分子プログラミング

2007 Fiscal Year Final Research Report Summary

• Project/Area Number: 14085101
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• Research Institution: The University of Tokyo
• Principal Investigator: 萩谷 昌己 The University of Tokyo, 大学院・情報理工学系研究科, 教授 (30156252)
• Co-Investigator(Kenkyū-buntansha): 有川 節夫 九州大学, 理事(研究職), 教授 (40037221) ; 小林 重信 東京工業大学, 大学院・総合理工学研究科, 教授 (40016697) ; 米澤 明憲 東京大学, 大学院・情報理工学系研究科, 教授 (00133116) ; 佐藤 雅彦 京都大学, 大学院・情報学研究科, 教授 (20027387) ; 小長谷 明彦 独立行政法人理化学研究所, ゲノム科学総合研究センター, プロジェクトディレクター (00301200)
• Project Period (FY): 2002 – 2007
• Keywords: DNAコンピュータ / 生体生命情報学 / 自己組織化 / ナノバイオ / バイオテクノロジー

Research Abstract

本研究領域の目標は,主としてDNA分子によって作られた分子システムのためのシステマティックな設計論を確立することである.本研究領域の研究項目は多岐に渡っており,その研究成果も膨大であるため、本研究領域の主目的である,分子計算のための計算分子と分子反応の設計論および応用に関係する研究成果の中から,領域全体を通して主要なものを取捨選択し簡潔にまとめると,以下のようになる.
1.計算分子(DNA配列)の設計論(1-1)望ましくない構造を作らない配列の設計(1-2)望ましい構造を作る配列の設計(1-3)自在に構造変化する配列の設計(1-4)構造変化の数理モデルと実験的検証
2.分子反応の設計論(2-1)反応の並列化(2-2)反応の精密化(2-3)進化のための反応
3.計算論的ナノテクノロジー応用(3-1)DNAナノ構造の高信頼アセンブリ(3-2)4*4DNAタイルによるバイナリカウンタの実現(3-3)ヘアピンとバルジによる並行計算(3-4)光ライゲーションによる耐熱性DNAナノ構造体の構築
4.合成生物学応用(4-1)in vitro論理演算素子,発振素子の構築(4-2)in vivo論理演算素子の構築(4-3)大腸菌を用いたバクテリアコンピュータの開発(4-4)WetTDGAによるaaRSの基質改変
(1),(2)は基礎的な設計技術に関する理論および実験であり、主として研究期間の前半の成果である.特に(1)の配列設計は, DNAを計算分子とするすべての分子計算に共通した基礎的成果である。(3),(4)は,分子プログラミングの次世代の展開として重要視されている計算論的ナノテクノロジーおよび合成生物学への応用研究であり,研究期間の後半の成果である.

Research Products

• [Journal Article] メタ戦略アルゴリズムに対するロバストな並列化 (2008)
  • Author(s): 石橋正裕, 小野廣隆, 朝廣雄一, 山下雅史
  • Journal Title: 数理解析研究所講究録 1325 Pages: 1-7
  • Peer Reviewed
• [Journal Article] Dynamics of an Abstract Chemical System with few molecular (2007)
  • Author(s): Y. Suzuki
  • Journal Title: Proc. of the International Symposium on Artificial Life and Robotics 1 Pages: OS13-3
  • Peer Reviewed
• [Journal Article] An Investigation Of The Brusselator On The Mesoscopic Scale (2007)
  • Author(s): Y. Suzuki
  • Journal Title: International Journal of Parallel, Emergent and Distributed Algorithms 22 Pages: 91-102
  • Peer Reviewed
• [Journal Article] 純粋λ計算の階層グラフ書換えへのエンコーディング (2007)
  • Author(s): 上田和紀
  • Journal Title: 第9回プログラミングおよびプログラミング言語ワークショップ(PPL2007) 1 Pages: 221-232
  • Peer Reviewed
• [Journal Article] Coupled Equilibrium Model of Hybridization Error for the DNA Microarray and Tag-Antitag Systems (2007)
  • Author(s): John A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama
  • Journal Title: IEEE Transactions on Nanobioscience Vol. 6, No. 1 Pages: 18-27
  • Peer Reviewed
• [Journal Article] Site-specific incorporation of non-natural amino acids into proteins in the mammalian cells with an expanded genetic code (2007)
  • Author(s): Nobumasa Hino, Akiko Hayashi, Kensaku Sakamoto, Shigeyuki Yokoyama
  • Journal Title: Nature protocols 1 Pages: 2957-2962
  • Peer Reviewed
• [Journal Article] Site-specific functionalization of proteins by organopalladium reactions (2007)
  • Author(s): Kodama, K., Fukuzawa, S., Nakayama, H., Sakamoto, K., Kigawa, T., Yabuki, T., Matsuda, N., Shirouzu, M., Takio, K., Yokoyama, S., Tachibana, K.
  • Journal Title: Chembiochem 8 Pages: 232-238
  • Peer Reviewed
• [Journal Article] Multi-fueled Approach to DNA Nano-robotics (2007)
  • Author(s): A. Nishikawa, S. Yaegashi, K. Ohtake, M. Hagiya
  • Journal Title: DNA13, Preliminary Proceedings 1 Pages: 162-171
  • Peer Reviewed
• [Journal Article] A Coupled Equilibrium Model for Hybridization Error Estimation for the DNA Microarray and Tag-Antitag Systems (2007)
  • Author(s): J. A. Rose, R. J. Deaton, M. Hagiya, A. Suyama
  • Journal Title: IEEE Transactions in NanoBioscience, Special Issueon Computational NanoBioscience 1 Pages: 1-2
  • Peer Reviewed
• [Journal Article] Unravel four hairpins! (2007)
  • Author(s): Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Satsuki Yaegashi, Masami Hagiya
  • Journal Title: Natural Computing Vol. 7, No. 2 Pages: 287-298
  • Peer Reviewed
• [Journal Article] DNA Memorty with 16.8M addresses (2007)
  • Author(s): Masahito Yamamoto, Satoshi Kashiwamura, Azuma Ohuchi
  • Journal Title: Preliminary Proceedings of the 13th International Meeting on DNA Computing 1 Pages: 19-29
  • Peer Reviewed
• [Journal Article] Combining Randomness and a High-capacity DNA Moemry (2007)
  • Author(s): Atsushi Kameda, Satoshi Kashiwamura, Masahito Yamamoto, Azuma Ohuchi, Masami Hagiya
  • Journal Title: Preliminary Proceedings of the 13th International Meeting on DNA Computing 1 Pages: 261-269
  • Peer Reviewed
• [Journal Article] Sequence Design Support System for 4×4 DNA Tiles (2007)
  • Author(s): Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Azuma Ohuchi
  • Journal Title: Preliminary Proceedings of the 13th International Meeting on DNA Computing 1 Pages: 270-278
  • Peer Reviewed
• [Journal Article] 分子計算のための一点から開始される探索法 (2007)
  • Author(s): 染谷博司, 山村雅幸, 坂本健作
  • Journal Title: 人工知能学会誌(J-STAGE) 22・4(採録)
  • Peer Reviewed
• [Journal Article] Promising Search Regions of Crossover Operators for Function Optimization (2007)
  • Author(s): Hiroshi Someya
  • Journal Title: Proc. IEA/AIE 2007 1 Pages: 434-443
  • Peer Reviewed
• [Journal Article] Selection-by-function : efficient enrichment of cathepsin E inhibitors froma DNA library (2007)
  • Author(s): Naimuddin M, Kitamura K., Kinoshita Y, Honda-Takahashi, Y., Murakami, M., Ito, M., Yamamoto, K., Hanada, K., Husimi, Y., Nishigaki, K.
  • Journal Title: J. Mol. Recognition, published online vol. 20, no1 Pages: 58-68
  • Peer Reviewed
• [Journal Article] Experimental Rugged Fitness Landscape in Protein Seguence Space (2007)
  • Author(s): Hayashi, S., Aita, T., Toyota, H., Husimi, Y., Urabe, I., Yomo, T.
  • Journal Title: PLoS ONE 1 Pages: 96
  • Peer Reviewed
• [Journal Article] Extracting characteristic properties of fitness landscape from in vitro evolution : A case study on infectivity of fd phage to E. coli (2007)
  • Author(s): Aita, T., Hayashi, S., Toyota, H., Husimi, Y., Urabe, I, Yomo, T.
