Peer-reviewed Journal Papers

  • T. Kotsuka, Y. Hori, "Stability analysis for large-scale multi-agent molecular communication systems," IEEE Transactions on Nanobioscience, 2024 (accepted). (doi:10.1109/TNB.2024.3404592) (preprint)
  • S. Kitada, T. Kotsuka, Y. Hori, "Analysis of Signal Distortion in Molecular Communication Channels Using Frequency Response," New Generation Computing, 2024 (accepted).
  • S. Hara, C.-Y. Kao, S. Z. Khong, T. Iwasaki, Y. Hori, "Exact Instability Margin Analysis and Minimum Norm Strong Stabilization -- phase change rate maximization --," IEEE Transactions on Automatic Control, vol. 69, no. 4, pp. 2084--2099, 2024 (doi:10.1109/TMBMC.2023.3290077 (preprint)
  • S. Nishikawa, G. Sato, S. Takada, S. Kohyama, G. Honda, M. Yanagisawa, Y. Hori, N. Doi, N. Yoshinaga, K. Fujiwara, "Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space," Advanced Science, 2308030, 2023. (DOI: 10.1002/advs.202308030).
  • T. Kwak, Y. Kim, Y. Hori, T.-H. Kim, "Graphical and Analytical Approaches for Analyzing Collective Behavior of Dynamic Multi-Agent Systems Governed by Generalized Cyclic Pursuit Mechanism," IEEE Access, vol. 11, pp. 140481--140495, 2023. (doi:10.1109/ACCESS.2023.3339195).
  • M. Minami, Y. Masumoto, Y. Okawa, T. Sasaki, Y. Hori, "Two-step reinforcement learning for model-free redesign of nonlinear optimal regulator," SICE Journal of Control, Measurement, and System Integration, vol. 16, no. 1, pp. 349--362, 2023. (doi:10.1080/18824889.2023.2278753).
  • T. Kotsuka, Y. Hori, "A Control-theoretic Model for Bidirectional Molecular Communication Systems," IEEE Transactions on Molecular, Biological and Multi-Scale Communications, vol. 9, no. 3, 274--285, 2023 (doi:10.1109/TMBMC.2023.3290077, preprint).
  • K. Uehara, Y. Hori, T. Ishigure, "Fabrication of Circular Cross-Section Microchannels with 3-D Lattice Arrangement and Their Use as On-Off Valves," Micro, vol. 3, No. 3, pp. 620--631, 2023 (doi:10.3390/micro3030043).
  • T. Chatani, S. Shiraishi, H. Miyazako, H. Onoe, Y. Hori, "L-2L ladder digital-to-analogue converter for dynamics generation of chemical concentrations," Royal Society Open Science, vol. 10, no. 4, 230085, 2023 ( (doi:10.1098/rsos.230085).
  • Y. Sakurai, Y. Hori, "Interval Analysis of Worst-case Stationary Moments for Stochastic Chemical Reactions with Uncertain Parameters," Automatica, vol. 146, no. 12, 110647, 2022 ( (doi:10.1016/j.automatica.2022.110647 preprint).
