Publications

November, 2019

Journal articles

  1. Naoto Sakamoto & Takashi Naka: Validity of transfer-function representation of input-output relation in allosteric models. BioSystems 19, 317-326 (1986)
  2. Takashi Naka & Naoto Sakamoto: Kinetics of membrane-bound enzymes: Validity of quasi-steady-state approximation for a Michaelis-Menten-type reaction. Journal of Membrane Science 74, 159-170 (1992)
  3. Takashi Naka, Kosuke Shiba & Naoto Sakamoto: A two-dimensional compartment model for the reaction-diffusion system of acetylcholine in the synaptic cleft at the neuromuscular junction. BioSystems 41, 17-27 (1997)
  4. Takashi Naka: Simulation analysis of the effects of the junctional folds on spontaneous generation of the miniature endplate current at neuromuscular junction. Mathematics and Computers in Simulation 46, 633-641 (1998)
  5. Takashi Naka: Evaluation of characteristic parameters for the neurotransmitter release mechanisms at the neuromuscular junction. BioSystems 49, 143-149 (1999)
  6. Takashi Naka & Naoto Sakamoto: Localization effects of acetylcholine release from a synaptic vesicle at the neuromuscular junction. BioSystems 51, 73-78 (1999)
  7. Takashi Naka & Naoto Sakamoto: Two-dimensional compartment model for generation of miniature endplate current at the neuromuscular junction. Comments on Theoretical Biology 6, 1-28 (2001)
  8. Takashi Naka & Naoto Sakamoto: Simulation analysis of the effects of the simultaneous release of quanta of ACh on the endplate current at the neuromuscular junction. Mathematics and Computers in Simulation 59, 87-94 (2002)
  9. Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Noriko Yumoto, Mio Ichikawa, Jae-Hoon Kim, Kazuki Saito, Mihoro Saeki, Mikako Shirouzu, Shigeyuki Yokoyama and Akihiko Konagaya: A computational model on the modulation of MAPK and Akt pathways in heregulin induced ErbB signaling, Biochemical Journal, 373, 451-463, (2003)
  10. Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya: OBIYagns : A grid-based biochemical simulator with parameter estimator. Bioinformatics 20. 1646-1648 (2004, July)
  11. Takashi Naka, Mariko Hatakeyama, Naoto Sakamoto, Akihiko Konagaya: Compensation effect of MAPK cascade on formation of Phospho-protein gradient. BioSystems 83. 167-177 (2006 February)
  12. Takashi Nakakuki, Noriko Yumoto, Takashi Naka, Mikako Shirouzu, Shigeyuki Yokoyama, Mariko Hatakeyama: Topological Analysis of MAPK Cascade for Kinetic ErbB Signaling. PLoS ONE 3. e1782 (2008 March)
  13. Yoshimi Naruo , Takeshi Nagashima , Ryoko Ushikoshi-Nakayama , Yuko Saeki , Takashi Nakakuki , Takashi Naka , Hiroshi Tanaka , Shih F Tsai and Mariko Okada-Hatakeyama: Epidermal growth factor receptor mutation in combination with expression of MIG6 alters gefitinib sensitivity. BMC Systems Biology 5:29 doi:10.1186/1752-0509-5-29 (2011 February).
  14. Bastiaens, P., M. R. Birtwistle, et al.: Silence on the relevant literature and errors in implementation. Nature Biotechnology 33(4): 336-339. (2015 April).
  15. Chinasa Sueyoshi, Takashi Naka: Stability Analysis for the Cellular Signaling Systems Composed of Two Phosphorylation-Dephosphorylation Cyclic Reactions. Computational Molecular Bioscience 2017, 7, 33-45. (2017 August).
  16. Takashi Naka: The partition representation of enzymatic reaction networks and its application for searching bi-stable reaction systems. PLOS ONE 26. https://doi.org/10.1371/journal.pone.0263111 (2022 Jan)