  • Journal Title: J. Theor. Biol. 246 (3) Pages: 538-550
  • Peer Reviewed
• [Journal Article] Numerical study of Thou less-Anderson-Palmer metastable states in three-body Ising spin glasses (2007)
  • Author(s): Y. Tonosaki, K. Takeda, Y. Kabashima
  • Journal Title: Phys. Rev. B 75 Pages: 94405-94411
  • Peer Reviewed
• [Journal Article] Spiking Neural P systems (2006)
  • Author(s): M. Ionescue, G. Paun, T. Yokomori
  • Journal Title: Fundamenta Informaticae 71 Pages: 279-308
  • Peer Reviewed
• [Journal Article] Probabilistic Inference in Test Tube and Its Application to Gene Expression Profiles (2006)
  • Author(s): Y. Sakakibara, T. Yokomori, S. Kobayashi, A. Suyama
  • Journal Title: Formal Models, Languages And Applications (edited by Subramanian et al. ), World Scientific Pub. 1 Pages: 304-319
  • Peer Reviewed
• [Journal Article] An Attempt to Analyze the Dynamics of Abstract Rewriting Systems on Multisets (2006)
  • Author(s): Y. Suzuki
  • Journal Title: Pre-proceedings of Membrane Computing, International Workshop 1 Pages: 501-506
  • Peer Reviewed
• [Journal Article] 階層グラフ書き換え言語LMNtal処理系とその応用例 (2006)
  • Author(s): 乾敦行, 原耕司, 水野謙, 上田和紀
  • Journal Title: 第8回プログラミングおよびプログラミング言語ワークショップ(PPL2006) 1 Pages: 119-133
  • Peer Reviewed
• [Journal Article] 分散プロセス計算のLMNtalへのエンコーディング (2006)
  • Author(s): 上田和紀
  • Journal Title: 日本ソフトウェア科学会第23回大会論文集 1 Pages: 1A-4
  • Peer Reviewed
• [Journal Article] LMNtal as a Unifying Declarative Language : Live Demonstration (2006)
  • Author(s): Kazunori Ueda, Norio Kato, Koji Hara, Ken Mizuno
  • Journal Title: Proc. 22nd Int. Conf. on Logic Programming (ICLP'06), LNCS, Springer-Verlag 4079 Pages: 457-458
  • Peer Reviewed
• [Journal Article] Constraint-Based Concurrency and Beyond (2006)
  • Author(s): Kazunori Ueda
  • Journal Title: Electronic Notes in Theoretical Computer Science 162 Pages: 327-331
  • Peer Reviewed
• [Journal Article] LMNtal as a Unifying Declarative Language (2006)
  • Author(s): Kazunori Ueda, Norio Kato, Koji Hara, Ken Mizuno
  • Journal Title: Proc. Third Workshop on Constraint Handling Rules (CHR2006) 1 Pages: 1-15
  • Peer Reviewed
• [Journal Article] Logic Programming and Concurrency : a Personal Perspective (2006)
  • Author(s): Kazunori Ueda
  • Journal Title: The ALP Newsletter 19(オンライン出版)
  • Peer Reviewed
• [Journal Article] A Probabilistic Model of DNA Conformational Change (2006)
  • Author(s): M. Shiozaki, H. Ono, K. Sadakane, M. Yamashita
  • Journal Title: Revised Selected Papers of the 12th International Meeting on DNA Computing (DNA12, LNCS) 4287 Pages: 274-285
  • Peer Reviewed
• [Journal Article] DNA Sequence Design by Dynamic Neighborhood Searches (2006)
  • Author(s): S. Kawashimo, H. Ono, K. Sadakane, M. Yamashita
  • Journal Title: Revised Selected Papers of the 12th International Meeting on DNA Computing (DNA12, LNCS) 4287 Pages: 157-171
  • Peer Reviewed
• [Journal Article] 局所探索法に基づくDNA配列設計手法 (2006)
  • Author(s): 川下優, 小野廣隆, 定兼邦彦, 山下雅史
  • Journal Title: 冬のLAシンポジウム予稿(京都大学数理解析研究所講究録) 1 Pages: 250-257
  • Peer Reviewed
• [Journal Article] サイズ3の最小ブロック転送問題の近似困難性 (2006)
  • Author(s): 朝廣雄一, 古川哲也, 池上佳一, 宮野英次
  • Journal Title: 電気関係学会九州支部連合大会, 予稿集(CDROM) 1 Pages: 343
  • Peer Reviewed
• [Journal Article] Multiple points of tilings associated with Pisot numeration systems (2006)
  • Author(s): Taizo Sadahiro
  • Journal Title: Theoretical Computer Science 359 Pages: 133-147
  • Peer Reviewed
• [Journal Article] The number of orbits of periodic box-ball systems (2006)
  • Author(s): A. Mikoda, S. Inokuchi, Y. Mizoguchi, M. Fujio
  • Journal Title: Lecture Notes in Computer Science 4135 Pages: 181-194
  • Peer Reviewed
• [Journal Article] On-Line Polygon Search by a Seven-State Boundary 1-Searcher (2006)
  • Author(s): T. Kameda, M. Yamashita, I. Suzuki
  • Journal Title: IEEE Transactions on Robotics 22(3) Pages: 446-460
  • Peer Reviewed
• [Journal Article] A Randomized l-Latent, Time-Adaptive and Safe Self-Stabilizing Mutual Exelusion Protocol (2006)
  • Author(s): J. Kiniwa, M. Yamashita
  • Journal Title: Parallel Processing Letters 16(1) Pages: 53-61
  • Peer Reviewed
• [Journal Article] Nogood-based Asynchronous Distributed Optimization (ADOPT-ng) (2006)
  • Author(s): Marius C. Silaghi, Makoto Yokoo
  • Journal Title: Proc. of the 5th International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS-2006) 1 Pages: 1389-1396
  • Peer Reviewed
• [Journal Article] Multiply constrained distributed constraint optimization (2006)
  • Author(s): Emma Bowring, Milind Tambe, Makoto Yokoo
  • Journal Title: Proc. of the 5th International Joint Conference on Autonomous Agents and Multiagent Systems(AAMAS-2006) 1 Pages: 1413-1420
  • Peer Reviewed
• [Journal Article] Winning back the cup for distributed POMDPs : Planning over continuous belief spaces (2006)
  • Author(s): Pradeep Varakantham, Ranjit Nair, Milind Tambe, Makoto Yokoo
  • Journal Title: Proceedings of the Fifth International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS-2006) 1 Pages: 289-296
  • Peer Reviewed
• [Journal Article] A Fault-Tolerant Content Addressable Network (2006)
  • Author(s): D. Takemoto, S. Tagashira, S. Fujita
  • Journal Title: IE ICE Trans. Inf. & Syst. E89-D(6) Pages: 1923-1930
  • Peer Reviewed
• [Journal Article] A Localization Scheme for Sensor Networks Based on Wireless Communication with Anchor Groups (2006)
  • Author(s): H. Ochi, S. Tagashira, S. Fujita
  • Journal Title: IEICE Trans. Inf. & Syst. E89-D (5) Pages: 1614-1621
  • Peer Reviewed
• [Journal Article] A Generic Solver based on Functional Parallelism for Solving Conmbinatorial Optimization Problems (2006)
  • Author(s): S. Tagashira, M. Mito, S. Fujita
  • Journal Title: IEICE Trans. Inf. & Syst. E89-D(6) Pages: 1940-1947
  • Peer Reviewed
• [Journal Article] 分散ネットワーク上の故障診断問題について (2006)
  • Author(s): 藤田聡
  • Journal Title: 電子情報通信学会論文誌A J89-A(6) Pages: 430-437
  • Peer Reviewed
• [Journal Article] A Local Search Based Barrier Height Estimation Algorithm for DNA Moleeular Transitions (2006)
  • Author(s): T. Takeda, H. Ono, K. Sadakane, M. Yamashita
  • Journal Title: DNA11, Lecture Notes in Computer Science 3892 Pages: 359-370
  • Peer Reviewed
• [Journal Article] 隠れマルコフモデルを用いたDNA配列設計 (2006)
  • Author(s): 前村一哉, 小野廣隆, 定兼邦彦, 山下雅史
  • Journal Title: 火の国情報シンポジウム2006 1 (予稿集, CD-ROM) Pages: 1-13
  • Peer Reviewed
• [Journal Article] Unravel Four Hairpins (2006)
  • Author(s): A. Kemada, M. Yamamoto, A. Ohuchi, S. Yaegashi, M. Hagiya
  • Journal Title: DNA12, Preliminary Proceedings 1 Pages: 65-74
  • Peer Reviewed
• [Journal Article] Towards Robust DNA Logic Gates (2006)
  • Author(s): Masami Hagiya, Satsuki Yaegashi
  • Journal Title: DNA12, Preliminary Proceedings 1 Pages: 413
  • Peer Reviewed
• [Journal Article] Azobenzene-tethered T7 promoter for Efficient Photoregulation of Transcription (2006)
  • Author(s): M. Liu, H. Asanuma, M. Komiyama
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 1009-1015
  • Peer Reviewed
• [Journal Article] Insertion of Two Pyrene Moieties to Oligodeoxyribonucleotides for the Efficient Detection of Insertion/Deletion Polymorphisms (2006)
  • Author(s): H. Kashida, H. Asanuma, M. Komiyama
  • Journal Title: Chem. Commun. 1 Pages: 2768-2770
  • Peer Reviewed
• [Journal Article] Exciplex Formation between Pyrene and N, N-Dimethylaniline in DNA for the Detection of One-base Deletion (2006)
  • Author(s): H. Kashida, M. Komiyama, H. Asanuma
  • Journal Title: Chem. Lett. 35(8) Pages: 934-935
  • Peer Reviewed
• [Journal Article] Enhancement of RNA cleavage activity of 10-23 DNAzyme by covalently introduced intercalator (2006)
  • Author(s): H. Asanuma, H. Hayashi, J. Zhao, X. Liang, A. Yamazawa, T. Kuramochi, D. Matsunaga, Y. Aiba, H. Kashida, M. Komiyama
  • Journal Title: Chem. Commun. 1 Pages: 5062-5064
  • Peer Reviewed
• [Journal Article] Incorporation of methyl group on azobenzene for the effective photo-regulation of hybridization and suppression of thermal isomerization (2006)
  • Author(s): H. Nishioka, H. Kashida, M. Komiyama, X. Liang, H. Asanuma
  • Journal Title: Nucleic Acids Res. Supple. 50 50 Pages: 85-86
  • Peer Reviewed
• [Journal Article] Activation of DNA enzyme 10-23 by tethering an intercalator to its backbone (2006)
  • Author(s): H. Hayashi, X. Liang, J. Zhao, M. Komiyama, H. Asanuma
  • Journal Title: Nucleic Acids Res. Supple. 50 50 Pages: 167-168
  • Peer Reviewed
• [Journal Article] DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing (2006)
  • Author(s): Ken Komiya, Kensaku Sakamoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Daisuke Kiga, Shigeyuki Yokoyama, Masami Hagiya
  • Journal Title: BioSysterns Vol. 83, No. 1 Pages: 18-25
  • Peer Reviewed
• [Journal Article] Experimental Validation of the statistical Thermodynamic Model for Prediction of the Behavior of Autonomous Molecular Computers Based on Hairpin Formation (2006)
  • Author(s): Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama, John A. Rose
  • Journal Title: DNA12, Preliminary Proceedings 1 Pages: 382-392
  • Peer Reviewed
• [Journal Article] Displacement Whiplash PCR : Optimized architecture and experimental validation (2006)
  • Author(s): John A. Rose, Ken Komiya, Satsuki Yaegashi, Masami Hagiya
  • Journal Title: DNA12, Preliminary Proceedings 1 Pages: 393-403
  • Peer Reviewed
• [Journal Article] An autonomous molecular computing system in cell-sized liposome (2006)
  • Author(s): K. Shohda, D. Kiga, M. Takinoue, K. Yoshiyuki, T. Sugawara, A. Suyama
  • Journal Title: Proceedings of NanoBio-Tokyo 2006 1 Pages: 357-358
  • Peer Reviewed
• [Journal Article] Bionano clock based on an autonomous biomolecular computing system (2006)
  • Author(s): M. Takinoue, D. Kiga, K. Shohda, A. Suyama
  • Journal Title: Proceedings of NanoBio-Tokyo 2006 1 Pages: 361-362
  • Peer Reviewed
• [Journal Article] Turing machine using RRACS (2006)
  • Author(s): Akira Suyama
  • Journal Title: Preliminary proceedings of DNA 12 1 Pages: 422
  • Peer Reviewed
• [Journal Article] Autonomous DNA computer in small vesicle (2006)
  • Author(s): D. Kiga, K. Shoda, M. Takinoue, A. Suyama
  • Journal Title: Preliminary proceedings of DNA 12 1 Pages: 420
  • Peer Reviewed
• [Journal Article] A numerical analysis of an autonomous molecular computing system (2006)
  • Author(s): Masahiro Takinoue, Daisuke Kiga, Akira Suyama
  • Journal Title: RTRACS. Preliminary proceedings of DNA 12 1 Pages: 411
  • Peer Reviewed
• [Journal Article] DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing (2006)
  • Author(s): K. Komiya, K. Sakamoto, A. Kameda, M. Yamamoto, A. Ohuchi, D. Kiga, S. Yokoyama, M. Hagiya
  • Journal Title: BioSystems Vol. 83, No. 1 Pages: 18-25
  • Peer Reviewed
• [Journal Article] Cation-π interaction in triterpene biosynthesis revealed by incorporating unnatural amino acids into the catalytic site of a squalene cyclase (2006)
  • Author(s): N. Morikubo, Y. Fukuda, K. Ohtake, N. Shinya, D. Kiga, K. Sakamoto, M. Asanuma, H. Hirota, S. Yokoyama, T. Hoshino
  • Journal Title: J. Am. Chem. Soc. 128 Pages: 13184-13194
  • Peer Reviewed
• [Journal Article] A New Protein Engineering Approach Combining Chemistry and Biology, Part I ; Site-Specific Incorporation of 4-Iodo-L-phenylalanine in vitro by Using Misacylated Suppressor tRNA (Phe) (2006)
  • Author(s): Kodama K, Fukuzawa S, Sakamoto K, Nakayama H, Kigawa T, Yabuki T, Matsuda N, Shirouzu M, Takio K, Tachibana K, Yokoyama s.
