Academy of Sciences, 104 2007: 18982-18987

Bennett, M.R., Volfson, D., Tsimring, L., and Hasty, J. Transient dynamics of genetic regulatory networks.  Biophys J, 92 2007: 3501-3512

Bennett, Matthew R; Volfson, Dmitri; Tsimring, Lev; Hasty, Jeff; Transient dynamics of genetic regulatory networks.  Biophysical journal, 92 2007: 3501-3512

Lindner, J.F., Bennett, M., and Wiesenfeld, K. Potential energy landscape and finite-state models of array-enhanced stochastic resonance.  Phys Rev E, 73 2006: 031107

Lindner, John F; Bennett, Matthew; Wiesenfeld, Kurt; Potential energy landscape and finite-state models of array-enhanced stochastic resonance.  Physical Review E, 73 2006: 031107

Bennett, Matthew Raymond; Synchronization and Signal Enhancement in Nonlinear and Stochastic Systems.   2006

Bennett, M.R. and Wiesenfeld, K. Towards a unified rate theory of stochastic resonance.  Fluct Noise Lett, 6 2006: L405-L413

Bennett, Matthew R; Wiesenfeld, Kurt; Towards a unified rate theory of stochastic resonance.  Fluctuation and Noise Letters, 6 2006: L405-L413

Lindner, J.F., Bennett, M., and Wiesenfeld, K. Stochastic resonance in the mechanoelectrical transduction of hair cells.  Phys Rev E, 72 2005: 051911

Lindner, John F; Bennett, Matthew; Wiesenfeld, Kurt; Stochastic resonance in the mechanoelectrical transduction of hair cells.  Physical Review E, 72 2005: 051911

Bennett, M. and Wiesenfeld, K. Averaged equations for distributed Josephson junction arrays.  Physica D, 192 2004: 196-214

Bennett, Matthew; Wiesenfeld, Kurt; Averaged equations for distributed Josephson junction arrays.  Physica D: Nonlinear Phenomena, 192 2004: 196-214

BENNETT, MATTHEW; WIESENFELD, KURT; JARAMILLO, FERNAN; Stochastic resonance in hair cell mechanoelectrical transduction.  Fluctuation and Noise Letters, 4 2004: L1-L10

Bennett, M., Wiesenfeld, K., and Jaramillo, F. Stochastic resonance in hair cells.  Fluct Noise Lett, 4 2004: L1-L10

Bennett, M., Schatz, M.F., Rockwood, H., and Wiesenfeld, K. Huygens' clocks.  Proc Roy Soc London A, 458 2002: 563-579

Bennett, Matthew; Schatz, Michael F; Rockwood, Heidi; Wiesenfeld, Kurt; Huygens's clocks.  Proceedings: Mathematics, Physical and Engineering Sciences 2002: 563-579

The Bennett Lab Website

  • B.S. Physics (2000) Georgia Institute of Technology
  • Ph.D. Physics (2006) Georgia Institute of Technology
  • Department of Bioengineering
  • Institute of Biosciences and Bioengineering
  • Systems, Synthetic, and Physical Biology
Research Areas
  • Synthetic Biology, Cellular Signaling, Computational Biology, Microfluidic Engineering
Contact Information
Email: matthew.bennett@rice.edu
Phone: 713-348-4161
Office: Keck Hall, 306