  • K. Kambe, Y. Hirokawa, A. Koshi, Y. Hori, "A parametric logistic equation with light flux and medium concentration for cultivation planning of microalgae," Journal of the Royal Society Interface, vol. 19, No. 19, 20220166, 2022 (doi:10.1098/rsif.2022.0166)
  • S. Hara, T. Iwasaki, Y. Hori, "Instability Margin Analysis for Parametrized LTI Systems with Application to Repressilator," Automatica, vol. 136, no. 2, 110047, 2022 (doi:10.1016/j.automatica.2021.110047 preprint)
  • T. Kotsuka, Y. Hori, "Spatial Frequency based Characterization of Disturbance Rejection in Molecular Communication Systems," IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, vol.8, no. 1, pp.36--43, 2022. (doi:10.1109/TMBMC.2021.3083726)
  • N. Takeuchi, S. Nakajima, R. Kawano, Y. Hori and H. Onoe, "Microfiber-shaped programmable materials with stimuli-responsive hydrogel," Soft Robotics, 2020. (doi:10.1089/soro.2020.0038)
  • R. Suzuki, T. Emura, Y. Tokura, N. Kawamura, Y. Hori, "A Quartz Crystal Microbalance based Portable Gas Sensing Platform for On-demand Human Breath Monitoring," IEEE Access, vol. 8, pp. 146166--146171, 2020. (doi:10.1109/ACCESS.2020.3013857)
  • T. Matsunaga, R. Uemura and Y. Hori, "Finite-time Stability Analysis for Resource Limited Chemical Reactions," IEEE Control Systems Letters, vol. 5, No. 3, pp. 815--820, 2020 (doi:10.1109/LCSYS.2020.3006052)
  • S. Hara, T. Iwasaki and Y. Hori, "Robust Stability Analysis for LTI Systems with Generalized Frequency Variables and its Application to Gene Regulatory Networks," Automatica, vol 105, pp. 96--106., 2019. (doi:10.1016/j.automatica.2019.03.019)
  • Y. Sakurai and Y. Hori, "Bounding Transient Moments of Stochastic Chemical Reactions," IEEE Control Systems Letters, vol 3, No. 2 (special issue on Control and Network Theory for Biological Systems), pp.290--295, 2019. (doi:10.1109/LCSYS.2018.2869639, arXiv)
  • Y. Hori and H. Miyazako, "Analysing Diffusion and Flow-driven Instability using Semidefinite Programming," Journal of the Royal Society Interface, vol.16, No. 150, 20180586, 2019. (doi:10.1098/rsif.2018.0586, arXiv)
  • 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)
  • 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]
  • V. Hsiao, Y. Hori. P. W. K. Rothemund, R. M. Murray, "A Population-based Temporal Logic Gate for Timing and Recording Chemical Events," Molecular Systems Biology, vol. 12, No. 5, 869, 2016. (doi:10.15252/msb.20156663, bioRxiv).
  • 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)
  • H. Niederholtmeyer*, Z. Z. Sun*, Y. Hori, E. Yeung, A. Verpoorte, R. M. Murray and S. J. Maerkl, "Rapid Cell-free Forward Engineering of Novel Genetic Ring Oscillators," eLife, vol. 4, e09771, 2015. (doi:10.7554/eLife.09771)
  • Y. Wang, Y. Hori, S. Hara and F. J. Doyle III, "Collective Oscillation Period of Inter-Coupled Biological Negative Cyclic Feedback Oscillators," IEEE Transactions on Automatic Control, vol. 60, No. 5, pp. 1392--1397, 2015. v(doi:10.1109/TAC.2014.2342072)
  • M. Takada, Y. Hori and S. Hara, "Comments and Corrections on Stability of Genetic Regulatory Networks With Time Delay," IEEE Transactions on Circuits and Systems I, vol. 61, No. 9, pp. 2771--2774, 2014. (doi:10.1109/TCSI.2014.2332245)
  • T. Nakamura, Y. Hori and S. Hara, "Hierarchical Modeling and Local Stability Analysis for Repressilators Coupled by Quorum Sensing," SICE Journal of Control, Measurement, and System Integration, vol. 7, No. 3, pp.133--140, 2014. (doi:10.9746/jcmsi.7.133) [Best Paper Award (Takeda Award)]
  • Y. Wang, Y. Hori, S. Hara and F. J. Doyle III, "Intercellular Delay Regulates the Collective Period of Repressively Coupled Gene Regulatory Oscillator Networks," IEEE Transactions on Automatic Control, vol. 59, issue 1, 2014. (doi:10.1109/TAC.2013.2270072)
  • 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)
  • 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)
  • T.-H. Kim, Y. Hori and S. Hara, ``Robust Stability Analysis of Gene-protein Regulatory Networks with Cyclic Activation repression Interconnections,'' Systems and Control Letters , vol. 60, No. 6, pp. 373--382, 2011. (doi:10.1016/j.sysconle.2011.03.003)
  • T.-H. Kim, S. Hara and Y. Hori, "Cooperative Control of Multi-agent Dynamical Systems in Target-enclosing Operations using Cyclic Pursuit Strategy," International Journal of Control, vol. 83, No. 10, pp. 2040--2052, 2010. (doi:10.1080/00207179.2010.504784)
  • S. Murata, A. Kuzuya, K. Fujiwara, J.Taira, I Kawamata, Y. Sato, M. Takinoue, S. M. Nomura, A. Kakugo, Y. Hori, K. Abe, ``Online Biomolecular Design Competition Across University Boundaries,'' Journal of JSEE, 2021 (accepted, in Japanese).