  • Journal Title: Chembiochem 7 Pages: 1577-1581
  • Peer Reviewed
• [Journal Article] Translation of' rare' Codons in a Cell-free Protein Synthesis System from Escherichia coli (2006)
  • Author(s): Chumpolkulwong N, Sakamoto K, Hayashi A, Iraha F, Shinya N, Matsuda N, Kiga D, Urushibata A, Shirouzu M, Oki K, Kigawa T, Yokoyama S.
  • Journal Title: J struct Funct Genomics 7 Pages: 31-36
  • Peer Reviewed
• [Journal Article] Microfluidic Device for Droplet-based DNA-PNA Hybridization and Separation (2006)
  • Author(s): S Kaneda, K. Somei, K. Ono, T. Yamamoto, T. Fujii
  • Journal Title: Proc. μTAS2006 2 Pages: 1151-1153
  • Peer Reviewed
• [Journal Article] 微量液滴ハンドリングデバイスによる反応・分析操作 (2006)
  • Author(s): 金田祥平, 染井康太郎, 小野航一, 山本貴富喜, 藤井輝夫
  • Journal Title: 第13回化学とマイクロ・ナノシステム研究会予稿集 PC-039 Pages: 1-5
  • Peer Reviewed
• [Journal Article] マイクロ流体デバイスによるバイオ分析 (2006)
  • Author(s): 金田祥平, 藤井輝夫
  • Journal Title: 精密工学会誌 72 Pages: 937-976
  • Peer Reviewed
• [Journal Article] Development of DNA Relational Database and Data Manipulation Experiments (2006)
  • Author(s): Masahito Yamamoto, Yutaka Kita, Satoshi Kashiwamura, Atsushi Kameda, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA12), Lecture Notes in ComputerScience 4287 Pages: 418-427
  • Peer Reviewed
• [Journal Article] Sequence Design for stable DNA Tiles (2006)
  • Author(s): Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA12), Lecture Notes in Computer Science 4287 Pages: 172-181
  • Peer Reviewed
• [Journal Article] Specificity of Hybridization between DNA Sequences Based on Free Energy (2006)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA11), Lecture Notes in Computer Science 3892 Pages: 371-379
  • Peer Reviewed
• [Journal Article] DNAタイル構造のための塩基配列設計支援システムの構築 (2006)
  • Author(s): 飯村直記, 山本雅人, 田中文昭, 大内東
  • Journal Title: 情報処理北海道シンポジウム2006 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] DNAを用いたタイル構造における接着結合部の塩基配列設計 (2006)
  • Author(s): 飯村直記, 山本雅人, 田中文昭, 大内東
  • Journal Title: 第5回情報科学技術フォーラム(FIT2006) 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] stability evaluation method of DNA tile structure (2006)
  • Author(s): Naoki Iimura, Masahito Yamamoto, Fumiaki Tanaka, Atsushi Kameda, Azuma Ohuchi
  • Journal Title: The Eleventh International Symposium on Artificial Life and Robotics (AROB11th) 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Data Manipulation of DNA Relational Database (2006)
  • Author(s): Yutaka Kita, Satoshi Kasbiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: The Eleventh International Symposium on Artificial Life and Robotics (AROB 11th'06) 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] DNAを用いた微小粒子のナノ位置決め (2006)
  • Author(s): 初澤毅, 小山内寛, 柳田保子
  • Journal Title: 精密工学会誌 Vol. 72, No. 11 Pages: 1407-1410
  • Peer Reviewed
• [Journal Article] A Microfluidic Device for DNA Tile Self-Assembly (2006)
  • Author(s): K. Somei, S. Kaneda, T. Fujii, S. Murata
  • Journal Title: 11th International Workshop on DNA Computing, Revised Selected Papers (DNA11) LNCS 3892 Pages: 325-335
  • Peer Reviewed
• [Journal Article] Hybridization in a Microfluidic Device for DNA Tile Self-Assembly (2006)
  • Author(s): K. Somei, S. Kaneda, T. Fujii, S. Murata
  • Journal Title: Proc. Foundations of Nanoscience, Self-Assembled Architectures and Devices (FNAN02006) 1 Pages: 148-152
  • Peer Reviewed
• [Journal Article] Reversible Signal Amplification by Linear Hybridization Chain Reaction (2006)
  • Author(s): Tomohiro Suzuki, Ken Komiya, Satoshi Murata
  • Journal Title: Preliminary Proceedings of 12^<th> International Meeting on DNA Computing (DNA11) 1 Pages: 418
  • Peer Reviewed
• [Journal Article] Self-Assembling Systems (2006)
  • Author(s): Satoshi Murata
  • Journal Title: 9^<th> Japanese-American Kavli Frontiers of Science Symposium, National Academy of Sciences (JAFoS) 1(CD-ROM)
  • Peer Reviewed
• [Journal Article] Computation by DNA Molecule (2006)
  • Author(s): Satoshi Murata
  • Journal Title: SCIS&ISIS 2006 (invited session) 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Photochemical Synthesis of R-Shaped DNA toward in vitro DNA Recombination and Processing (2006)
  • Author(s): Masayuki Ogino, Kenzo Fujimoto
  • Journal Title: Angewandte Chemie Int. Ed. 45 Pages: 7223-7225
  • Peer Reviewed
• [Journal Article] SNP Genotyping using Photochemical Ligation (2006)
  • Author(s): Shinzi Ogasawara, Kenzo Fujimoto
  • Journal Title: Angewandte Chemie Int. Ed. 45 Pages: 4512-4515
  • Peer Reviewed
• [Journal Article] Highly selective and sensitive template-directed photoligation of DNA via 5-carbamoylvinyl-2-deoxyuridine (2006)
  • Author(s): Yoshinaga Yoshimura, Daisuke Okamura, Masayuki Ogino, Kenzo Fujimoto
  • Journal Title: Org. Lett. 8(22) Pages: 5049-5052
  • Peer Reviewed
• [Journal Article] Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside (2006)
  • Author(s): Yoshinaga Yoshimura, Kenzo Fujimoto
  • Journal Title: Chem. Lett. 35(4) Pages: 386-389
  • Peer Reviewed
• [Journal Article] Template-directed DNA photoligation in rapid and selective detection of RNA point mutations (2006)
  • Author(s): Yoshinaga Yoshimura, Yuuki Noguchi, Kenzo Fujimoto
  • Journal Title: ChemBioChem 7(4) Pages: 598-601
  • Peer Reviewed
• [Journal Article] Biofilm formation by a Bacillus subtilis strain that producesgamma-polyglutamate (2006)
  • Author(s): Morikawa, M., Kagihiro, S., Haruki, M., Takano, K., Branda, S., Kolter, R., Kanaya, S.
  • Journal Title: Microbiology 152 Pages: 2801-2807
  • Peer Reviewed
• [Journal Article] A Hypertheriophilic Protein Acquires Function at the Cost of Stability (2006)
  • Author(s): Mukaiyama, A., Haruki, M,. Ota, M., Koga, Y., Takano, K., Kanay, a S.
  • Journal Title: Biochemistry 45 Pages: 12673-12679
  • Peer Reviewed
• [Journal Article] Modified substrate specificity of pyrroloquinoline quinone glucose dehydrogenase by biased mutation-assembling with optimized amino acid substitution (2006)
  • Author(s): Hamamatsu, N., Suzumura, A., Nomiya, Y., Sato, M., Aita, T., Nakajima, M., Husimi, Y., Shibanaka, Y.
  • Journal Title: Applied Microbiology and Biotechnology 73 Pages: 607-617
  • Peer Reviewed
• [Journal Article] Accumulation of ami no acid substitutions for thermostabilization of lactate oxidase with less deterioration of catalytic activity (2006)
  • Author(s): Hamamatsu, N., Nomiya, Y., Aita, T., Nakajima, M., Husimi, Y., Shibanaka, Y
  • Journal Title: Protein Eng. Design and Selection 19 Pages: 483-489
  • Peer Reviewed
• [Journal Article] Solid-phase translation and RNA-protein fusion : a novel approach for folding Quality control and direct immobilization of protein using anchored mRNA (2006)
  • Author(s): Biyani, M., Husimi, Y., Nemoto, N.
  • Journal Title: Nucleic Acids Res. Advanced publication online 1 Pages: On line
  • Peer Reviewed
• [Journal Article] 実験室内分子進化過程の熱力学的および情報論的解釈 (2006)
  • Author(s): 相田拓洋, 伏見譲
  • Journal Title: 生物物理 46 Pages: 137-143
  • Peer Reviewed
• [Journal Article] Analysis of CDMA systems that are characterized by eigenvalue spectrum (2006)
  • Author(s): K. Takeda, S. Uda, Y. Kabashima
  • Journal Title: Europhysics Letters 76 Pages: 1193-1199
  • Peer Reviewed
• [Journal Article] Tutorial on Brain-Inspired Computing Part 5 : statistical Mechanics of Communication and Computation (2006)
  • Author(s): Y. Kabashima
  • Journal Title: New Generation Computing 24 Pages: 403-420
  • Peer Reviewed
• [Journal Article] Survey propagation for the cascading Sourlas code (2006)
  • Author(s): JPL. Hatchet, Y. Kabashima
  • Journal Title: JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL 39・34 Pages: 10659-10672
  • Peer Reviewed
• [Journal Article] 有望探索領域を重点探索する交叉と形質遺伝性を考慮した世代交代による実数値GA (2006)
  • Author(s): 染谷博司
  • Journal Title: 計測自動制御学会システム・情報部門学術講演会2006講演論文集(計測自動制御学会システム・情報部門奨励賞) Nov Pages: 3-8
  • Peer Reviewed
• [Journal Article] Stabilization of E. coli Ribonuclease HI by the 'stabilityprofile of mutant protein' (SPMP)-inspired random and non-random mutagenesis (2006)
  • Author(s): Haruki, M., Saito, Y., Ota, M., Nishikawa, K., Kanaya, S.
  • Journal Title: J. Biotechnol. 1 Pages: 512-522
  • Peer Reviewed
• [Journal Article] Gene cloning and in vivo characterization of a dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans (2006)
  • Author(s): Hirano, S., Haruki, M., Takano, K., Imanaka, T., Morikawa, M., Kanaya, S.
