Hori group's research interests are in feedback control theory, optimization and their application to synthetic biology. Our research works are particularly focused on streamlining the process of biocircuit synthesis from systems and control engineering perspectives. For this purpose, we combine tools in feedback control theory and mathematical optimization to develop system theoretic model identification, analysis and design methodologies. Our research also includes development of system-oriented experimental platforms such as combined computational and microfluidic devices that can supplement model prediction with theoretically meaningful data.

Keywords: feedback control, synthetic biology, DNA circuits, optimization, microfluidics

Yutaka Hori will be on sabbatical leave at the University of Oxford from April 2025 to March 2026.

News

• Dec. 11th, 2025: Akito Igarashi will present "Parameter Invariance Analysis of Moment Equations Using Dulmage-Mendelsohn Decomposition" (A. Igarashi, Y. Hori; ThA15.8) at IEEE Conference on Decision and Control (Rio de Janerioro, Brazil) (paper).
• Sep. 9th, 2025: Manao Ito will present "Patterned Polyacrylamide Gel as a Testbed for Molecular Communication" (M. Ito, Y. Hori) at International Workshop on Biodesign Automation (IWBDA) (Boston, MA, USA)．
• July 10th, 2025: Ryoma Yasunaga will present "Orthogonal Modal Representation in Long-Term Risk Quantification for Dynamic Multi-Agent Systems" (R. Yasunaga, Y. Nakahira, Y. Hori; ThC03.6) at American Control Conference (Denver, USA) (paper)．
• June 10th, 2025: Yutaka Hori will present "Learning and Optimizing Dynamic DNA Circuits through Control-Inspired Microfluidic Platforms" at International Symposium on Molecular Cybernetics.
• May 2025: Our paper "Parameter Invariance Analysis of Moment Equations Using Dulmage-Mendelsohn Decomposition" (A. Igarashi, Y. Hori) is published in IEEE Control Systems Letters．
• Apr. 2025: Yutaka Hori started a sabbatical year at the Control Group of the University of Oxford (until March, 2026).
• Feb. 16-20th, 2025: Haruno Namura will present "Dynamic Control of Plasmid Copy Number for Adjusting the Gain of Genetic Circuits" at Winter q-bio conference.
• Jan. 2025: Our paper "Orthogonal Modal Representation in Long-Term Risk Quantification for Dynamic Multi-Agent Systems" (R. Yasunaga, Y. Nakahira, Y. Hori) is published in IEEE Control Systems Letter. This is a joint work with Prof. Yorie Nakahira at Carnegie Mellon University.
• Dec. 26th, 2024: Yutaka Hori will give an online seminar on Mathematical Optimization for Bounding Moments of Stochastic Chemical Reactions at National Center for Theoretical Sciences (NCTS) of National Tsing Hua University (Taiwan)
• Dec., 2024: Our joint paper "Evaluation of the microenvironment formed by interferon-β" is accepted for publication in Frontiers in Chemical Biology. This is a joint work with the team of Dr. Yoshitaka Shirasaki and Dr. Osamu Ohara (paper)
• Jul. 2024: Masaya Miyazaki received Best Student Paper Award at Asian Control Conference (Dalian, China)
• Jul. 2024: Masaya Miyazaki will be presenting "Parameter-preserving model order reduction of chemical master equations with a priori error bound" at Asian Control Conference (Dalian, China). Our paper is selected for the Finalist of Best Student Paper Award.
• June 2024: Our paper "Stability analysis for large-scale multi-agent molecular communication systems" (T. Kotsuka, Y. Hori) is accepted for publication in IEEE Transactions on NanoBiosciences (paper) (preprint)
• Apr. 2024: Our paper "Analysis of Signal Distortion in Molecular Communication Channels Using Frequency Response" (S. Kitada, T. Kotsuka, Y. Hori) is accepted for publication in New Generation Computing.