Conference proceedings

  1. Takashi Naka & Naoto Sakamoto: Simulation analysis of the effects of the simultaneous release of quanta of ACh on the endplate current at the neuromuscular junction. Proc. of the IMACS (International Association for Mathematics and Computers in Simulation) International Congress on Modelling and Simulation,561-566 (1999)
  2. Takashi Naka & Naoto Sakamoto: Simulation analysis of the effects of quantum size of acetylcholine on generation of endplate current at the neuromuscular junction. Proc. of the 16th IMACS World Congress on Scientific Computation, Applied Mathematics and Simulation, 6 pages on CD-ROM (2000)
  3. Mariko Hatakeyama, Shuhei Kimura, Noriko Yumoto, Mio Ichikawa, Takuji Kawasaki, Takashi Naka, & Akihiko Konagaya: A Mathematical Modeling of Signal Transduction Cascade on Raf-Akt Cross-Talk, Genome Informatics 13 (Proceedings of GIW2002 -The 13th International Conference on Genome Informatics), 359-360(2002)
  4. Takuji Kawasaki, Shuhei Kimura, Mariko Hatakeyama, Takashi Naka, & Akihiko Konagaya: Development of Biochemical System Simulator with Parameter Estimator, Genome Informatics 13 (Proceedings of GIW2002 -The 13th International Conference on Genome Informatics), 463-464(2002)
  5. Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, & Akihiko Konagaya: OBIYagns: A Biochemical Simulator in Grid Environment, Genome Informatics 14 (Proceedings of GIW2003 -The 14th International Conference on Genome Informatics), 621-622(2003)
  6. Shuhei Kimura, Mariko Hatakeyama, Takuji Kawasaki, Takashi Naka, Akihiko Konagaya: Parameter Estimation for the Simulation of Biochemical Pathways. Proceedings of 15th IASTED International Conference on Modelling and Simulation (MS2004). 266-271 (2004, March)
  7. Takashi Naka: Effect of the EGF binding cooperativity on EGFR activation on the cell surface. Porc. of GIW2008 - The 19th International Conference on Genome Informatics, 2 pages on CD-ROM (Gold Coast, Australia, 2008, December)
  8. Takashi Naka: Simulation analysis of lateral propagation mechanism of EGF signaling on cell surface, Proceedings of ICCSA2009 ( International Conferences on Computational Science and Its Applications 2009), 183-188 (Yongin, Korea, 2009 June)
  9. Takashi Naka: Stochastic Aspects of Kinase Cascade Pathways in Cellular Signaling, Proceedings of ICCSA2010 ( International Conferences on Computational Science and Its Applications 2010), 300-302 (Fukuoka, Japan, 2010 March)
  10. Chinasa Sueyoshi, Takashi Naka: Exhaustive Analysis for the Effects of a Feedback Regulation on the Bi-Stability in Cellular Signaling Systems, Springer International Publishing AG 2017 O. Gervasi et al. (Eds.): ICCSA 2017, Part I, LNCS 10404, pp. 159?173, 2017. DOI: 10.1007/978-3-319-62392-4_12 (Trieste, Italy, 2017 July)
  11. Chinasa Sueyoshi, Takashi Naka: Stability Analysis for the Cellular Signaling Systems with a Feedback Regulation, Proceedings of EECS2019 ( International Conferences on Electrical Engineering and Computer Science 2019), 302-314 (Singapre, 2019 February)
  12. Takashi Naka: Validity of the Michaelis-Menten Approximation for the Stability Analysis in Regulatory Reaction Networks, Proceedings of BIOSTEC 2020 (13th International Joint Conference on Biomedical Engineering Systems and Technologies), Volume 3: BIOINFORMATICS, 176-182, (Valletta, Malta, 2020 February)
  13. Takashi Naka: Identification of Bistability in Enzymatic Reaction Networks Using Hysteresis Response, Proceedings of BIOSTEC 2022 (17th International Joint Conference on Biomedical Engineering Systems and Technologies), BIOINFORMATICS; ISBN 978-989-758-688-0; ISSN 2184-4305, SciTePress, pages 479-486. DOI: 10.5220/0012416000003657

Technical reports

  1. Takashi Naka: Pseudo Japanese specification tool. FASET (Formal Approach to Software Environment Technology) Technical Report 1, 29-32 (1987)
  2. Takashi Naka & Masahiro Matsuo: A lisp program development support tool applying stepwise refinement technique to natural language. FASET Technical Report 2, 29-32 (1989)