  • Journal Title: Appl Microbiol Biotechnol 69 Pages: 672-681
  • Peer Reviewed
• [Journal Article] Linearizer and Doubler : Two mappings to unify melocular computing models based on DNA complementarity (2005)
  • Author(s): Kaoru Onodera, Takashi Yokomori
  • Journal Title: Proceedings of 11th International Meeting on DNA Based Computers 1 Pages: 139-150
  • Peer Reviewed
• [Journal Article] Efficient algorithm for testing structure freeness of finite set of biomolecular sequences (2005)
  • Author(s): Atsushi Kijima, Satoshi Kobayashi
  • Journal Title: Proceedings of 11th International Meeting on DNA BasedComputers 1 Pages: 278-288
  • Peer Reviewed
• [Journal Article] Development of an in vivo computer based on Escherichia coli (2005)
  • Author(s): H. Nakagawa, K. Sakamoto, Y. Sakakibara
  • Journal Title: Proceedings of 11th International Meeting on DNA Based Computers 1 Pages: 68-77
  • Peer Reviewed
• [Journal Article] Intensive in vitro experiments of implementing and executing finite automata in test tube (2005)
  • Author(s): J. Kuramochi, Y. Sakakibara
  • Journal Title: Proceedings of 11th International Meeting on DNA Based Computers 1 Pages: 59-67
  • Peer Reviewed
• [Journal Article] Modeling p53 signaling pathways by using Multiset Processing (2005)
  • Author(s): Y. Suzuki, H. Tanaka
  • Journal Title: Applications of Membrane Computing 1 Pages: 203-214
  • Peer Reviewed
• [Journal Article] LMNtal : a language model with links and membranes. (2005)
  • Author(s): K. Ueda, N. Kato
  • Journal Title: Proc. Fifth Int. Workshop on Membrane Computing (WMC2004), LNCS, Springer-Verlag 3365 Pages: 110-125
  • Peer Reviewed
• [Journal Article] Constraint-Based Concurrency and Beyond. (2005)
  • Author(s): K. Ueda
  • Journal Title: Proc. Workshop on Algebraic Process Calculi, The First Twenty Years (PA'05), BRICS Notes Series, NS-05-3 1 Pages: 227-230
  • Peer Reviewed
• [Journal Article] LMNtal処理系におけるグラフ構造の操作機能の設計と実装 (2005)
  • Author(s): 工藤晋太郎, 加藤紀夫, 上田和紀
  • Journal Title: 情報科学技術レターズ LA-003 Pages: 9-12
  • Peer Reviewed
• [Journal Article] LMNtalコンパイラにおける並び替えとグループ化を用いた命令列の最適化 (2005)
  • Author(s): 櫻井健, 加藤紀夫, 水野謙, 上田和紀
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005) 1 Pages: 33-36
  • Peer Reviewed
• [Journal Article] 階層グラフ書換え言語LMNtal処理系における非同期実行の実現 (2005)
  • Author(s): 水野謙, 加藤紀夫, 原耕司, 上田和紀
  • Journal Title: 日本ソフトウェア科学会第22回大会講演論文集 1 Pages: 213-221
  • Peer Reviewed
• [Journal Article] Modeling DNA Conformation Change and Theoretical Analysis on the Reaction Rate (2005)
  • Author(s): M. Shiozaki, H. Ono, R. Sadakane, M. Yamashita
  • Journal Title: Preproceedings of the 11th International Meeting on DNA Computing, DNA11 1 Pages: 408
  • Peer Reviewed
• [Journal Article] Simple Greedy Methods for DNA Word Design (2005)
  • Author(s): Y. Asahiro
  • Journal Title: Proc. 9th World Multi-Conference on Systemics, Cybernetics and Informatics III Pages: 186-191
  • Peer Reviewed
• [Journal Article] On Linkage Identification in EC for Solving Combinatorial Optimization Problems (2005)
  • Author(s): S. Umezane, S. Fujita
  • Journal Title: Proc. IEEE SMC Vol. 4(CD-ROM) Pages: 3071-3076
  • Peer Reviewed
• [Journal Article] Circuit Switched Broadcastings and Digit Tilings on Torus Networks (2005)
  • Author(s): R. Okazaki, H. Ono, T. Sadahiro, M. Yamashita
  • Journal Title: Proceedings of 4th Japanese-Hungarian Sympothium on Discrete Mathematics and Its Applications 1 Pages: 288-295
  • Peer Reviewed
• [Journal Article] Tagged Choice Graph Transformations (Abstract) (2005)
  • Author(s): Y. Mizoguchi, W. Kahl
  • Journal Title: Proc. Of the 11th International Meeting on DNA computing 1 Pages: 405
  • Peer Reviewed
• [Journal Article] Transversal Merge Operation : A Nondominated Coterie Construction Method for Distributed Mutual Exclusion (2005)
  • Author(s): T. Harada, M. Yamashita
  • Journal Title: IEEE Transactions on Parallel and Distributed Systems 16-2 Pages: 183-192
  • Peer Reviewed
• [Journal Article] An Asynchronous Complete Method for Distributed Constraint Optimization (2005)
  • Author(s): Pragnesh Jay Modi, Wei-Min Shen, Milind Tambe, Makoto Yokoo
  • Journal Title: Artificial Intelligence Journal 161, 1-2 Pages: 149-180
  • Peer Reviewed
• [Journal Article] Secure Distributed Constraint Satisfaction : Reaching Agreement without Revealing Private Information (2005)
  • Author(s): Makoto Yokoo, Koutarou Suzuki, Katsutoshi Hirayama
  • Journal Title: Artificial Intelligence Journal 161, 1-2 Pages: 229-246
  • Peer Reviewed
• [Journal Article] Networked Distributed POMDPs : A Synthesis of Distributed Constraint Optimization and POMDPs (2005)
  • Author(s): Ranjit Nair, Pradeep Varakantham, Milind Tambe, Makoto Yokoo
  • Journal Title: Twentieth National Conference on Artificial Intelligence (AAAI-05) 1 Pages: 133-149
  • Peer Reviewed
• [Journal Article] 分子構造変化のモデル化と反応度の理論的解析 (2005)
  • Author(s): 塩崎真史, 小野廣隆, 定兼邦彦, 山下雅史
  • Journal Title: 2005年冬のLAシンポジウム, 数理解析研究所講究録1426 1 Pages: 232-237
  • Peer Reviewed
• [Journal Article] Generalized partitioned quantum cellular automata and Quantization of classical CA (2005)
  • Author(s): S. Inokuchi, Y. Mizoguchi
  • Journal Title: International Journal of Unconventional Computing 1 Pages: 149-160
  • Peer Reviewed
• [Journal Article] Computing with Hairpins and Secondary structures of DNA (2005)
  • Author(s): Masami Hagiya, Satsuki Yaegashi, Keiichiro Takahashi
  • Journal Title: Science and Computation, Natural Computing Series 1 Pages: 293-308
  • Peer Reviewed
• [Journal Article] Minimum Basin Algorithm : An Effective Analysis Technique for DNA Energy Landscapes (2005)
  • Author(s): Mitsuhiro Kubota, Masami Hagiya
  • Journal Title: DNA10, Lecture Notes in Computer Science 3384 Pages: 202-214
  • Peer Reviewed
• [Journal Article] バイオナノデバイスとしての人工DNA (2005)
  • Author(s): 浅沼浩之
  • Journal Title: 化学と教育 53 Pages: 12-15
  • Peer Reviewed
• [Journal Article] Design of Light-switchable Phage Promoter for Efficient Photo-regulation of Gene-expression (2005)
  • Author(s): M. Liu, M. Komiyama, H. Asanuma
  • Journal Title: Nucleic Acids Res. Supple. No. 49 49 Pages: 283-284
  • Peer Reviewed
• [Journal Article] Clear-cut photo-regulation of the formation and dissociation of the DNA duplex by modified oligonucleotide involving Multiple azobenzenes (2005)
  • Author(s): H. Asanuma, D. Matsunaga, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. No. 49 49 Pages: 35-36
  • Peer Reviewed
• [Journal Article] Thermal Ratchetを用いたDNAタイルのエラーフリーアセンブリ (2005)
  • Author(s): 小川賢一, 藤林健一, 村田 智
  • Journal Title: 第17回自律分散システムシンポジウム資料 1 Pages: 147-152
  • Peer Reviewed
• [Journal Article] Photo- and Thermoregulation of DNA Nanomachines (2005)
  • Author(s): Keiichiro Takahashi, Satsuki Yaegashi, Hiroyuki Asanuma, Masami Hagiya
  • Journal Title: DNA11 Preliminary Proceedings 1 Pages: 147-156
  • Peer Reviewed
• [Journal Article] Chain Reaction Systems Based on Loop Dissociation of DNA (2005)
  • Author(s): Keiichiro Takahashi, Satsuki Yaegashi, Atsushi Kameda, Masami Hagiya
  • Journal Title: DNA11 Preliminary Proceedings 1 Pages: 343-353
  • Peer Reviewed
• [Journal Article] A simple classifications of the volvocine algae by formal languages (2005)
  • Author(s): H. Yoshida, T. Yokomori, A. Suyama
  • Journal Title: Bull. Math. Biol. 67 Pages: 1339-1354
  • Peer Reviewed
• [Journal Article] DigiTag assay for multiplex single nucleotide polymorphism typing with highsuccess rate (2005)
  • Author(s): K. Hashido, K. Hirayasu, M. Takasu, A. Suyama, K. Tokunaga
  • Journal Title: Anal. Biochem. 346 Pages: 281-288
  • Peer Reviewed
• [Journal Article] Methods for manipulating DNA molecules in a micrometer scale using optical techniques (2005)
  • Author(s): Y. Ogura, T. Rawakami, F. Sumiyama, S. Irie, A. Suyama, J. Tanida
  • Journal Title: Led. Notes Comput. Sc. 3384 Pages: 258-267
  • Peer Reviewed
• [Journal Article] Control of DNA molecules on a microscopic bead using optical techniques for photonic DNA memory (2005)
  • Author(s): Y. Ogura, T. Beppu, M. Takinoue, A. Suyama, J. Tanida
  • Journal Title: Preliminary proceedings of DNA 11 1 Pages: 78-88
  • Peer Reviewed
• [Journal Article] Normalized molecular encoding method for quantitative gene expression profiling (2005)
  • Author(s): O. Gotoh, Y. Sakai, Y. Mawatari, W. Gunji, Y. Murakami, A. Suyama
  • Journal Title: Preliminary proceedings of DNA 11 1 Pages: 395
  • Peer Reviewed
• [Journal Article] Realization of RTRAC : Reverse transcription and Transcription-based Autonomous Computer (2005)
  • Author(s): D. Kiga, T. Mochida, M. Takinoue, A. Suyama
  • Journal Title: Preliminary proceedings of DNA 11 1 Pages: 397
  • Peer Reviewed
• [Journal Article] Amorphous DNA memory constructed with hairpin DNA immobilized on a soliud surface (2005)
  • Author(s): M. Takinoue, Y. Hatano, Y. Endoh, A. Suyama
  • Journal Title: Preliminary proceedings of DNA 11 1 Pages: 410
  • Peer Reviewed
• [Journal Article] Programmable step-by-step assembly of DNA nanostructures (2005)
  • Author(s): M. Tagawa, D. Kiga, T. Yoshinobu, H. Iwasaki, A. Suyama
  • Journal Title: Proc. Foundations of Nanoscience 2005 1 Pages: 192
  • Peer Reviewed
• [Journal Article] 細胞の中で働くコンピュータ(前編) (2005)
  • Author(s): 陶山明
  • Journal Title: BIONICS 7月号 Pages: 58-60
  • Peer Reviewed
• [Journal Article] 細胞の中で働くコンピュータ(後編) (2005)
  • Author(s): 陶山明
  • Journal Title: BIONICS 8月号 Pages: 54-56
  • Peer Reviewed
• [Journal Article] DNAエンコード技術を用いた発現解析 (2005)
  • Author(s): 陶山明
  • Journal Title: 蛋白質核酸酵素 50(16) Pages: 2300
  • Peer Reviewed
• [Journal Article] Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid (2005)
  • Author(s): Hino N., Okazaki Y., Kobayashi T., Hayashi A., Sakamoto K., Yokoyama s.