  • Y. Hori, "A Control Engineering Approach to Designing and Building Genetic Circuits," Systems, Control and Information, Vol. 61, No. 5, pp. 194--199, 2017 (in Japanese).
  • H. Miyazako, Y. Hori and S. Hara, "Analysis of Turing Instability in Reaction-Diffusion Systems Using a Single Diffuser," Transactions of the Society of Instrument and Control Engineers, Vol. 49, No. 12, pp.1164--1171, 2013 (in Japanese). (doi:10.9746/sicetr.49.1164)
  • S. Osawa, Y. Hori and S. Hara, "Robust Stability Analysis for Cyclic Gene Regulatory Networks," Transactions of the Society of Instrument and Control Engineers, Vol. 48, No. 6, pp. 318--325, 2012 (in Japanese). (JOI: DN/JST.JSTAGE/sicetr/48.318)
  • Y. Hori and S. Hara, "Oscillation Profile Analysis for Cyclic Gene Regulatory Networks," Transactions of the Society of Instrument and Control Engineers, Vol. 48, No. 4, pp. 241--247, 2012 (in Japanese). (JOI: DN/JST.JSTAGE/sicetr/48.241)
  • S. Hara, Y. Hori and T.-H. Kim, "Cyclic Pursuit Based Formation Control for Cooperative Target-enclosing," Transactions of the Society of Instrument and Control Engineers, Vol. 45, No. 3, pp. 160--167, 2009 (in Japanese). (JOI: JST.JSTAGE/sicetr/45.160)

Review Papers

  • Y. Hori, "Modeling and Analysis of Stochastic Reaction Kinetics in Biomolecular Systems," New Generation Computing, vol. 38, pp. 367--377, 2020. (doi: 10.1007/s00354-020-00095-y)

Peer-reviewed Conference Papers/Abstract

  • M. Miyazaki, Y. Hori, "Parameter-preserving model order reduction of chemical master equations with a priori error bound," Proceedings of Asian Control Conference, 2024 (accepted).
  • M. Saita, Y. Hori, "Parallel Kinetics Measurement of of Temperature-Dependent DNA Devices," DNA29, 2023
  • C.-Y. Kao, S. Hara, Y. Hori, T. Iwasaki, S. Z. Khong, "On Phase Change Rate Maximization with Practical Applications," Proceedings of IFAC World Congress (IFAC-Papers Online), vol. 56, no. 2, pp. 5805--5810, 2023 (doi:10.1016/j.ifacol.2023.10.558arXiv).
  • Shoichiro Kitada, Taishi Kotsuka, Yutaka Hori, "Analysis of Signal Distortion in Molecular Communication Channels," Proceedings of IFAC World Congress, 2023.
  • T. Kotsuka, Y. Hori, "Stability analysis for circulant structured multi-agent molecular communication systems," Proceedings of the 7th Workshop on Molecular Communications, 2023 (arXiv).
  • K. Uehara, Y. Hori, T. Ishigure, "Fabrication for circular cross-sectional microchannels and their application for on-off valves," Proceedings of IEEE CPMT Symposium Japan, pp. 119-122, 2022 (10.1109/ICSJ55786.2022.10034705.
  • S. Shiraishi, T. Chatani, H. Miyazako, H. Onoe, Y. Hori, "L-2L LADDER MICROFLUIDICS FOR DYNAMIC GENERATION OF CHEMICAL CONCENTRATIONS", Proceedings of Miniaturized Systems for Chemistry and Life Sciences (MicroTAS) , 2022.
  • A. Nakajima, T. Yamamoto, T. Kotsuka, Y. Hori, "Model-based analysis and rapid prototyping of genetic circuits with decoy transcription factor binding sites", Proceedings of SICE Annual Conference, 2022.
  • T. Kotsuka, Y. Hori, "Frequency response of diffusion-based molecular communication channels in bounded environment", Proceedings of European Control Conference, pp. 327--332, 2022 (doi:10.23919/ECC55457.2022.9838248 arXiv).