• Dec. 2023: Our paper "Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space" (S. Nishikawa, G. Sato, S. Takada, S. Kohyama, G. Honda, M. Yanagisawa, Y. Hori, N. Doi, N. Yoshinaga, K. Fujiwara) was published in Advanced Science (paper ).
• Dec. 2023: Our paper "Graphical and Analytical Approaches for Analyzing Collective Behavior of Dynamic Multi-Agent Systems Governed by Generalized Cyclic Pursuit Mechanism" (T. Kwak, Y. Kim, Y. Hori, T.-H. Kim) was published in IEEE Access (paper )．
• Nov. 2023: Our paper "Stability analysis for large-scale multi-agent molecular communication systems" (T. Kotsuka, Y. Hori) was published on arXiv (preprint ).
• Nov. 2023: Our paper "Two-step reinforcement learning for model-free redesign of nonlinear optimal regulator" (M. Minami, Y. Masumoto, Y. Okawa, T. Sasaki, Y. Hori) was published in SICE Journal of Control, Measurement, and System Integration (paper ).
• Oct. 2023: Our paper "Exact Instability Margin Analysis and Minimum-Norm Strong Stabilization - phase change rate maximization -" (S. Hara, C.-Y. Kao, S. Z. Khong, T. Iwasaki, Yutaka Hori) was accepted for IEEE Transactions on Automatic Control. paper (arXiv)
• Sep. 2023: Mei Minami participated in "Girls in Control", a programming class for girls, as a staff.
• Sep. 2023: Mamoru Saita is going to present "Parallel Kinetics Measurement of of Temperature-Dependent DNA Devices" at DNA29
• Sep. 6th-9th, 2023: Taishi Kotsuka is going to present "Stability analysis for multi-agent molecular communication systems" at SICE2023
• Jul., 2023: Our paper "A Control-theoretic Model for Bidirectional Molecular Communication Systems" (by Taishi Kotsuka and Yutaka Hori) is published in IEEE Transactions on Molecular, Biological and Multi-Scale Communications (arXiv)
• Jul. 12th, 2023: Prof. Chung-Yao Kao is presenting a co-authored paper "On Phase Change Rate Maximization with Practical Applications" (Chung-Yao Kao, Shinji Hara, Yutaka Hori, Tetsuya Iwasaki, Sei Zhen Khong) at the IFAC World Congress 2023 (arXiv)
• Jul. 10th, 2023: Shoichiro Kitada is presenting our paper "Analysis of Signal Distortion in Molecular Communication Channels" (Shoichiro Kitada, Taishi Kotsuka, Yutaka Hori) at the IFAC World Congress 2023.
• Jul. 9th, 2023: Yutaka Hori is organizing a tutorial on Control Systems in Synthetic Biology with Prof. Mustafa Khammash at ETC Zurich at the IFAC World Congress. Detailed information is available. Registration is required.
• Apr., 2023: Our paper "L-2L ladder digital-to-analogue converter for dynamics generation of chemical concentrations" (T. Chatani, S. Shiraishi, H. Miyazako, H. Onoe, Y. Hori) was published in Royal Society Open Science
• Apr. 14th, 2023: Yutaka Hori gave a Tutorial Talk "Theory-based Design and Control of Biomolecular Circuits and Communication Systems" at the 7th Workshop on Molecular Communications
• Apr. 12th, 2023: Taishi Kotsuka gave a talk "Stability analysis for circulant structured multi-agent molecular communication systems" at the 7th Workshop on Molecular Communications (accompanying paper on arXiv)
• Jan. 24th, 2023: Our paper "Stability analysis for circulant structured multi-agent molecular communication systems" (T. Kotsuka and Y. Hori) was published on arXiv．
• Nov. 12th, 2022: Python codes for the two-step reinforcement learning algorithm for controller design were published at GitHub. The accompanying paper is available on arXiv.