  • Journal Title: Nature Methods 2 2 Pages: 201-206
  • Peer Reviewed
• [Journal Article] structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion (2005)
  • Author(s): Kobayashi T, Sakamoto K, Takimura T, Sekine R, Vincent K, Kamata K, Nishimura s, Yokoyama s.
  • Journal Title: Proc. Natl. Acad. Sci. USA 102 120 Pages: 1366-1371
  • Peer Reviewed
• [Journal Article] Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase (2005)
  • Author(s): Kobayashi T, Takimura T, Sekine R, Vincent K, Kamata K, Sakamoto K, Nishimura S, Yokoyama S.
  • Journal Title: J Mol. Biol. 346 346 Pages: 105-117
  • Peer Reviewed
• [Journal Article] 生きた細胞で超タンパク質を作る (2005)
  • Author(s): 坂本健作, 横山茂之
  • Journal Title: 化学 60 (4) Pages: 70-71
  • Peer Reviewed
• [Journal Article] 人工的なアミノ酸をタンパク質に導入することによる動物細胞内での光クロスリンク法 (2005)
  • Author(s): 樋野展正, 坂本健作, 横山茂之
  • Journal Title: 実験医学 23(13) Pages: 2047-2051
  • Peer Reviewed
• [Journal Article] 二次構造の解離に基づく汎用分子システム (2005)
  • Author(s): 萩谷昌己
  • Journal Title: シミュレーション Vol. 24, No. 4 Pages: 21-24
  • Peer Reviewed
• [Journal Article] Discrete state Transition Systems on Continuous Space-Time : A Theoretical Model for Amorphous Computing (2005)
  • Author(s): Masami Hagiya
  • Journal Title: Lecture Notes in Computer Science 3699 Pages: 117-129
  • Peer Reviewed
• [Journal Article] DNAコンピュータ制御コードの最適化 (2005)
  • Author(s): 阿部正佳, 萩谷昌己, 瀬川修
  • Journal Title: 日本ソフトウェア科学会第22回大会論文集 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] A Retargetable Code Generator for the Generic Intermediate Language in COINS (2005)
  • Author(s): Seika Abe, Masami Hagiya, Ikuo Nakata
  • Journal Title: IPSJ Transactions on Programming Vol. 46, No. SIG14 Pages: 12-29
  • Peer Reviewed
• [Journal Article] Aqueous Computing with DNA Hairpin-Based RAM (2005)
  • Author(s): Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: DNA Computers (DNA10), Lecture Notes in Computer Science 3384 Pages: 355-364
  • Peer Reviewed
• [Journal Article] Specificity of Hybridization between DNA Sequences Based on Free Energy (2005)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of DNA11 1 Pages: 366-375
  • Peer Reviewed
• [Journal Article] Experimental Challenge of Scaled-up Hierarchical DNA Memory (2005)
  • Author(s): S. Kashiwamura, M. Yamamoto, A. Kameda, A. Ohuchi
  • Journal Title: Proceedings of DNA11 1 Pages: 396
  • Peer Reviewed
• [Journal Article] DNAタイルによる自己組織的ナノ構造制御 (2005)
  • Author(s): 山本 雅人
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005), イベント企画チュートリアル「分子計算の仕組み」 1 Pages: 7-11
  • Peer Reviewed
• [Journal Article] 自由エネルギーを用いたDNAナノ構造形成のための塩基配列設計 (2005)
  • Author(s): 飯村直記, 山本 雅人, 田中文昭, 亀田充史, 大内 東
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005) 1 Pages: 371-373
  • Peer Reviewed
• [Journal Article] 自由エネルギーに基づいた塩基配列設計に関する研究 (2005)
  • Author(s): 田中文昭, 亀田充史, 山本雅人, 大内東
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005) 1 Pages: 375-377
  • Peer Reviewed
• [Journal Article] DNAを記憶素子として用いた分子メモリの開発と大容量化に関する検討 (2005)
  • Author(s): 柏村 聡, 山本 雅人, 亀田 充史, 大内 東
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005) 1 Pages: 367-369
  • Peer Reviewed
• [Journal Article] DNA分子を利用したリレーショナルデータベースの開発 (2005)
  • Author(s): 北 豊, 柏村 聡, 亀田 充史, 山本 雅人, 大内 東
  • Journal Title: 第4回情報科学技術フォーラム(FIT2005) 1 Pages: 21-23
  • Peer Reviewed
• [Journal Article] DNAタイル構造の安定性評価法 (2005)
  • Author(s): 飯村 直記, 山本 雅人, 田中 文昭, 亀田 充史, 大内 東
  • Journal Title: 北海道情報処理シンポジウム 1 Pages: 126-127
  • Peer Reviewed
• [Journal Article] DNAタイルによる計算論的ナノテクノロジー (2005)
  • Author(s): 山本 雅人, 飯村 直記, 田中 文昭, 亀田 充史, 大内 東
  • Journal Title: 第98回日本分子生物学会年会 シンポジウム「ナノバイオテクノロジー・分析から構築の科学へ」 Pages: 40-40
  • Peer Reviewed
• [Journal Article] Potential for enlarging DNA memory : the validity of experimental operations of scaled-up nested primer molecular memory (2005)
  • Author(s): Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Biosystems Vol. 80, No. 1 Pages: 99-112
  • Peer Reviewed
• [Journal Article] Design of nucleic acid seguences for DNA computing based on a thermodynamic approach (2005)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Nucleic Acids Research Vol. 33, No. 3 Pages: 903-911
  • Peer Reviewed
• [Journal Article] Design of Soccer-ball-shape DNA Molecules and Preliminary Experiments in Vitro (2005)
  • Author(s): Yutaka Kita, Atsushi Rameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of The 10th International Symposiumon Artificial Life and Robotics 1 Pages: 563-566
  • Peer Reviewed
• [Journal Article] P-cats : Prediction of catalytic residues in proteins from the tertiary structures (2005)
  • Author(s): K. Kinoshita, M. *Ota
  • Journal Title: Bioinformatics 21 Pages: 3570-3571
  • Peer Reviewed
• [Journal Article] Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8 : X-ray crystallographic analysis and calorimetry (2005)
  • Author(s): Y. Asada, M. Sawano, K. Ogasahara J. Nakamura, M. Ota, C. Kuroishi, M. Sugahara, K. Yutani, N. Kunishima
  • Journal Title: J Biochem 138 Pages: 343-353
  • Peer Reviewed
• [Journal Article] Design of lambda Cro Fold : Solution Structure of a Monomeric Variant of the De Novo Protein (2005)
  • Author(s): Y. Isogai, Y. Ito, T. Ikeya, I, Shiro, M. Ota
  • Journal Title: J. Mol. Biol. 354 Pages: 801-814
  • Peer Reviewed
• [Journal Article] Security and Reliability of LDPC Based Public-Key Cryptosysterns (2005)
  • Author(s): D. Saad, N. Skantzos, Y. *Kabashima
  • Journal Title: Prog. Theor. Phys. 157 Pages: 229-236
  • Peer Reviewed
• [Journal Article] Statistical Mechanics of Source Coding with a Fidelity Criterion (2005)
  • Author(s): Y. Kabashima, T. Hosaka
  • Journal Title: Prog. Theor. Phys. 157 Pages: 197-204
  • Peer Reviewed
• [Journal Article] An Exact Analytic Continuation to Complex Replica Number in the Discrete Random Energy Model of Finite System Size (2005)
  • Author(s): K. Ogure, Y. Kabashima
  • Journal Title: Prog. Theor. Phys. 157 Pages: 103-106
  • Peer Reviewed
• [Journal Article] Replicated Bethe Free Energy : A Variational Principle behind Survey Propagation (2005)
  • Author(s): Y. Kabashima
  • Journal Title: J. Phys. Soc. Jpn. 74 Pages: 2133-2136
  • Peer Reviewed
• [Journal Article] Statistical Mechanical Development of a Sparse Bayesian Classifier . (2005)
  • Author(s): S. Uda, Y. Kabashima
  • Journal Title: J. Phys. Soc. Jpn. 74 Pages: 2233-2242
  • Peer Reviewed
• [Journal Article] Biased mutation-assembling : an efficient method for rapid directed evolution through simultaneous mutation accumulation (2005)
  • Author(s): Hamamatsu N., Aita T., Nomiya Y., Uchiyama H., Nakajima M., HusimiY., Shibanaka Y.
  • Journal Title: Protein Eng. Design & Selection 18(6) Pages: 265-271
  • Peer Reviewed
• [Journal Article] Thermodynamical Interpretation of Evolutionary Dynamics on a Fitness Landscape in an Evolution Reactor, II (2005)
  • Author(s): Aita T., Morinaga S., Husimi Y.
  • Journal Title: Bulletin of Mathematical Biology 67(3) Pages: 613-661
  • Peer Reviewed
• [Journal Article] マルコフ連鎖モンテカルロ法の分子計算による実現の一検討 (2005)
  • Author(s): 染谷博司, 山村雅幸, 坂本健作
  • Journal Title: 電気学会電子・情報・システム部門大会2005論文集 OS3-4 Pages: 466-469
  • Peer Reviewed
• [Journal Article] A Robust Real-Coded Evolutionary Algorithm with Toroidal Search Space Conversion (2005)
  • Author(s): Someya, H. Yamamura, M.
