Publications

Refereed Papers

  1. Makoto Komori*, Ken Komiya*(* equyally contributed), Takuma Shirakawa, Takamitsu J. Morikawa and Toru Yoshimura
    “Measurement of microRNA with isothermal DNA amplification on fully automated immunoassay analyzers”
    (Analytical and Bioanalytical Chemistry, 2019, in press)
    # Featured as Paper in Forefront
  2. Ken Komiya, Makoto Komori, Chizuru Noda, Satoshi Kobayashi, Toru Yoshimura and Masayuki Yamamura
    “Leak-free million-fold DNA amplification with locked nucleic acid and targeted hybridization in one pot”
    (Organic and Biomolecular Chemistry, 2019, Vol. 17, Iss. 23, pp. 5708-5713)
    # Featured as the outside front cover
  3. Nobuya Kimoto, Ken Komiya, Kenzo Fujimoto and Satoshi Kobayashi
    “Monotonically controlling right linear grammars with unknown behaviors to output a target string”
    (Theoretical Computer Science, 2019, in press)
  4. John. A. Rose, Ken Komiya and Satoshi Kobayashi
    “Engineering multistate DNA molecules: a tunable thermal band-pass filter”
    (Micro & Nano Letters, 2016, Vol. 11, Iss. 10, pp. 595-601)
  5. John A. Rose and Ken Komiya *nominated for Best Conference Paper Award
    “Analysis and Design of a Single-Molecule DNA Nanodevice for Thermal Band-Pass Filters”
    (Proceedings of the 11th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems (IEEE-NEMS 2016), 2016, (6 pages))
  6. Ken Komiya and Masayuki Yamamura
    “Cascading DNA Generation Reaction for Controlling DNA Nanomachines at a Physiological Temperature”
    (New Generation Computing, 2015, Vol. 33, No. 3, pp. 213-229)
  7. Satoshi Kobayashi, Kazuya Yanagibashi, Kenzo Fujimoto, Ken Komiya and Masami Hagiya *invited
    “Analog DNA Computing Devices Toward the Control of Molecular Robots”
    (Proceedings of Workshop on Self-organization in Swarm of Robots: from Molecular Robots to Mobile Agents (WSSR 2014), 2014, pp. 147-157)
  8. Ryo Hirose, Satoshi Kobayashi and Ken Komiya
    “DNA Logic Circuits with a DNA Polymerase and a Nicking Enzyme”
    (Proceedings of the 2011 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA’11), 2011, pp. 713-719)
  9. 小宮健，ジョン A. ローズ，山村雅幸
    “自律DNA分子計算　‐ in vitro インテリジェンスの構築”
    Ken Komiya, John A. Rose and Masayuki Yamamura
    “Autonomous DNA-Molecule Computing
    —Towards Construction of in vitro Intelligence—”
    （計測自動制御学会論文集, 2010, Vol. 46, No. 11, 700-705）
  10. Ken Komiya, Masayuki Yamamura and John A. Rose
    “Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states”
    (Nucleic Acids Research, 2010, Vol. 38, No. 13, pp. 4539-4546)
  11. Ken Komiya, Masayuki Yamamura and John A. Rose
    “Experimental Validation and Optimization of Signal Dependent Operation in Whiplash PCR”
    (Natural Computing, 2010, Vol. 9, No. 1, pp. 207-218)
  12. Ken Komiya, Masayuki Yamamura and John A. Rose
    “Experimental Validation of Signal Dependent Operation in Whiplash PCR”
    (Lecture Notes in Computer Science, 2009, Vol. 5347, pp. 1-10)
  13. Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga and Masayuki Yamamura
    “A Design and Feasibility Study of Reactions Comprising DNA Molecular Machine that Walks Autonomously by using a Restriction Enzyme”
    (Natural Computing, 2008, Vol. 7, No. 3, pp. 303-315)
  14. Ken Komiya, Noriko Hirayama and Masayuki Yamamura
