Journal Papers

• Ohkubo T, Sakumura Y, Kunida K, On-Line Reoptimization of Mammalian Fed-Batch Culture Using a Nonlinear Model Predictive Controller, New Generation Computing, doi:10.1007/s00354-023-00235-0, 2023.

• Fujikawa R, Okimura C,  Kozawa S, Ikeda K, Inagaki N, Iwadate Y,  Sakumura Y*, Bayesian traction force estimation using cell boundary-dependent force priors, Biophyscal Journal, doi:10.1016/j.bpj.2023.10.032, 2023.

• Ong ALC, Kokaji T,  Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N, Acquisition of neural fate by combination of BMP blockade and chromatin modification, 29, 10 doi:10.1016/j.isci.2023.107887, 2023.

• Sakumura Y, Kunida K, Extracting quantitative relationships between cell motility and molecular activities (Analytical approaches and implications),  Journal of Biomechanical Science and Engineering,  doi:10.1299/jbse.23-00336, 2023.

• Ohkubo T, Soma Y, Sakumura Y, Hanai T, Kunida K, A hybrid in silico/in-cell controller for microbial bioprocesses with process-model mismatch, Scientific Reports volume 13, doi: 10.1038/s41598-023-40469-y, 2023.

• Itoh T, Koyama Y, Sakumura Y, Akamatsu T, Tsuruta A, Masuda Y, Shin W, Discrimination of volatile organic compounds using a sensor array via a rapid method based on linear discriminant analysis, Sensors and Actuators B: Chemical, 387, doi: 10.1016/j.snb.2023.133803, 2023.

• Kunida K, Takagi N, Aoki K, Ikeda K, Nakamura T, Sakumura Y, Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities, Cell Reports, 42, 2, doi: 10.1016/j.celrep.2023.112071, 2023.

• Kokaji T, Eto M, Hatano A, Yugi K, Morita K, Ohno S, Fujii M, Hironaka K, Ito Y, Egami R, Uematsu S, Terakawa A, Pan Y, Maehara H, Li D, Bai Y, Tsuchiya T, Ozaki H, Inoue H, Kubota H, Suzuki Y, Hirayama A, Soga T, and Kuroda S, In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states, Scientific Reports, 12, 13719, doi: 10.1038/s41598-022-17964-9,  2022.

• Minegishi T, Fujikawa R, Kastian RF, Sakumura Y, Inagaki N, Analyses of Actin Dynamics, Clutch Coupling and Traction Force for Growth Cone Advance, J. Vis. Exp. (176), e63227, doi: 10.3791/63227, 2021.

• Wong JH, Kato T, Belteton S, Shimizu R, Kinoshita N, Higaki T, Sakumura Y, Szymanski DB, Hashimoto T, Basic proline-rich protein-mediated microtubules are essential for lobe growth and flattened cell geometry, Plant Physiology, doi:10.1104/pp.19.00811, 2019.

• Okimura C, Sakumura Y, Shimabukuro K, & Iwadate Y, Sensing of substratum rigidity and directional migration by fast-crawling cells Okimura C, Sakumura Y, Shimabukuro K, & Iwadate Y, Physical Review E, 97 doi:10.1103/PhysRevE.97.052401, 2018.

• Yamada T, Nishiyama M, Oba S, Jimbo HC, Ikeda K, Ishii S, Hong K & Sakumura Y, Computational Methods for Estimating Molecular System from Membrane Potential Recordings in Nerve Growth Cone, Scientific Reports, 8 doi:10.1038/s41598-018-22506-3, 2018.

• Sakumura Y, Koyama Y, Tokutake H, Hida T, Sato K, Itoh T, Akamatsu T, Shin W, Diagnosis by volatile organic compounds in exhaled breath from lung cancer patients using support vector machine algorithm. Sensors, 17, 287, doi:10.3390/s17020287, 2017.

• Okimura C, Ueda K, Sakumura Y and Iwadate Y, Fast-crawling cell types migrate to avoid the direction of periodic substratum stretching. Cell Adhesion & Migration, DOI:10.1080/19336918.2015.1129482, 2016.