  • Journal Title: Soft Computing Vol. 9, No. 4 Pages: 254-269
  • Peer Reviewed
• [Journal Article] 分子コンピューティングの現状と新展開 (2005)
  • Author(s): 山村雅幸, 萩谷昌己
  • Journal Title: 日本建築学会第28回情報・システム・利用・技術シンポジウム論文集 1 Pages: 286-293
  • Peer Reviewed
• [Journal Article] DNAコンピューティングのための配列設計 (2004)
  • Author(s): 小林聡
  • Journal Title: 情報処理 4 5 Pages: 164-169
  • Peer Reviewed
• [Journal Article] Testing Structure Freeness of Regular Sets of Biomolecular Sequences (2004)
  • Author(s): Satoshi Kobayashi
  • Journal Title: Proceedings of 10th International Meeting on DNA Based Computers 1 Pages: 395-404
  • Peer Reviewed
• [Journal Article] Evaluating Biomolecular Sequences Using Hydrogen Bond Network Graph (2004)
  • Author(s): Kazuya Nagatsu, Atsushi Kijima, Satoshi Kobayashi
  • Journal Title: Proceedings of 10th International Meeting on DNA Based Computers 1 Pages: 441
  • Peer Reviewed
• [Journal Article] DNA計算のための配列集合評価アルゴリズム (2004)
  • Author(s): 小林聡
  • Journal Title: 第52回数理モデル化と問題解決研究会予稿集 MPS-52 Pages: 89-92
  • Peer Reviewed
• [Journal Article] 分子計算の理論モデル (2004)
  • Author(s): 小林聡, 榊原康文, 横森貴
  • Journal Title: 「分子コンピュータの現状と展望」(萩谷編), サイエンス社 1 Pages: 32-40
  • Peer Reviewed
• [Journal Article] A DNA-based Computational Model using a Specific Type of Restriction Enzymes (2004)
  • Author(s): Y. Sakakibara, H. Imai
  • Journal Title: Journal of Automata, Languages and Combinatorics 9・1 Pages: 111-119
  • Peer Reviewed
• [Journal Article] 分子コンピューティングの新しいモデル (2004)
  • Author(s): 榊原康文
  • Journal Title: 「分子コンピュータの現状と展望」(萩谷編), サイエンス社 1 Pages: 84-90
  • Peer Reviewed
• [Journal Article] On the Power of Membrane Division in P Systems (2004)
  • Author(s): Gh. Paun, Y. Suzuki, H. Tanaka, T. Yokomori
  • Journal Title: Theoretical Computer Science 324 Pages: 61-85
  • Peer Reviewed
• [Journal Article] Emergence of auto-catalytic structure in stochastic self-reinforcing reaction networks (2004)
  • Author(s): Y. Suzuki, P. Davis, H. Tanaka
  • Journal Title: Journal of Artificial Life and Robotics 7 Pages: 210-213
  • Peer Reviewed
• [Journal Article] Toward a novel computational framework for molecular computing : chemical reactionas computation (2004)
  • Author(s): Y. Suzuki, D. Besozzi, C. Zandron, H. Tanaka, G. Mauri
  • Journal Title: Preproceedings of DNA10 1 Pages: 455
  • Peer Reviewed
• [Journal Article] 言語モデルLMNtal (2004)
  • Author(s): 上田和紀, 加藤紀夫
  • Journal Title: コンピュータソフトウェア 21 Pages: 44-60
  • Peer Reviewed
• [Journal Article] LMNtalにおけるルールセット不変性の検査 (2004)
  • Author(s): 圷弘明, 加藤紀夫, 上田和紀
  • Journal Title: 第6回プログラミングおよびプログラミング言語ワークショップ(PPL2004)論文集 1 Pages: 211-216
  • Peer Reviewed
• [Journal Article] 並行言語モデルLMNtalにおけるプロセス構造の解析 (2004)
  • Author(s): 加藤紀夫, 上田和紀
  • Journal Title: 第6回プログラミングおよびプログラミング言語ワークショップ(PPL2004)論文集 1 Pages: 217-222
  • Peer Reviewed
• [Journal Article] Pseudorandomness of SPN-Type Transformations (2004)
  • Author(s): W. Lee, M. Nandi, P. Sarkar, D. Chang, S. Lee, K. Sakurai
  • Journal Title: Information Security and Privacy : 9th Australasian Conference, ACISP 2004, LNCS 3108 Pages: 212-223
  • Peer Reviewed
• [Journal Article] DNA計算における局所探索法による反応障壁近似計算 (2004)
  • Author(s): 武田勉, 小野廣隆, 定兼邦彦, 山下雅史
  • Journal Title: 信学技報, vol. 104, no. 339, COMP2004-49 1 Pages: 41-46
  • Peer Reviewed
• [Journal Article] An Improved Heuristic for Solving TSP Based on the Evolution of Easy Instances (2004)
  • Author(s): S. Fujita, S. Umezane
  • Journal Title: Proc. International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2004) 1 Pages: 324-330
  • Peer Reviewed
• [Journal Article] Advantages of Backward Searching --- Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays (2004)
  • Author(s): V. Makinen, G. Navarro, K. Sadakane
  • Journal Title: Algorithms and Computation, 15th International Symposium, ISAAC 2004 1 Pages: 681-692
  • Peer Reviewed
• [Journal Article] Compressed Index for Dynamic Text (2004)
  • Author(s): W. K. Hon, T. W. Lam, K. Sadakane, W. R. Sung, S. M. Yiu
  • Journal Title: IEEE Data Compression Conference (DCC 2004) 1 Pages: 102-111
  • Peer Reviewed
• [Journal Article] グラフの集合を表現するラベル付グラフについて (2004)
  • Author(s): 溝口佳寛, 森雅生
  • Journal Title: 火の国情報シンポジウム2004 1 (予稿集CD-ROM) Pages: A-2-4,22
  • Peer Reviewed
• [Journal Article] ランダムタイリングの数値シミュレーション (2004)
  • Author(s): 貞廣泰造
  • Journal Title: 数理解析研究所講究録 1381 Pages: 182-189
  • Peer Reviewed
• [Journal Article] k-Coteries for Tolerating Network 2-Partition (2004)
  • Author(s): T. Harada, M. Yamashita
  • Journal Title: IEEE Trans. Parallel and Distributed Systems 15-7 Pages: 666-672
  • Peer Reviewed
• [Journal Article] Communication for Improving Policy Computation in Distributed POMDPs (2004)
  • Author(s): Ranjit Nair, Tambe Milind, Maayan Roth, Makoto Yokoo
  • Journal Title: Third International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS2004) 3 Pages: 1098-1105
  • Peer Reviewed
• [Journal Article] Multiagent Planning as Control Synthesis (2004)
  • Author(s): Kiam Tian Seow, Chuan Ma, Makoto Yokoo
  • Journal Title: Third International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS2004) 1 Pages: 972-979
  • Peer Reviewed
• [Journal Article] High Speed Formations of Reconfigurable Modular Robotic Systems (2004)
  • Author(s): A. Dumitrescu, I. Suzuki, M. Yamashita
  • Journal Title: Int'l Journal on Robotic Research 23(6) Pages: 583-593
  • Peer Reviewed
• [Journal Article] Motion Planning for Metamorphic Systems : Feasibility, Decidability and Distributed Reconfiguration (2004)
  • Author(s): A. Dumitrescu, I. Suzuki, M. Yamashita
  • Journal Title: IEEE Trans. Robotics and Automation 20(3) Pages: 409-418
  • Peer Reviewed
• [Journal Article] Towards Molecular Programming - a Personal Report on DNA8 and Molecular Computing (2004)
  • Author(s): Masami Hagiya
  • Journal Title: Natural Computing Series 1 Pages: 125-140
  • Peer Reviewed
• [Journal Article] Minimum Basin Algorithm : An Effective Analysis Technique for DNA Energy Landscapes (2004)
  • Author(s): Mitsuhiro Kubota, Masami Hagiya
  • Journal Title: DNA10, Preliminary Proceeding 1 Pages: 202-213
  • Peer Reviewed
• [Journal Article] DNA Nanorobotics and Sequence Design (2004)
  • Author(s): Masami Hagiya
  • Journal Title: Proc. SICE Annual Conference 1 Pages: 2774-2778
  • Peer Reviewed
• [Journal Article] On Computation of Minimum Free Energy and Partition Function of Multiple Nucleic Acid Seguences (2004)
  • Author(s): Keiichiro Takahashi, Masami Hagiya
  • Journal Title: Proc. FIT2004 Vol. 1 Pages: 91-92
  • Peer Reviewed
• [Journal Article] Preliminary Experiments on Hairpin Structure Dissociation for Constructing Robust DNA Machines (2004)
  • Author(s): Keiichiro Takahashi, Masami Hagiya
  • Journal Title: Proc. of the 2004 IEEE 1 Pages: 285-290
  • Peer Reviewed
• [Journal Article] 光機能性DNAの設計と応用 (2004)
  • Author(s): 浅沼浩之, 樫田啓
  • Journal Title: 高分子加工 53(1) Pages: 37-43
  • Peer Reviewed
• [Journal Article] Photo-regulation of RNA Digestion by RNase H with Azobenzene-Tethered DNA (2004)
  • Author(s): D. Matsunaga, H. Asanuma, M. Komiyama
  • Journal Title: J. Am. Chem. Soc. 126 Pages: 11452-11453
  • Peer Reviewed
• [Journal Article] Photoregulation of in vitro transcription/translation of GFP by tethering an azobenzene to T7 promoter (2004)
  • Author(s): J. Zhao, J. Zhou, M. Liu, H. Asanuma, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. 4 1 Pages: 199-200
  • Peer Reviewed
• [Journal Article] Real time monitoring of the interaction of T7 RNA polymerase with azobenzene-tethered T7 promoter by affinity biosensor (2004)
  • Author(s): M. Liu, H. Asanuma, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. 4 1 Pages: 221-222
  • Peer Reviewed
• [Journal Article] Interstrand H aggregation of cationic dyes for narrowing the absorption spectra and stabilizing the duplex (2004)
  • Author(s): H. Asanuma, H. Kashida, M. Komiyama
  • Journal Title: Supramol. Chem. 16 Pages: 459-464
  • Peer Reviewed
• [Journal Article] Azobenzene-tethered DNA towards the photo-regulation of molecular machine (2004)
  • Author(s): H. Asanuma, D. Matsunaga, M. Komiyama
  • Journal Title: DNA10, Preliminary Proceedings 1 Pages: 434
  • Peer Reviewed