• Nov. 11th. 2022: Our collaborator (Kaori Uehara) will be presenting "Fabrication for circular cross-sectional microchannels and their application for on-off valves" (K. Uehara, Y. Hori, T. Ishigure) at IEEE CPMT Symposium Japan (ICSJ2022)．
• Oct. 27. 2022: Our preprint "A Control-theoretic Model for Bidirectional Molecular Communication Systems" (T. Kotsuka and Y. Hori) is published on arXiv (preprint)．
• Oct. 23-27. 2022: Suguru Shiraishi will be presenting his work on "L-2L LADDER MICROFLUIDICS FOR DYNAMIC GENERATION OF CHEMICAL CONCENTRATIONS" (S. Shiraishi, T. Chatani, H. Miyazako, H. Onoe, Y. Hori) at MicroTAS2022．
• Sep. 12th. 2022: Our paper "Two-step reinforcement learning for model-free redesign of nonlinear optimal regulator" (M. Minami, Y. Masumoto, Y. Okawa, T. Sasaki, Y. Hori) was published on arXiv．
• Sep. 8th, 2022: Ayumi Nakajima was selected as the winner of the SICE Annual Conference Young Author's Award at SICE2022．
• Sep. 8th, 2022: Ayumi Nakajima is giving a talk on "Model-based analysis and rapid prototyping of genetic circuits with decoy transcription factor binding sites" (A. Nakajima, T. Yamamoto, T. Kotsuka, Y. Hori) at SICE2022．
• Sep. 2022: Ayumi Nakajima was selected as the Finalist of SICE Annual Conference Young Author's Award at SICE2022．
• Aug. 2022: Our paper "Interval Analysis of Worst-case Stationary Moments for Stochastic Chemical Reactions with Uncertain Parameters" (Y. Sakurai and Y. Hori) was accepted for publication in Automatica ( preprint).
• Jul. 13th, 2022: Taishi Kotsuka is giving a talk "Frequency Response of Diffusion-Based Molecular Communication Channels in Bounded Environment" (T. Kotsuka and Y. Hori) at European Control Conference 2022 (arXiv).
• June 2022: Our paper "A parametric logistic equation with light flux and medium concentration for cultivation planning of microalgae" (K. Kambe, Y. Hirokawa, A. Koshi, Y. Hori) was published in Journal of the Royal Society Interface. (bioRxiv)
• Mar. 14th, 2022: Yutaka Hori gave a talk "A Mathematical Optimization for the Analysis and Design of Uncertain Biocircuits" at International Workshop on Molecular Cybernetics: Toward Chemical AI.
• Feb. 2022: Our paper "A parametric logistic equation with light flux and media concentration for cultivation planning of microalgae" (K. Kambe, Y. Hirokawa, A. Koshi, Y. Hori) is published on bioRxiv.
• Feb. 2022: Our paper "Exact Instability Margin Analysis and Minimum Norm Strong Stabilization - phase change rate maximization -" (S. Hara, C.-Y. Kao, S. Z. Khong, T. Iwasaki, Y. Hori) is published on arXiv.org
• Oct. 2021: Our paper "Instability Margin Analysis for Parametrized LTI Systems with Application to Repressilator" (Shinji Hara, Tetsuya Iwasaki, Yutaka Hori) was accepted for publication in Automatica (preprint).
• Sep. 14th, 2021: Yutaka Hori is going to present "Theory-based Design and Control of Biomolecular Systems" in the Tutorial Workshop at IFAC Conference on Modelling, Identification and Control of Nonlinear Systems (MICNON 2021).
• Sep. 2021: Seishu Hara is going to present "Modeling and Stability Analysis for Multi-Agent Molecular Communication Systems: A Case Study for Two Agents" at SICE2021.
• May. 2021: Our paper "Spatial Frequency based Characterization of Disturbance Rejection in Molecular Communication Systems" by Taishi Kotsuka and Yutaka Hori was accepted for publication in IEEE Transactions on Molecular, Biological, and Multi-Scale Communications (T-MBMC).
