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Journals and Writings

Invited Paper

  • Daisuke Kiga and Masayuki Yamamura:
    Synthetic Biology, Tutorial on Programming Natural Systems:
    Part2. Programming Cells, New Generation Computing, Vol.26, No.4, pp.347-364 (2008.04).

International Journals and Writings

  • Akifumi Nishida, Vera Thiel, Mayuko Nakagawa, Shotaro Ayukawa, and Masayuki Yamamura.
    gEffect of light wavelength on hot spring microbial mat biodiversityh
    (PLoS One, 2018 13(1): e0191650, https://doi.org/10.1371/journal.pone.0191650)
  • Yasuda S, Zhou Y, Wang Y, Yamamura M and Wang JY4.
    gA model integrating tonic and antigen-triggered BCR signals to predict the survival of primary B cells.h
    (Scientific Reports, 2017, Vol. 7, No. 1, DOI: 10.1038/s41598-017-13993-x)
  • Ken Komiya and Masayuki Yamamura
    gCascading DNA Generation Reaction for Controlling DNA Nanomachines at a Physiological Temperatureh
    (New Generation Computing, 2015, Vol. 33, No. 3, to appear)
  • Ryoji Sekine, Masayuki Yamamura
    "Design and control of synthetic biological systems," Proceedings in
    Information and Communications Technology, vol. 6, pp. 104-114, 2013
  • Ryoji Sekine, Daisuke Kiga, Masayuki Yamamura,
    "Design strategy for an initial state-independent diversity generator,"
    Chem-Bio Informatics Journal 2012 12: 39-49
  • Ryoji Sekine, Masayuki Yamamura, Shotaro Ayukawa, Kana Ishimatsu, Satoru Akama, Masahiro Takinoue, Masami Hagiya , and Daisuke Kiga:
    Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling,
    Proceedings of the National Academy of Sciences 2011 108:17969-17973
  • Ken Komiya, Masayuki Yamamura and John A. Rose:
    Experimental Validation and Optimization of Signal Dependent Operation in Whiplash PCR,
    Natural Computing, Volume 9, Number 1, 207-218, DOI: 10.1007/s11047-009-9140-1 (2010)
  • Hiromi Arai; Satoru Watanabe; Takanori Kigawa; Masayuki Yamamura
    A new modeling method in feature construction for the HSQC spectra screening problem,
    Bioinformatics 2009 25: 948-953
  • Hiroshi Sekiguchi, Ken Komiya, Daisuke Kiga, Masayuki Yamamura:
    A Realization of DNA Molecular Machine that Walks Autonomously by using a Restriction Enzyme,
    Lecture Notes on Computer Science 4848 (DNA13), pp.54-65 (2008).
  • K. Komiya, N. Hirayama, M. Yamamura,
    An Interface for a Computing Model Using Methylation to Allow Precise Population Control by Quantitative Monitoring,
    Lecture Notes on Computer Science 4848 (DNA13), pp.191-200 (2008).
  • Hiroshi Sekiguchi, Daisuke Kiga, Ken Komiya, Masayuki Yamamura:
    A Design and Feasibility Study of Reactions Comprising DNA Molecular Machine that Walks Autonomously by using a Restriction Enzyme,
    Natural Computing, # DOI: 10.1007/s11047-008-9077-9 (2008).
  • Hiroshi Sekiguchi, Daisuke Kiga, Ken Komiya, Masayuki Yamamura:
    A Design and Feasibility Study of Reactions Comprising DNA Molecular Machine that Walks Autonomously by using a Restriction Enzyme,
    Natural Computing, Vol.7, No.3, pp.303-315 (2008).
  • Ken Komiya, Kensaku Sakamoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Daisuke Kiga, Shigeyuki Yokoyama and Masami Hagiya,
    DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing,
    BioSytems, 83: 18-25, 2006
  • Kenichi Wakabayashi, Masayuki Yamamura,
    A Design for Cellular Evolutionary Computation by using Bacteria,
    Natural Computing, Vol.4, pp.275-292 (2005).
  • Kenichi Wakabayashi, Masayuki Yamamura:
    A design for cellular evolutionary computation by using bacteria, Rozenberg G and Spaink H.P. (eds)
    Natural Computing, (under publication)->2005
  • Atsushi Kajita, Masayuki Yamamura, Yuji Kohara,
    Computer Simulation of the Cellular Arrangement using Physical Model in Early Cleavage of the Nematode Caenorhabditis Elegans,
    Bioinformatics, 19(6):704-716, 2003
  • Masayuki Yamamura, Tom Head, Masami Hagiya,
    Biomolecular Computing - Preface,
    New Generation Computing, 20(2): 215-216, 2002
  • Akio Nishikawa, Masayuki Yamamura, Masami Hagiya,
    DNA computation simulator based on abstract bases,
    Soft Computing, 5(1): 25-44, 2001

Domestic Journals and Writings

  • Shigeo Doi, Masayuki Yamamura,
    BntNetL and its evaluation on a situation of congestion,
    Electronics and Communications in Japan, 85(9):31-41, 2002
  • Hajime Kimura, Masayuki Yamamura, Shigenobu Kobayashi,
    Reinforcement Learning in Partially Observable Markov Decision Processes: A Stochastic Gradient Method,
    Journal of Japanese Society for Artificial Intelligence, 11(5):787-794, 1996
  • Masayuki Yamamura, Kazuteru Miyazaki, Shigenobu Kobayashi,
    A survey on learning for agents,
    Journal of Japanese Society for Artificial Intelligence, 10(5):683-689, 1995