  • S. Hara, T. Kotsuka, Y. Hori, "Modeling and stability analysis for multi-agent molecular communication systems: a case study for two agents", Proceedings of SICE Annual Conference, 2021.
  • S. Hara, T. Iwasaki, Y. Hori, "Robust Instability Radius for Multi-agent Dynamical Systems with Cyclic Structure," Proceedings of SICE International Symposium on Control Systems, 2021. (arXiv)
  • S. Hara, T. Iwasaki and Y. Hori, "Robust Instability Analysis with Application to Neuronal Dynamics," Proceedings of the IEEE Conference on Decision and Control, pp. 6156-6161, 2020. (doi:10.1109/CDC42340.2020.9304320, arXiv)
  • N. Takeuchi, S. Nakajima, R. Kawano, Y. Hori, H. Onoe , "Locally Bendable Stimuli-Responsive Hydrogel Actuator with Axially Patterned Functional Materials," IEEE International Conference on Micro Electro Mechanical Systems (MEMS), 2019. (doi:10.1109/MEMS46641.2020.9056321)
  • Y. Hori and H. Miyazako, "Semidefinite programming for Turing instability analysis in molecular communication networks," IEEE Conference on Decision and Control, pp. 1874-1880, 2019. (doi:10.1109/CDC40024.2019.9029976)
  • T. Kotsuka, Y. Hori, "Disturbance response analysis of cell-to-cell communication systems based on spatial frequency decomposition," IFAC-PapersOnLine (Proceedings of the IFAC Foundations of Systems Biology in Engineering), vol. 52, No. 26, pp. 65-69, 2019 (doi:10.1016/j.ifacol.2019.12.237,bioRxiv)
  • A. Wakamei and Y. Hori, "A microfluidic actuator for dynamic control of chemical reactions," Proceedings of SICE Annual Conference, pp.1767--1769, 2018.
  • T. Yamada, Y. Hori, S. Suzuki, S. Kawasaki, N. Hiroi, H. Saito and A. Funahashi, "Mathematical modeling identifies the conditions required for RNA-based oscillator," Proceedings of SICE Annual Conference, pp.1574--1578, 2018.
  • Y. Sakurai and Y. Hori, "A Convex Approach to Steady State Moment Analysis for Stochastic Chemical Reactions," Proceedings of IEEE Conference on Decision and Control, pp.1206--1211, 2017. doi:10.1109/CDC.2017.8263820)
  • Y. Hori, "Model-based Feedback Control of Synthetic Biomolecular Circuits," Proceedings of International Symposium on Micro-NanoMechatronics and Human Science (MHS), 2017. doi:10.1109/MHS.2017.8305288) [Keynote Talk]
  • M. Yamagishi, Y. Hori, S. Uemura, O. Ohara and Y. Shirasaki, "Time evolution of microenvironment around cells regulated by the secretion activity and culture density of the cells," Proceedings of International Symposium on Micro-NanoMechatronics and Human Science (MHS), 2017. doi:10.1109/MHS.2017.8305247).
  • T. Uchiyama, Y. Hori and K. Suzuki, "Estimation of tibialis anterior muscle stiffness during the swing phase of walking with various footwear," Proceedings of Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 4131--4134, 2017. doi:10.1109/EMBC.2017.8037765).
  • Y. Hori and R. M. Murray, "Engineering Principles of Synthetic Biochemical Oscillators with Negative Cyclic Feedback," Proceedings of IEEE Conference on Decision and Control, pp. 584--589, 2015. (doi:10.1109/ECC.2015.7330878)
  • 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)
  • Y. Hori, S. Kumagai and S. Hara, "Network Structure for Turing Instabilizability in Reaction-Diffusion Systems with One Diffuser: A Case Study for Three-gene Networks," Proceedings of SICE Annual Conference, pp. 892--895, 2014.
