Hori group's research interests lie in feedback control theory, mathematical optimization and their applications to synthetic biology. We develop theoretical and experimental platforms including model identification methods, design and analysis theory, and mathematical optimization for the rational design of synthetic biocircuits. We also build microfluidic devices that synergistically work together with computational modeling tools to streamline the design process of synthetic biomolecular circuits.

Control theory and mathematical optimization for synthetic molecular feedback systems

Our research work ranges from fundamental mathematical theory of biomolecular feedback control to computational tools for the design of synthetic biomolecular systems.

Selected publications
  • Parameter/System identification
    1. Y. Hori and R. M. Murray, "A State-space Realization Approach to Set Identification of Biochemical Kinetic Parameters," Proceedings of European Control Conference, pp. 2280--2285, 2015. (doi:10.1109/CDC.2015.7402292)
    2. Y. Hori, M. H. Khammash and S. Hara, "Efficient Parameter Identification for Stochastic Biochemical Networks Using a Reduced-order Realization," Proceedings of European Control Conference, pp.4154--4159, 2013. (IEEE Xplore)
  • Analysis and Design of stochastic/deterministic biomolecular systems
    1. Y. Sakurai and Y. Hori, "Optimization-based synthesis of stochastic biocircuits with statistical specifications," Journal of the Royal Society Interface, vol. 15, No. 138, 20170709, 2018 (doi:10.1098/rsif.2017.0709, bioRxiv)
    2. Y. Hori and H. Miyazako, "Analysing diffusion and flow-driven instability using semidefinite programming," Journal of the Royal Society Interface, 20180586, 2019. doi:10.1098/rsif.2018.0586
    3. Y. Hori, M. Takada and S. Hara, "Biochemical oscillations in delayed negative cyclic feedback: Existence and profiles," Automatica, vol 49, No. 9, pp. 2581--2590, 2013. (doi:10.1016/j.automatica.2013.04.020)
    4. Y. Hori, T.-H. Kim and S. Hara, ``Existence Criteria of Periodic Oscillations in Cyclic Gene Regulatory Networks,'' Automatica, vol. 47, No. 6 (special issue on Systems Biology), pp. 1203-1209, 2011. (doi:10.1016/j.automatica.2011.02.042)
    5. Y. Hori, H. Miyazako, S. Kumagai and S. Hara, "Coordinated Spatial Pattern Formation in Biomolecular Communication Networks," IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, vol. 1, No. 2, pp.111--121, 2015 (invited paper). (doi:10.1109/TMBMC.2015.2500567; preprint)
Microfluidic devices for optimization and control of synthetic biocircuits

The design-build-test cycles of synthetic biocircuits involve time-consuming iterations of sample preparation, verification and cloning. To accelerate this process, we develop experimental platforms that specifically fullfill the need for model identification and control of shynthetic biocircuits. We use cell-free protein expression systems with microfludics to enable high-throughput characterization of the input/output response of synthetic biocircuits in well-controlled in vitro environements. We are also developing a microfluidic platform combined with model based controllers to enable real-time feedback control of biocircuits.

  1. Y. Hori, C. Kantak, R. M. Murray and A. R. Abate "Cell-free Extract based Optimization of Biomolecular Circuits with Droplet Microfluidics," Lab on a Chip, vol. 17, pp. 3037-3042, 2017 (doi:10.1039/C7LC00552K) [Selected for the front cover]
  2. A. Wakamei and Y. Hori, "A microfluidic actuator for dynamic control of chemical reactions," Proceedings of SICE Annual Conference, pp.1767--1769, 2018.