• Katsuno H, Toriyama M, Hosokawa Y, Mizuno K, Ikeda K, Sakumura Y, Inagaki N. Actin Migration Driven by Directional Assembly and Disassembly of Membrane-Anchored Actin Filaments, Cell Reports, 12, 1–13, 2015.

• Fujimuro T, Matsui T, Nitanda Y, Matta T, Sakumura Y, Saito M, Kohno K, Nakahata Y, Bessho Y, Hes7 3′UTR is required for somite segmentation function, Scientific Reports, doi:10.1038/srep06462, 2014.

• Pham TM, Tan KW, Sakumura Y, Okumura K, Maki H, Akiyama MT. A single-molecule approach to DNA replication in Escherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed, Mol. Microbiol. doi:10.1111/mmi.12386, 2013

• Kozawa S, Sakumura Y, Toriyama M, Inagaki N, Ikeda K. Bayesian Cell Force Estimation Considering Force Directions, Neural Processing Letters, DOI 10.1007/s11063-013-9320-y, 2013

• Toriyama M, Kozawa S, Sakumura Y, Inagaki N, Conversion of a Signal into Forces for Axon Outgrowth through Pak1-mediated Shootin1 Phosphorylation, Curr. Biol. 23, 529–534, 2013.

• Kaneko-Kawano T, Takasu F, Naoki H, Sakumura Y, Ishii S, Ueba T, Eiyama A, Okada A, Kawano Y, Suzuki K. Dynamic Regulation of Myosin Light Chain Phosphorylation by Rho-kinase. PLoS ONE 7(6): e39269. 2012.

• Kim W, Matsui T, Yamao M, Ishibashi M, Tamada K, Takumi T, Kohno K, Oba S, Ishii S, *Sakumura Y, and *Bessho Y, The period of the somite segmentation clock is sensitive to Notch activity, Mol. Biol. Cell, 22:18 3541-3549, 2011. (*corresponding authors)

• Inagaki N, Toriyama M, Sakumura Y, Systems Biology of Symmetry-Breaking during Neuronal Polarity Formation, Dev. Neurobiol., 71(6), 584-593, 2011.

• Toriyama M, *Sakumura Y, Shimada T, Ishii S, *Inagaki N, A Diffusion-based neurite length sensing mechanism involved in neuronal symmetry-breaking, Mol. Syst. Biol., 6:394, 2010. (*corresponding authors)

• Hayashi S, Shimoda T, Nakajima M, Tsukada Y, Sakumura Y, Dale JK, Maroto M, Kohno K, Matsui T, Bessho Y. Sprouty4, an FGF inhibitor, displays cyclic gene expression under the control of the notch segmentation clock in the mouse PSM. PLoS One. 4(5):e5603, 2009.

• Tsukada Y, Aoki K, Nakamura T, Sakumura Y, Matsuda M, Ishii S. Quantification of local morphodynamics and local GTPase activity by edge evolution tracking. PLoS Comput. Biol., 4(11): e1000223, 2008.

• Honda N, Sakumura Y, Ishii S. Stochastic Control of Spontaneous Signal Generation for Gradient Sensing in Chemotaxis. J. Theor. Biol., 255, 259-266, 2008.

• Toriyama M, Shimada T, Kim KB, Mitsuba M, Nomura E, Katsuta K, Sakumura Y, Roepstorff P, Inagaki N. Shootin1: A protein involved in the organization of an asymmetric signal for neuronal polarization. J. Cell Biol. 175(1), 147-157, 2006.

• Igarashi Y, *Sakumura Y, and Ishii S. The role of short-term depression in sustained neural activity in the prefrontal cortex: A simulation study. Neural Networks, 19, 1137-1152, 2006. (*corresponding author)

• Sakumura Y. and Ishii S. Stochastic Resonance with Differential Code in Feedforward Network with Intra-layer Random Connections. Neural Networks, 19, 469-476, 2006.

• Naoki H, Sakumura Y, and Ishii S. Local Signaling with Molecular Diffusion as a Decoder of Ca2+ Signals in Synaptic Plasticity, Mol. Syst. Biol., 1:2005.0027, 2005.

