Publications

Refereed Papers

  1. Yusuke Sato, Ken Komiya, Ibuki Kawamata, Satoshi Murataa and Shin-ichiro M. Nomura
    Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles
    (Chemical Communications, 2019, Vol. 55, Iss. 62, pp. 9084-9087))
    https://doi.org/10.1039/C9CC03277K
    # Featured as the back cover
  2. 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, Vol. 411, Iss. 17, pp. 3789-3800)
    https://doi.org/10.1007/s00216-019-01878-z
    # Featured as Paper in Forefront
  3. 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)
    https://doi.org/10.1039/C9OB00521H
    # Featured as the outside front cover
  4. 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, Vol. 777, pp. 387-408)
    https://doi.org/10.1016/j.tcs.2019.01.009
  5. 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)
    http://dx.doi.org/10.1049/mnl.2016.0345
  6. John A. Rose and Ken Komiya
    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))
    https://doi.org/10.1109/NEMS.2016.7758205
    # Nominated for Best Conference Paper Award
  7. 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)
    https://doi.org/10.1007/s00354-015-0304-5
  8. 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)
    https://doi.org/10.1109/SRDSW.2014.7468414
  9. 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)
  10. 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)
  11. 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)
    https://doi.org/10.1093/nar/gkq250
  12. 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)
    https://doi.org/10.1007/s11047-009-9140-1
  13. 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)
    https://doi.org/10.1007/978-3-642-03076-5_1
  14. 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)
    https://doi.org/10.1007/s11047-008-9077-9
  15. 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)
    https://doi.org/10.1007/978-3-540-77962-9_20
  16. 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)
    https://doi.org/10.1007/978-3-540-77962-9_6
  17. 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)
  18. 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)
    https://doi.org/10.1007/11925903_34
  19. 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)
    https://doi.org/10.1007/11925903_31
  20. 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)
    https://doi.org/10.1016/j.biosystems.2005.07.005
  21. 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)
    https://doi.org/10.1109/CEC.2003.1299408
  22. 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)
    https://doi.org/10.1016/S0304-3975(02)00095-6
  23. 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)
    https://doi.org/10.1007/3-540-44992-2_2
  24. 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)
  25. 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)
    https://doi.org/10.1126/science.288.5469.1223
  26. 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)
    https://doi.org/10.1016/S0303-2647(99)00035-0

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Non-refereed Papers

  1. 池田亮太,小林聡,小宮健
    “Hill 型の融解曲線を持つDNA塩基配列の設計”
    (研究報告バイオ情報学(BIO), Vol. 2019-BIO-59, pp. 1-2, 2019)
  2. 矢光隆太郎,小宮健,藤本健造,小林 聡
    “反応システムの制御によるブール関数の計算”
    (電子情報通信学会技術研究報告, Vol. 118, pp. 9-16, 2018)
  3. 木元達哉,小宮健,藤本健造,小林 聡
    “未知の振る舞いを持つ正則文法とその制御”
    (電子情報通信学会技術研究報告, Vol. 118, pp. 1-8, 2018)
  4. 小宮健,山村雅幸
    “DNA応答型ナノマシンの動作を指定するDNAシグナル生成機構の構築”
    (日本機械学会 第6回マイクロ・ナノ工学シンポジウム講演論文集, 2014年, 21pm2-F4)
  5. 外舘悠仁,小宮健,山村雅幸
    “DNAナノマシンによる歩行動作の温度特性の検証”
    (日本機械学会 第6回マイクロ・ナノ工学シンポジウム講演論文集, 2014年, 221pm3-PM024)
  6. 光成更,井上貴彦,林孝文,河村秀樹,喜屋武竜一,菅谷快斗,張子聡,松川寛,川又生吹,萩谷昌己,小長谷明彦,木賀大介,山村雅幸,小宮健,瀧ノ上正浩
    “マイクロサイズの分子ロボット「DNA繊毛虫」の開発”
    (システム・情報部門 学術講演会 2011 (SSI2011) 講演論文集,2011年,pp. 396-398)
  7. 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”
    (システム・情報部門 学術講演会 2009 (SSI2009) 講演論文集,2009年,pp. 480-485)
  8. 坂本健作,小宮健,横山茂之,萩谷昌己
    “DNA分子の自己会合反応の解析”
    (新しい計算パラダイムシンポジウム2000 論文集, 情報処理学会シンポジウムシリーズ, 2000年, Vol. 2000, No. 16, pp. 115-121)
  9. 萩谷昌己,小宮健,坂本健作
    “SAT Engineの計算量の解析 −確率アルゴリズムとしてのDNAアルゴリズム−”
    (新しい計算パラダイムシンポジウム2000 論文集, 情報処理学会シンポジウムシリーズ, 2000年, Vol. 2000, No. 16, pp. 109-114)

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解説など

解説・翻訳・コラム

  1. 小宮健
    “DNAナノマシン”
    (近代化学, No. 548, pp. 32-35, 2016)
  2. 小宮健 訳
    “ナノサイズの「DNAからくり箱」が患部にお届けします”
    (パリティ, Vol. 28, No. 8, pp. 47-49, 2013)
  3. 小宮健
    “大学生のうちに世界と闘おう!: 国際生体分子デザインコンペテイション BIOMOD”
    (パリティ, Vol. 28, No. 8, pp. 48-49, 2013)
  4. 小宮健パリティ2012年1月号表紙
    “分子ロボット創製に向けた動的DNAナノテクノロジーの展開”
    (パリティ, Vol. 27, No. 1 ※2012年1月号 特集「物理科学,この1年」, pp. 72-74, 2012)
  5. 小宮健日本ロボット学会誌
    “分子計算”
    (日本ロボット学会誌, Vol. 28, No. 10 ※「分子ロボティクス」特集号, pp. 1168-1171, 2010)

学会・領域ニュースレター

  1. 小宮健
    “一本鎖DNAを生成するプログラマブルな等温反応系”
    新学術領域「分子ロボティクス」, No. 18, pp. 11, 2016)
  2. 小宮健
    “分子プログラミング、分子ロボティクスと高感度に核酸を検出する等温指数増幅反応系の構築”
    日本化学会 生体機能関連化学部会, Vol. 30, No. 2, pp. 6-9, 2015)

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著書

  1. 分子ロボティクス研究会(浅沼浩之,遠藤政幸,葛谷明紀,小宮健,小長谷明彦,萩谷昌己,藤本健造,松浦和則 ほか全30名(共著)),
    “分子ロボティクス概論 分子のデザインでシステムを創る”
    ((村田智 編),情報計算化学生物学会(CBI学会)出版,全312頁,2019,ISBN: 978-4-9909076-4-8)
  2. 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)
  3. 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)
  4. 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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特許

  1. 発明者:小宮健, 出願人:東京工業大学
    “標的核酸の検出方法及びキット”
    (特願2010-275948,2010年12月10日基礎出願,
     PCT/JP2011/078717,2011年12月12日国際出願,
     WO2012/077819,2012年6月14日国際公開,
     指定国移行済み)
  2. 他、海外出願 3件

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