    “An Interface for a Computing Model Using Methylation to Allow Precise Population Control by Quantitative Monitoring”
    (Lecture Notes in Computer Science, 2008, Vol. 4848, pp. 191-200)
  15. Hiroyuki Sekiguchi, Ken Komiya, Daisuke Kiga and Masayuki Yamamura
    “A realization of DNA molecular machine that walks autonomously by using a restriction enzyme”
    (Lecture Notes in Computer Science, 2008, Vol. 4848, pp. 54-65)
  16. Masayuki Yamamura, Ken Komiya and Noriko Hirayama
    “An Implementation of Aqueous Memory Molecules with Light Responsive DNAs”
    (Proceedings of 2007 IEEE Congress on Evolutionary Computation (CEC2007), 2007, pp. 1843-1848)
  17. Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama and John A. Rose
    “Experimental Validation of the Statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on DNA Hairpin Formation”
    (Lecture Notes in Computer Science, 2006, Vol. 4287, pp. 428-438)
  18. John A. Rose, Ken Komiya, Satsuki Yaegashi and Masami Hagiya
    “Displacement Whiplash PCR: Optimized architecture and experimental validation”
    (Lecture Notes in Computer Science, 2006, Vol. 4287, pp. 393-403)
  19. 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”
    (BioSystems, 2006, vol. 83, pp. 18-25)
  20. Mitsuhiro Kubota, Kazumasa Ohtake, Ken Komiya, Kensaku Sakamoto and Masami Hagiya
    “Branching DNA Machines Based on Transitions of Hairpin Structures”
    (Proceedings of 2003 Congress on Evolutionary Computation (CEC2003), 2003, pp. 2542-2548)
  21. Masami Hagiya, John A. Rose, Ken Komiya and Kensaku Sakamoto *invited
    “Complexity analysis of the SAT engine: DNA algorithms as probablistic algorithms”
    (Theoretical Computer Science, 2002, Vol. 287, pp. 59-71)
  22. Ken Komiya, Kensaku Sakamoto, Hidetaka Gouzu, Shigeyuki Yokoyama, Masanori Arita, Akio Nishikawa and Masami Hagiya
    “Successive State Transitions with I/O Interface by Molecules”
    (Lecture Notes in Computer Science, 2001, Vol. 2054, pp. 17-26)
  23. Masanori Arita, Akio Nishikawa, Masami Hagiya, Ken Komiya, Kensaku Sakamoto, Hidetaka Gouzu and Shigeyuki Yokoyama
    “Improving Sequence Design for DNA Computing”
    (Proceedings of Fifth Genetic and Evolutionary Computation Conference (GECCO2000), 2000, pp. 875-882)
  24. Kensaku Sakamoto, Hidetaka Gouzu, Ken Komiya, Shigeyuki Yokoyama,
    Takashi Yokomori and Masami Hagiya
    “Molecular Computation by DNA Hairpin Formation”
    (Science, 2000, vol. 288, pp. 1223-1226)
  25. Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu,
    Shigeyuki Yokoyama, Shuji Ikeda, Hiroshi Sugiyama and Masami Hagiya
    “State Transitions by Molecules”
    (Biosystems, 1999, vol. 52, pp. 81-91)

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Books

  1. 村田智，浜田省吾，多田隈尚史，野村慎一郎，葛谷明紀，小宮健，川又生吹，中茎隆，角五彰　ほか全２２名（共著），
    “DNA分子デザインのすべて ～国際学生コンテストBIOMOD虎の巻～”
    （（分子ロボティクス研究会 編），情報計算化学生物学会（CBI学会）出版，222頁，2016，ISBN: 978-4-9903708-9-3)
  2. 小宮健，瀧ノ上正浩，田中文昭，浜田省吾，村田智
    “DNAナノエンジニアリング”
    (ナチュラルコンピューティング・シリーズ（萩谷昌己，横森貴　編） 第2巻，近代科学社，216頁，2011，ISBN: 978-4-7649-0402-6)
  3. Masami Hagiya, Satoshi Kobayashi, Ken Komiya, Fumiaki Tanaka, Takashi Yokomori
    “Molecular Computing Machineries – Computing Models and Wet Implementations”
    (in Natural Computing Handbook (G. Rozenberg et al. Eds.), Springer-Verlag, 1700 pages, 2010, ISBN: 978-3-540-92909-3)

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