• [Journal Article] Alternating hetero H-aggregation of different dyes by interstrand stacking from two DNA-dye conjugates (2004)
  • Author(s): H. Asanuma, H. Kashida, M. Komiyama
  • Journal Title: Angew. Chem. Int. Ed. Engl 43 Pages: 6522-6525
  • Peer Reviewed
• [Journal Article] A Method of Error Suppression for Self-Assembling DNA Tiles (2004)
  • Author(s): K. Fujibayashi, S. Murata
  • Journal Title: Proc. DNA10 1 Pages: 284-293
  • Peer Reviewed
• [Journal Article] Self-Assembling DNA Tiles -Mechanisms of Error Suppression (2004)
  • Author(s): S. Murata
  • Journal Title: Proc. SICE Annual Conference 1 Pages: 2764-2767
  • Peer Reviewed
• [Journal Article] Application of AFM Anodic Oxidation to Patterning of Biomolecules on Si (2004)
  • Author(s): T. Yoshinobu, W. -C. Moon, A. Nishikawa, J. Suzuki, H. Iwasaki
  • Journal Title: Sensors and Materials 16 Pages: 421-428
  • Peer Reviewed
• [Journal Article] Autonomous biomolecular computer modeled after retroviral replication (2004)
  • Author(s): N. Nitta, A. Suyama
  • Journal Title: Lect. Notes Comput. Sc. 2943 Pages: 03-212
  • Peer Reviewed
• [Journal Article] Parallel translation of DNA clusters by VGSEL array trapping and temperature control with laser illumination (2004)
  • Author(s): Y. Ogura, T. Kawakami, F. Sumiyama, A. Suyama, J. Tanida
  • Journal Title: Lect. Notes Comput. Sc. 2943 Pages: 1-18
  • Peer Reviewed
• [Journal Article] DNAコンピュータとナノテクノロジー (2004)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 23(2) Pages: 241-246
  • Peer Reviewed
• [Journal Article] DNAコンピュータの現状と将来 (2004)
  • Author(s): 陶山明
  • Journal Title: 臨時別冊・数理科学 SGCライブラリ 31 Pages: 129-135
  • Peer Reviewed
• [Journal Article] バイオコンピュータ・DNAデバイス (2004)
  • Author(s): 陶山明
  • Journal Title: 新訂版・表面科学の基礎と応用, 日本表面科学会編 1 Pages: 1365-1367
  • Peer Reviewed
• [Journal Article] DNA二重らせんの安定性を解く-その理論と応用 (2004)
  • Author(s): J. A. Rose, 陶山明
  • Journal Title: 東京大学バイオインフォマティクス集中講義 1 Pages: 60-67
  • Peer Reviewed
• [Journal Article] Molecular reactions for a molecular memory based on hairpin DNA (2004)
  • Author(s): M. Takinoue, A. Suyama
  • Journal Title: CBI J. 4(3) Pages: 112-120
  • Peer Reviewed
• [Journal Article] Equilibrium Model of DNA Chip Hybridization Error (2004)
  • Author(s): John A. Rose, Masami Hagiya, Akira Suyama
  • Journal Title: The 15^<th> International Conference on Genome Informatics 1 Pages: 1-2
  • Peer Reviewed
• [Journal Article] ソフトリソグラフィーを用いたマイクロ・ナノ構造の製作技術 (2004)
  • Author(s): 金田祥平, 藤井輝夫
  • Journal Title: 高分子 53 Pages: 341
  • Peer Reviewed
• [Journal Article] A Microfluidic Device of Write-in and Read-out Operations of a Molecular Memory (2004)
  • Author(s): K. Mogi, S. Kaneda, K. Ono, T. Fukuba, T. Fujii
  • Journal Title: Proc. ・ TAS 2004 1 Pages: 569-571
  • Peer Reviewed
• [Journal Article] 整数線形計画法を用いたDNAコンピュータ制御コードの生成 (2004)
  • Author(s): 阿部正佳, 萩谷昌己
  • Journal Title: 情報処理学会論文誌プログラミング Vol. 45, No. SIG9 Pages: 1-13
  • Peer Reviewed
• [Journal Article] Code Generation for a DNA Computer by Integer Linear Programming (2004)
  • Author(s): Seika Abe, Masami Hagiya, Takao Nakajima
  • Journal Title: Proceedings of the 2004 IEEE Conference on Cybernetics and Intelligent Systems 1 Pages: 268-273
  • Peer Reviewed
• [Journal Article] Thermodynamic Parameters, Based on a Nearest-Neighbor Model for DNA Seauences with a Single-Bulge Loop (2004)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Biochemistry Vol. 43, No. 22 Pages: 7143-7150
  • Peer Reviewed
• [Journal Article] Two-step Search for DNA Sequence Design, IEICE TRANSACTIONS on Fundamentals of Electronics (2004)
  • Author(s): Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Communications and Computer Sciences Vol. E87-A, N0. 6 Pages: 1446-1453
  • Peer Reviewed
• [Journal Article] Development, Evaluation and Benchmarking of Simulation Software for Biomolecule-based Computing (2004)
  • Author(s): S. -Y. Shin, B. -T. Zhang, S. Kashiwamura. M. Yamamoto, A. Kameda, A. Ohuchi
  • Journal Title: Natural Computing Vol. 3, No. 4 Pages: 427-442
  • Peer Reviewed
• [Journal Article] Conformational Addressing Using the Hairpin structure of Single-Strand DNA (2004)
  • Author(s): A. Kameda, M. Yamamoto, H. Uejima, M. Hagiya, R. Sakamoto, A. Ohuchi
  • Journal Title: DNA Computers (DNA9), LNCS Vol. 2943 Pages: 219-224
  • Peer Reviewed
• [Journal Article] Aqueous Computing with DNA hairpin-based RAM (2004)
  • Author(s): Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Preliminary Proceedings of DNA10 1 Pages: 50-59
  • Peer Reviewed
• [Journal Article] Probabilistic state Transition Model based on PCR (2004)
  • Author(s): Atsushi Kameda, Keisuke Hashimoto, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Preliminary Proceedings of DNA10 1 Pages: 448-448
  • Peer Reviewed
• [Journal Article] サッカーボール型DNA分子の設計と基礎実験 (2004)
  • Author(s): 北 豊, 亀田 充史, 山本 雅人, 大内 東
  • Journal Title: 情報処理北海道シンポジウム2004講演論文集 1 Pages: 14-15
  • Peer Reviewed
• [Journal Article] DNAヘアピンを利用したRAMによるアクエアスコンピューティング (2004)
  • Author(s): 高橋 直人, 亀田 充史, 山本 雅人, 大内 東
  • Journal Title: 情報処理北海道シンポジウム2004講演論文集 1 Pages: 16-17
  • Peer Reviewed
• [Journal Article] Nearest-Neighbor Thermodynamics of DNA Seauences with Single Bulge Loop (2004)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA9), LNCS 2943 Pages: 170-179
  • Peer Reviewed
• [Journal Article] Conformational Addressing Using the Hairpin structure of Single-Strand DNA (2004)
  • Author(s): Atsushi Kameda, Masahito Yamamoto, Hiroki Uejima, Masami Hagiya, Kensaku Sakamoto, Azuma Ohuchi
  • Journal Title: 9th International Workshop on DNA Based Computers(DNA9) 2943 Pages: 219-224
  • Peer Reviewed
• [Journal Article] General Protocol for Evaluating the Degree of Occurrence of Mis-Hybridization (2004)
  • Author(s): Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the Ninth International Symposium on Artificial Life and Robotics (AROB 9th'04) 1 Pages: 303-308
  • Peer Reviewed
• [Journal Article] Construction and Verification of DNA Hairpin-based RAM (2004)
  • Author(s): Naoto Takahashi, Atsushi Kaieda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the Ninth International Symposium on Artificial Life and Robotics (AROB 9th'04) 2 Pages: 388-391
  • Peer Reviewed
• [Journal Article] DNAコンピューティングと最適化 (2004)
  • Author(s): 山本 雅人, 大内 東
  • Journal Title: 平成16年電気学会全国大会講演論文集 Vol. 4-S19 Pages: 13-16
  • Peer Reviewed
• [Journal Article] 分子プログラミング大容量分子メモリと分子 (2004)
  • Author(s): 萩谷昌己, 山本雅人, 亀田充史
  • Journal Title: 臨時別冊・数理科学SGCライブラリー31 分子コンピュータの現状と展望-分子プログラミングへの展開- 1 Pages: 112-118
  • Peer Reviewed
• [Journal Article] The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus (2004)
  • Author(s): Y. Hioki, K. Ogasahara K, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S. Kuramitsu, K. Yutani
  • Journal Title: Eur. J. Biochem 271 Pages: 2624-2635
  • Peer Reviewed
• [Journal Article] Possible involvement of an FKBP family member protein from a psychrotrophic bacterium Shewanella sp. SIB1 in cold-adaptation (2004)
  • Author(s): Suzuki., Y, Haruki, M., Takano, K., Morikawa, M., Kanaya, S.
  • Journal Title: Eur J Biochem 271 Pages: 1372-81
  • Peer Reviewed
• [Journal Article] A design for cellular evolutionary computation by using bacteria (2004)
  • Author(s): Wakabayashi K., Yamamura M.
  • Journal Title: Preliminary Proceedings of 10^<th> International Meeting on DNA based computers (DNA10) 1 Pages: 304-313
  • Peer Reviewed
• [Journal Article] タンパク質工学のための遺伝的アルゴリズムの設計 (2004)
  • Author(s): 坂本健作, 山村雅幸, 染谷博司
  • Journal Title: 電気学会電子・情報・システム部門大会2004講演論文集 OS5 Pages: 10
  • Peer Reviewed
• [Journal Article] Toward "Wet" Implementation of Genetic Algorithm for Protein Engineering (2004)
  • Author(s): K. Sakamoto, M. Yamamura, H. Someya
  • Journal Title: In Preliminary Proceedings of 10th international Workshop on DNA-Based Computers 3384 Pages: 308-318
  • Peer Reviewed
• [Journal Article] statistical mechanics of low-density parity-check, codes (2004)
  • Author(s): Y. Kabashima, D. Saad
  • Journal Title: J. Phys. A37, R1 Pages: R1-R43
  • Peer Reviewed
• [Journal Article] Thermodynamic Interpretation of evolutionary dynamics on a Mt. Fuji-type fitness landscape (2004)
  • Author(s): Aita T., Husimi Y.