• Mar. 2021: Our paper "Model-free two-step design for improving transient learning performance in nonlinear optimal regulator problems" by Y. Masumoto, Y. Okawa, T. Sasaki, Y. Hori is available at arXiv (preprint)
• Mar. 2021: Our paper "Robust Instability Radius for Multi-agent Dynamical Systems with Cyclic Structure" by S. Hara, T. Iwasaki, Y. Hori will be presented at SICE International Symposium on Control Systems (ISCS) (preprint)
• Feb. 2021: Our paper "Interval Analysis of Worst-case Stationary Moments for Stochastic Chemical Reactions with Uncertain Parameters" by Y. Sakurai and Y. Hori is available at arXiv. (preprint)
• Nov. 2020: "Microfiber-shaped programmable materials with stimuli-responsive hydrogel" by N. Takeuchi, S. Nakajima, R. Kawano, Y. Hori and H. Onoe is accepted for publication in Soft Robotics.
• Aug. 2020: Our new paper "Instability Margin Analysis with Application to Biological Oscillations" by Shinji Hara, Tetsuya Iwasaki and Yutaka Hori is now available at arXiv. preprint.
• Jul. 2020: Our paper "Robust Instability Analysis with Application to Neuronal Dynamics" by Shinji Hara, Tetsuya Iwasaki and Yutaka Hori is accepted for IEEE CDC2020. preprint.
• Jul. 2020: Our recent paper "Finite-Time Stability Analysis for Resource Limited Chemical Reactions" by Tomoki Matsunaga, Ryosuke Uemura and Yutaka Hori is accepted for the presentation in IEEE CDC2020.
• Jun. 2020: Our paper "Finite-Time Stability Analysis for Resource Limited Chemical Reactions" by Tomoki Matsunaga, Ryosuke Uemura and Yutaka Hori is accepted for publication in IEEE Control Systems Letters.
• May. 2020: Our paper "Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems" by Yutaka Hori is published in New Generation Computing.
• Mar. 2020: Our paper "Robust Instability Analysis with Application to Neuronal Dynamics" by Shinji Hara, Tetsuya Iwasaki and Yutaka Hori is published on arXiv.org.
• Dec. 2019: Asuka Koshi presented "Droplet based characterization of temperature dependent kinetics of DNA circuits" (with Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Risako Morita presented "Parameter set identification for uncertainty quantification of muscle mechanical models" (with T. Uchiyama and Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Ayaka Wakamei presented "A microfluidic actuator for dynamic control of biomolecular reactions" (with Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Ryosuke Uemura presented "Outer approximation of solution sets for uncertain dynamic polynomial systems" (with Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Tatsuya Yamamoto presented "Gain Control of Genetic Circuits using Decoy Promoters" (with Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Daichi Imai presented "Position feedback control of micro particles using dielectrophoresis" (with S.H. Kim, A.J. Genot, Y. Monnai, T. Fujii and Y. Hori) at Industry-UCB-UEC-keio Workshop 2019.
• Dec. 2019: Yutaka Hori presented "Semidefinite programming for Turing instability analysis in molecular communication networks" by Y. Hori and H. Miyazako at IEEE Conference on Decision and Control.
• Oct. 2019: Taishi Kotsuka presented "Disturbance response analysis of cell-to-cell communication systems based on spatial frequency decomposition" by T. Kotsuka and Y. Hori at IFAC Conference on Foundations of Systems Biology in Engineering.
• Sep. 2019: Yutaka Hori gave a seminar talk at the Shonan meeting on formal methods for the synthesis of biomolecular circuits.
• Jul. 2019: Our paper "Robust stability analysis for LTI systems with generalized frequency variables and its application to gene regulatory networks" by S. Hara, T. Iwasaki and Y. Hori was accepted for publication in Automatica.