  • H. Miyazako, Y. Hori and S. Hara, "Turing Instability in Reaction-Diffusion Systems with a Single Diffuser: Characterization Based on Root Locus," Proceedings of IEEE Conference on Decision and Control, pp. 2671--2676, 2013. ( IEEE Xplore, arXiv)
  • 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)
  • Y. Hori and S. Hara, "Noise-Induced Spatial Pattern Formation in Stochastic Reaction-Diffusion Systems, Proceedings of IEEE Conference on Decision and Control, pp. 1053--1058, 2012. ( IEEE Xplore, arXiv,) ( Errata and supplementary info)
  • Y. Wang, Y. Hori, S. Hara and F. J. Doyle III, ``The Collective Oscillation Period of Inter-coupled Goodwin Oscillators," Proceedings of IEEE Conference on Decision and Control, pp. 1627--1632, 2012. ( IEEE Xplore, arXiv)
  • T. Nakamura, S. Hara and Y. Hori, ``Local Stability Analysis for a Class of Quorum-Sensing Networks with Cyclic Gene Regulatory Networks," Proceedings of the SICE Annual Conference, pp. 2111--2116, 2011. [T. N. received Annual Conference International Award] ( IEEE Xplore)
  • Y. Hori and S. Hara, ``Time Delay Effects on Oscillation Profiles in Cyclic Gene Regulatory Networks: Harmonic Balance Approach,'' Proceedings of American Control Conference, pp. 2891--2896, 2011. ( IEEE Xplore)
  • S. Osawa, Y. Hori and S. Hara, ``Robust Stability Analysis for Cyclic Gene Regulatory Networks with Uncertainty,'' Proceedings of Asian Control Conference, pp. 869--874, 2011. [Finalist of Best Paper Award] [S. O. received Shimemura Young Author Award] ( IEEE Xplore)
  • Y. Hori and S. Hara, "Oscillation Pattern Analysis for Gene Regulatory Networks with Negative Cyclic Feedback," Proceedings of IEEE Conference on Decision and Control, pp. 5798--5803, 2010. (doi:10.1109/CDC.2010.5717982)
  • Y. Hori, S. Hara and T.-H. Kim, "Periodic Oscillations in Cyclic Repressor Networks: Analytic Existence Criteria with Biological Insight," Proceedings of IEEE Multi-conference on Systems and Control, pp.824--829, 2010. [Finalist of Best Student Paper Award] (doi:10.1109/CCA.2010.5611167)
  • M. Takada, Y. Hori and S. Hara, "Existence Conditions for Periodic Oscillations in Cyclic Gene Regulatory Networks with Time Delay," Proceedings of IEEE Multi-conference on Systems and Control, pp.830--835, 2010. (doi:10.1109/CCA.2010.5611130)
  • Y. Hori, T.-H. Kim and S. Hara, “Graphical and Analytic Criteria for the Existence of Protein Level Oscillations in Cyclic Gene Regulatory Networks,” Proceedings of IEEE Conference on Decision and Control, pp. 3521--3526, 2009. (doi:10.1109/CDC.2009.5400718)
  • Y. Hori, T.-H. Kim and S. Hara, “Robust Stability Analysis of Gene-Protein Regulatory Networks with Cyclic Activation-Inhibition interconnections,” Proceedings of Asian Control Conference, pp.1334--1339, 2009.
  • Y. Hori, A. Takabe and S. Hara, “On the Existence of Oscillatory Behavior in Gene Regulatory Networks with Cyclic Interconnections,” Proceedings of ICROS-SICE International Joint Conference, pp.2525--2530, 2009. [Annual Conference Young Author's Award] ( IEEE Xplore)
  • S. Hara, T.-H. Kim and Y. Hori, "Distributed Formation Control for Target-Enclosing Operations Based on a Cyclic Pursuit Strategy," Proceedings of International Federation of Automatic Control World Congress, pp. 6602--6607, 2008. (doi:10.3182/20080706-5-KR-1001.01113)
Patents
  • Japanese Patent No. 5057334 (LINEAR PREDICTION COEFFICIENT CALCULATOR, LINEAR PREDICTION COEFFICIENT CALCULATION METHOD, LINEAR PREDICTION COEFFICIENT CALCULATION PROGRAM, AND STORAGE MEDIUM)
  • Japanese Patent No. 5013293 (ENCODING DEVICE, DECODING DEVICE, ENCODING METHOD, DECODING METHOD, PROGRAM, AND RECORDING MEDIUM )