• Sakumura Y, Tsukada Y, Yamamoto N, and Ishii S. A Molecular Model for Axon Guidance Based on Crosstalk between Rho GTPases. Biophys. J., 89, pp.812-822, 2005.

• Sakumura Y. and Aihara K. Stochastic Resonance and Coincidence Detection in Single Neurons. Neural Processing Letters, 16(3), pp.235-242, 2002.

• Sakumura Y, Konno N. and Aihara K. Markov Chain Model Approximating the Hodgkin-Huxley Neuron, Artificial Neural Networks, Lecture Notes in Computer Science, 2130, pp.1153-1160, 2001.

• Sakumura Y, Konno N. and Aihara K. Approximating Markov Chain Model of the Hodgkin-Huxley Neuron. Trans. of the Materials Research Society of Japan, 26(1), pp.457-460, 2001.

• Sakumura Y. and Aihara K. A Neuronal Time Window for Coincidence Detection. IEICE Transactions on Fundamentals, E81-A(9), pp.1818-1823, 1998.

Books & Review Articles

• Kokaji T & Kuroda S,  Construction of an inter-organ transomic network for whole-body metabolism, Current Opinion in Endocrine and Metabolic Research, 25, 100361. doi: 10.1016/j.coemr.2022.100361, 2022.

• 作村諭一, 伊藤敏雄: 呼気ガスの簡易検知器開発と機械学習によるがん診断への応用, 「においのセンシング、分析技術と可視化」, 技術情報協会, 2020年8月

• 伊藤敏雄, 作村諭一: 半導体式ガスセンサによる呼気分析と統計解析, 電気化学, 2018

• Sakumura Y, Inagaki N, Quantitative Modeling of Neuronal Polarization, Technological Advancements in Biomedicine for Healthcare Application, 354-361, IGI global, 2012.

• 鳥山道則, 作村諭一, 稲垣直之：神経細胞が軸索の長さを検知する仕組みと神経細胞の対称性の破れ, 遺伝, 65, 80-86, 2011.

• 塚田 祐基, 作村 諭一: 細胞形態変化の定量と現象論的モデル, 細胞工学 339-343, 2010.

• 石井 信, 作村 諭一: 神経の可塑性と発達の生体反応モデリング. ゲノム情報と生命現象の統合的理解2007, 実験医学増刊(2007年2月), 198-204, 2007.

Patents

• 出願番号：特願2018-044724

• 発明者：作村 諭一、山田 達也、西山 誠、ホン キョンスウ　

• 発明の名称：膜電位時系列を用いた細胞内分子群の生化学反応経路の推定方法及び装置

• 出願人：国立大学法人奈良先端科学技術大学院大学

• 出願日：2018-03-12

International Conference (2000-)

• Chen X, Sasai N, Kunida K, Kokaji T, Sakumura Y, Estimating Shh-induced Gene Regulatory Network Based on a Strong-constrained LASSO Regression, the 14th International Conference on Bioscience, Biochemistry and Bioinformatics (ICBBB 2024), Kyoto, 2024.

• Sakumura Y & Kunida K, Extraction of Biomolecular Signals Controlling Complex Behavior of Biological Cells, Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA-ASC), Lanzhou, 2019. (Best Special Session Paper Award)

• Kosaka K, Ikeda K and Sakumura Y, “Estimation of intracellular key enzymes by applying machine learning algorithm,” The 20th International Conference on Systems Biology, 2 Nov. 2019

• Shirone S, Miyauchi M, Ouhara K, Kurihara J, Takata T, Hyogo H, Ito T, Shin W, Tanaka A, Sato K, Ikeda K and Sakumura Y, “Machine learning diagnosis of multiple liver-related diseases by exhaled breath gas components,” The 20th International Conference on Systems Biology, 2 Nov. 2019

• Koyama Y, Ikeda K, Sakumura Y, Feature Selection using Distance from Classification Boundary and Monte Carlo Simulation, The 25th International Conference on Neural Information Processing (ICONIP 2018), Siem Reap, 2018.