Conference presentations

  1. Naoto Sakamoto & Takashi Naka: Characterization of transverse and radial diffusion system of acetylcholine in the synaptic cleft at neuromuscular junction.First East Asian Symposium on Biophysics (1994)
  2. Takashi Naka: Simulation analysis of the effects of the junctional folds on spontaneous generation of the miniature endplate current at neuromuscular junction. IMACS Symposium on Mathematical Modelling (1997)
  3. Takashi Naka, Mariko Hatakeyama, Mio Ichikawa, Naoto Sakamoto, & Akihiko Konagaya: Formulation of the estimation methods for the kinetic parameters in cellular dynamics using object-oriented database. ISMB2001 (The 9th International Conference on Intelligent Systems for Molecular Biology) (2001)
  4. Shuhei Kimura, Takashi Naka, Mariko Hatakeyama, & Akihiko Konagaya: Parameter Estimation of Signal Transduction Pathways using Real-Coded Genetic Algorithms. ISMB2001 (The 9th International Conference on Intelligent Systems for Molecular Biology) (2001)
  5. Takashi Naka, Mariko Hatakeyama, Naoto Sakamoto, & Akihiko Konagaya: Development of a Model System for the Essential Mechanisms in Cellular Signaling. SIAM Symposium on Computational Models and Simulation for Intra-Cellular Processes (2002)
  6. Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Fumikazu Konishi, Akihiko Konagaya: Computer Simulation of ErbB Signaling in Grid Environment. Biomedical Information Science and Technology Initiative (BISTI) 2003 Symposium, Digital Biology: The Emerging Paradigm, WasingtonDC (2003)
  7. Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya: OBIYagns: A biochemical simulator in Grid environment. Genome Informatics Workshop, Yokohama (2003)
  8. Mariko Hatakeyama, Shuhei Kimura, Takashi Naka, Takuji Kawasaki, Noriko Yumoto, Mio Ichikawa, Mikako Shirouzu, Shigeyuki Yokoyama, Akihiko Konagaya: A computational model on Raf-Akt cross-talk in ErbB Signaling. International conference Pathways, Networks, and Systems: Theory and Experiments. Santorini, Greece (2003)
  9. Mariko Hatakeyama, Noriko Yumoto, Takashi Naka, Shuhei Kimura and Akihiko Konagaya: Computer simulation of ErbB signaling . Meeting on Protein Phosphorylation and Cell Signaling, The Salk Institute (San Diego, 2004, June)
  10. Mariko Hatakeyama, Atsushi Suenaga, Takashi Naka, Shuhei Kimura, Makoto Taiji, Akihiko Konagaya: Integration of molecular and network computer simulations for virtual drug assay. Systems Biology: Pathways to Molecular Medicine, Beyond Genome (San Francisco, 2004, June)
  11. Takashi Naka, Mariko Hatakeyama, Naoto Sakamoto, Akihiko Konagaya: Compensation effect of MAPK cascade on formation of phospho-protein gradient. 5th International Conference on Systems Biology (ICSB2004) (Heidelberg, 2004, October)
  12. Mariko Hatakeyama, Atsushi Suenaga, Shuhei Kimura, Takashi Naka, Makoto Taiji, Boris N. Kholodenko, Akihiko Konagaya: Molecular simulation for system modeling. 5th International Conference of Systems Biology (ICSB2004) (Heidelberg, 2004, October)
  13. Mariko Hatakeyama, Shuhei Kimura, Yoshiki Yamaguchi, Kaori Ide, Atsushi Suenaga, Makoto Taiji, Takashi Naka, Akihiko Konagaya: Modeling of intracellular signal transduction and gene expression dynamics of ErbB signaling. International Consortium on Systems Biology of Receptor Tyrosine Kinase Regulatory Networks (RTK Consortium) The first discussion and organizational meeting (Yokohama, 2005, January)
  14. Kaori Ide, Takeshi Nagashima, Yoshiki Yamaguchi, Takashi Naka, Shuhei Kimura, Atsushi Suenaga, Makoto Taiji, Mariko Hatakeyama: Computer simulation analysis of ErbB signaling for understanding of cellular transformation mechanism. FEBS 1st FEBS Advanced Lecture Course - SysBio2005　Systems Biology: From Molecules & Modeling To Cells (Austria, 2005, Feburary)
  15. Mariko Hatakeyama, Yoshiki Yamaguchi, Shuhei Kimura, Takashi Naka, Atsushi Suenaga, Makoto Taiji and Akihiko Konagaya: Dynamic analysis of ErbB signal transduction pathways. Nature Biotechnology Winter Symposia; Signal Transduction in Cancer (Florida, 2005, Feburary)
  16. Takashi Naka, Naoto Sakamoto, Mariko Hatakeyama: Dynamics of MAPK cascade in a double spherical configuration of cell space, 4th European Conference on Computational Biology 2005 (ECCB05), (Madrid, 2005, September)
  17. Yoshimi Naruo, Takeshi Nagashima, Ryoko Nakayama, Yuko Saeki, Takashi Nakakuki, Takashi Naka, Hirosi Tanaka (Ikashika), Shih-Feng Tsai (NHRI), Mariko Okada: Cell-specific control of EGFR signaling activity associated with lung cancer. CBI-KSBSB Joint Cconference (Busan, Korea, 2009 November)
  18. Takashi Naka: Stochastic aspects of cellular signaling dynamics in kinase cascades. The 22nd international conference on genome informatics (GIW2011) (Busan, Korea, 2011 December)
  19. Takashi Naka: The effect of enzyme saturation level and Damkoehler number on cellular signaling speed in kinase cascades. The 23nd international conference on genome informatics (GIW2012) (Tainan, Taiwan, 2012 December)
  20. Takashi Naka: Systematic model construction and simulation analysis for regulatory networks in cellular signal transduction systems. The 25nd international conference on genome informatics (GIW2014) (Odaiba, Japan, 2014 December)
  21. Chinasa Sueyoshi, Takashi Naka: Exhaustive analysis for the effects of network structures and reaction saturation levels on the multi-stability in cellular signaling systems. 5th International Conference on the Theory and Practice of Natural Computing (TPNC2016) (Sendai, Japan, 2016 December)
  22. Takashi Naka: Validity of quasi-steady-state approximation for a Michaelis-Menten-type reaction in regulatory reaction networks. The 20th International Conference on Systems Biology (ICSB2019) (Okinawa, Japan, 2019 November)
  23. Chinasa Sueyoshi, Takashi Naka: Validity of Using the Same Values for the Michaelis Constants on the Stability Analysis in Cellular Signalling Systems, ACSW 2020 (the 2020 Australasian Computer Science Week), (Melbourne, Australasia, 2020 February)

Thesis

  1. Estimation of functional and structural parameters in the chemical transmission process at the neuromuscular junction, Doctoral Program in Engineering, University of Tsukuba Graduate School (1998)