• Kozawa S, Sakumura Y, Toriyama M, Inagaki N, Ikeda K, An Estimation of Cell Forces with Hierarchical Bayes Approach Considering Cell Morphology, 19th International Conference on Neural Information Processing (ICONIP 2012), Doha, 501-508, 2012

• Sakumura Y. Simulation Analysis of the Network of the Stochastic Spike Generation Model Imitating the Hodgkin-Huxley Neuron, Asia Simulation Conference (JSST2011) .

• Yamada T, Jimbo HC, Ishii S, Nishiyama M, Hong K, Sakumura Y. Identification of a molecular system that regulates growth cone membrane potential during growth cone guidance, Computational Neuroscience Society 2011 (CNS*2011), 2011.

• Sakumura Y, Inagaki N. Neural polarization by an economizing system in neurite elongation. EMBO Conference Series on Systems Dynamics of Intracellular Communication (SPATIAL 2011), 2011.

• Dauwels, J., Tsukada, Y., Sakumura, Y., Ishii, S., Aoki, K., Nakamura, T., Matsuda, M., Vialatte, F., Cichocki, A. On the synchrony of morphological and molecular signaling events in cell migration. International Conference on Neural Information Processing (ICONIP 2008), 2008.

• Tsukada, Y., Aoki,K., Sakumura, Y., Nakamura, T., Matsuda, M., and Ishii, S., Quantitative Morphodynamic Analysis of FRET time-lapse imaging. International Conference on Systems Biology (ICSB 2008), DS2-1-54 pp.104, 2008.

• Tsukada, Y., Sakumura, Y., Ishii, S. Quantitative Morphodynamic Analysis of Time-Lapse Imaging by Edge Evolution Tracking. International Conference on Neural Information Processing (ICONIP 2007), 2007．

• Naoki, H., Sakumura, Y., and Ishii, S. Spontaneous signal generation induced by reaction noise for gradient sensing in chemotaxis. International Conference of Systems Biology (ICSB 2007), pp.46, 2007.

• Naoki, H., Sakumura, Y., and Ishii, S. Local signaling with diffusion process as a decorder of Ca2+ signals in synaptic plasticity. The Assembly and Function of Neuronal Circuits. pp.79, 2005.

• Tsukada Y., Aoki K., Sakumura Y., Nakamura T., Matsuda M., and Ishii S. Quantitative Analysis of Morphological Dynamics and the Activity of Rho-family GTPases during Neurite Outgrowth. The Sixth International Conference on Systems Biology (ICSB 2005), pp.316, 2005.

• Sakumura, Y., Tsukada, Y., Yamamoto, N., and Ishii, S. Axon guidance regulated by interactions of Rho family small GTPases. The Sixth International Conference on Systems Biology (ICSB 2005), pp.279, 2005.

• Igarashi, Y., Sakumura, Y., and Ishii, S. Short-term depression stabilizes sustained neural activities in the prefrontal cortex: a computational study, Society for Neuroscience, 35th Annual Meeting, 41.17, 2005.

• Sakumura, Y., Tsukada Y., Yamamoto, N., and Ishii, S. Axon guidance based on cross talk between Rho GTPases requires switching mechanism, Society for Neuroscience, 35th Annual Meeting, 146.8, 2005.

• Igarashi, Y., Sakumura, Y., Ishii, S. The role of short term depression for sustained neural activities in the prefrontal cortex: a simulation study, International Symposium on Nonlinear Theory and its Applications (NOLTA 2004), 509-512, 2004.

• Sakumura, Y., Tsukada Y., and Ishii, S. Spike Synchronization Represents Temporal Difference of Neural Population Activity in a Cortical Model. New Horizons in Molecular Sciences and Systems: An Integrated Approach, 51, 2003.

• Sakumura, Y. and Ishii, S. The differential operation by neural assembly. International Symposium on Nonlinear Theory and its Applications, 323-326, 2002.

• Sakumura, Y., Konno, N., and Aihara, K. Approximating Markov Chain Model of the Hodgkin-Huxley Neuron, The 12th Symposium of the Materials Research Society of Japan, 213, 2000.