  • Journal Title: Bulletin Math. Biology 66 Pages: 1371-1403
  • Peer Reviewed
• [Journal Article] On the computational power of Insertion-Deletion Systems (2003)
  • Author(s): A. Takahara, T. Yokomori
  • Journal Title: Natural Computing 2 Pages: 321-336
  • Peer Reviewed
• [Journal Article] Extracting Globally Structure Free Sequences by Local Structure Freeness (2003)
  • Author(s): S. Kobayashi. T. Kondo. K. Okuda, E. Tomita
  • Journal Title: Proc. of9th International Meeting on DNA Based Computers 1 Pages: 206
  • Peer Reviewed
• [Journal Article] A method for extracting globally structure free set of sequences (2003)
  • Author(s): Satoshi Kobayashi, Tomohiro Kondo, Kohei Okuda, Etsuji Tomita
  • Journal Title: Technical Report of IEICE COMP2003-16 Pages: 1-6
  • Peer Reviewed
• [Journal Article] Structure Free Sequences for Biomolecular Computing (2003)
  • Author(s): Satoshi Kobayashi
  • Journal Title: The 990th American. Mathematical Society Fall EasternSectional Meeting 1 Pages: 80
  • Peer Reviewed
• [Journal Article] An Algorithm for Testing Structure Freeness of Biomolecular Sequences (2003)
  • Author(s): Satoshi Kobayashi, Takashi Yokomori, Yasubumi Sakakibara
  • Journal Title: Lecture Notes in Computer Science 2950 Pages: 266-277
  • Peer Reviewed
• [Journal Article] 分子計算のための配列設計(招待講演) (2003)
  • Author(s): 小林聡
  • Journal Title: 第6回情報論的学習理論ワークショップ予稿集 1 Pages: 307-314
  • Peer Reviewed
• [Journal Article] DNA-based Algorithms for Learning Boolean Formulae (2003)
  • Author(s): Yasubumi Sakakibara
  • Journal Title: Natural Computing 2 Pages: 153-171
  • Peer Reviewed
• [Journal Article] In Vitro Translation-based Computations (2003)
  • Author(s): Y. Sakakibara, T. Hohsaka
  • Journal Title: Proceedings of 9th International Meeting on DNA Based Computers 1 Pages: 175-179
  • Peer Reviewed
• [Journal Article] DNA・分子コンピュータ (2003)
  • Author(s): 榊原康文
  • Journal Title: 「ナノテクノロジーハンドブック」, オーム社 1 Pages: 196-199
  • Peer Reviewed
• [Journal Article] 分子コンピュータを用いた計算と学習アルゴリズム(招待講演) (2003)
  • Author(s): 榊原康文
  • Journal Title: 第6回情報論的学習理論ワークショップ予稿集 1 Pages: 29-306
  • Peer Reviewed
• [Journal Article] Modeling p53 signaling pathways by using P Systems (2003)
  • Author(s): Y. Suzuki, S. Ogishima, H. Tanaka
  • Journal Title: Preproceedings of the Workshop on Membrane Computing 1 Pages: 449-454
  • Peer Reviewed
• [Journal Article] The Language Model LMNtal (2003)
  • Author(s): Kazunori Ueda, Norio Kato
  • Journal Title: Proc. Nineteenth Int. Conf. on Logic Programming(ICLP'03), LNCS, Springer-Verlag 2916 Pages: 517-518
  • Peer Reviewed
• [Journal Article] LMNtalプロセスの振舞いの定式化 (2003)
  • Author(s): 加藤紀夫, 上田和紀
  • Journal Title: 日本ソフトウェア科学会第20回大会論文集 1 Pages: 16-20
  • Peer Reviewed
• [Journal Article] LMNtalプロトタイプ処理系の設計と実装 (2003)
  • Author(s): 矢島伸吾, 永田貴彦, 加藤紀夫, 上田和紀
  • Journal Title: 日本ソフトウェア科学会第20回大会論文集 1 Pages: 21-25
  • Peer Reviewed
• [Journal Article] A Combinatorial Auction among Versatile Experts and Amateurs (2003)
  • Author(s): Takayuki Ito, Makoto Yokoo, Shigeo Matsubara
  • Journal Title: Third International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS2004) 8 Pages: 69-74
  • Peer Reviewed
• [Journal Article] Independent and Cooperative Parallel Search Methods for the Generalized Assignment Problem (2003)
  • Author(s): M. Ishibashi, Y. Asahiro, M. Yamashita
  • Journal Title: Optimization Methods and Software 18(2) Pages: 129-141
  • Peer Reviewed
• [Journal Article] 局所情報を用いたランダムウォークの拡張 (2003)
  • Author(s): J. Jansson, 定兼邦彦, W. K. Sung, 塩崎真史, 山下雅史
  • Journal Title: IPSJ SIG Notes, SIGAL-92-3 110 Pages: 17-23
  • Peer Reviewed
• [Journal Article] New Text Indexing Functionalities of the Compressed Suffix Arrays (2003)
  • Author(s): K. Sadakane
  • Journal Title: Journal of Algorithms 48(2) Pages: 292-313
  • Peer Reviewed
• [Journal Article] Breaking a Time-and-Space Barrier in Constructing Full-Text Indices (2003)
  • Author(s): W. K. Hon, K. Sadakane, W. K. Sung
  • Journal Title: Proc. IEEE FOCS 1 Pages: 251-260
  • Peer Reviewed
• [Journal Article] Constructing Compressed Suffix Arrays with Large Alphabets (2003)
  • Author(s): W. K. Hon, T. W. Lam, K. Sadakane, W. K. Sung
  • Journal Title: Proc. ISAAC, LNCS 2906 1 Pages: 240-249
  • Peer Reviewed
• [Journal Article] A Vehicle Scheduler for On-Demand Bus Systems Based on a Heuristic Cost Estimation (2003)
  • Author(s): S. Fujita, A. Nakatani
  • Journal Title: IEEE 2003 International Conference on Intelligent Transportation Systems (ITS 2003) 1 Pages: 1194-1199
  • Peer Reviewed
• [Journal Article] 巡回型量子セルオートマトンの挙動について (2003)
  • Author(s): 井口修一, 溝口佳寛
  • Journal Title: 応用数学合同研究集会報告集(2003/12) 1 Pages: 85-88
  • Peer Reviewed
• [Journal Article] Graph transformation approach for the shortest path search and lengthcalculation (2003)
  • Author(s): M. Mori, Y. MIzoguchi
  • Journal Title: Bull. of Informatics and Cybernetics 35, 5 Pages: 7-67
  • Peer Reviewed
• [Journal Article] Proposal and Evaluation of Obfuscation Scheme for Java Source Codes by Partial Destruction of Encapsulation (2003)
  • Author(s): K. Fukushima, T. Tabata, K. Sakurai
  • Journal Title: International Symposium on Information Science and Electrical Engineering 2003 (ISEE 2003) 1 Pages: 389-392
  • Peer Reviewed
• [Journal Article] A Software Fingerprinting Scheme for Java Using Classfiles Obfuscation (2003)
  • Author(s): K. Fukushima, K. Sakurai
  • Journal Title: Proc. of the 4th International Workshop on Information Security Applications (WISA2003) 1 Pages: 337-350
  • Peer Reviewed
• [Journal Article] Impact of Local Topological Information on Random Walks on Finite Graphs (2003)
  • Author(s): S. Ikeda, I. Kubo, N. Okumoto, M. Yamashita
  • Journal Title: Proc. 30th International Colloquiunm on Automata, Languages and Programming (ICALP2003) 1 Pages: 1054-1067
  • Peer Reviewed
• [Journal Article] Reducing the Hitting and the Cover Times of Random Walks on Finite Graphs by Local Topological Information (2003)
  • Author(s): S. Ikeda, I. Kubo, M. Yamashita
  • Journal Title: The 2003 International Conference on VLSI(VLSI' 03) 1 Pages: 203-207
  • Peer Reviewed
• [Journal Article] Transversal Merge Operation and Nondominated Grid Coteries (2003)
  • Author(s): T. Harada, M. Yamashita
  • Journal Title: Proc. 15th IASTED International Conference Parallel and Distributed Computing and Systems (PDCS 2003) 1 Pages: 128-133
  • Peer Reviewed
• [Journal Article] DNA Computing (2003)
  • Author(s): Masami Hagiya, Azuma Ohichi
  • Journal Title: DNA8 Lecture Notes in Computer Science Vol. 2568 Pages: 231-246
  • Peer Reviewed
• [Journal Article] Branching DNA Machines Based on Transitions of Hairpin structures (2003)
  • Author(s): Mitsuhiro Kubota, Kazumasa Ohtake, Ken Komiya, Kensaku Sakamoto, Masami Hagiya
  • Journal Title: Proceedings of the 2003 Congress on Evolutionary Computation (CEC'03) 1 Pages: 2542-2548
  • Peer Reviewed
• [Journal Article] Secondary structure Design of Multi-State DNA Machines Based on Sequential Structure Transitions (2003)
  • Author(s): Hiroki Uejima, Masami Hagiya
  • Journal Title: DNA9 Preliminary Proceedings 1 Pages: 80-91
  • Peer Reviewed
• [Journal Article] Analyzing Secondary Structure Transition Paths of DNA/RNA Molecules (2003)
  • Author(s): Hiroki Uejima, Masami Hagiya
  • Journal Title: DNA9 Preliminary Proceedings 1 Pages: 92-96
  • Peer Reviewed
• [Journal Article] Conformational Addressing using the hairpin structure of single-strand DNA (2003)
  • Author(s): A. Kameda, M. Yamamoto, H. Uejima, M. Hagiya, K. Sakamoto, A. Ohuchi
  • Journal Title: DNA9 Preliminary Proceedings 1 Pages: 197-201
  • Peer Reviewed
• [Journal Article] DNA-Dye conjugates for controllable H*aggregation (2003)
  • Author(s): H. Asanuma, T. Takarada, K. Shirasuka, M. Komiyama
  • Journal Title: J. Am. Chem. Soc. 125 Pages: 2217
  • Peer Reviewed
• [Journal Article] DNAの光機能化 (2003)
  • Author(s): 浅沼浩之
  • Journal Title: 高分子 52(3) Pages: 139
  • Peer Reviewed
• [Journal Article] Photo-regulation of DNA function by azobenzene-tethered oligonucleotides (2003)
  • Author(s): H. Asanuma, D. Matsunaga, M. Liu, X. Liang, J. Zhao, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. 3 1 Pages: 117-118
  • Peer Reviewed
• [Journal Article] Eifective photo-regulation of transcription reaction by SP6RNA polymerase with modified DNA tethering multiple azobenzenes (2003)
  • Author(s): M. Liu, H. Asanuma, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. 3 1 Pages: 265-266
  • Peer Reviewed
• [Journal Article] NMR study on the Photo-responsive DNA Tethering an Azobenzene. Assignment of the Absolute Configuration of Two Diastereomers and structure Determination of their Duplexes in the trans-Form. (2003)
  • Author(s): X. Liang, H. Asanuma, H. Kashida, A. Takasu, T. Sakamoto, G. Kawai, M. Komiyama
  • Journal Title: J. Am. Chem. Soc. 125 Pages: 16408-16415
  • Peer Reviewed
• [Journal Article] Synergistic Effect of the Two Azobenzenes in the Promoter on the Photo-Regulation of Transcription Reaction with SP6 RNA Polymerase (2003)
  • Author(s): M. Liu, D. Tamaru, H. Asanuma, M. Komiyama
  • Journal Title: Chem. Lett. 32(12) Pages: 1174-1175
  • Peer Reviewed
• [Journal Article] DNA-Naphthyl Red conjugate as a visualizing probe of DNA hybridization (2003)
  • Author(s): H. Asanuma, H. Kashida, M. Komiyama
  • Journal Title: Chem. Commun. 1 Pages: 1536-1537
  • Peer Reviewed
• [Journal Article] Development of a probe DNA which accompanies color change by hybridization (2003)
  • Author(s): H. Kashida, H. Asanuma, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple. 3 1 Pages: 143-144
  • Peer Reviewed
• [Journal Article] 遺伝子発現の人工的制御 (2003)
  • Author(s): 浅沼浩之
  • Journal Title: バイオマテリアル-生体材料 21(4) Pages: 289-296
  • Peer Reviewed
• [Journal Article] AFM Fabrication of Oxide Patterns and Immobilization of Biomolecules on Si Surface (2003)
  • Author(s): T. Yoshinobu, J. Suzuki, H. Kurooka, W. C. Moon, H. Iwasaki
  • Journal Title: Electrochimica Acta 48 Pages: 3131-3135
  • Peer Reviewed
• [Journal Article] Biomolecules Patterning on Si Surface by AFM Oxidation (2003)
  • Author(s): W. C. Moon, *T. Yoshinobu, A. Nishikawa, H. Iwasaki
  • Journal Title: Proc. ISSIN-2003 1 Pages: 1
  • Peer Reviewed
• [Journal Article] Patterned Surface as a Template for DNA-Based Nanotechnology (2003)
  • Author(s): W. C. Moon, A. Nishikawa, T. Yoshinobu, H. Iwasaki
  • Journal Title: proc. CEC 2003 vol. 4 Pages: 2727-2732
  • Peer Reviewed
• [Journal Article] 超並列コンピュータの誕生 : エーデルマンの実験 (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(1) Pages: 75-79
  • Peer Reviewed
• [Journal Article] 汎用型DNAコンピュータを目指して (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(3) Pages: 348-352
  • Peer Reviewed
• [Journal Article] Autonomous biomolecular computer modeled after retroviral reprication (2003)
  • Author(s): N. Nitta, A. Suyama
  • Journal Title: Proc. of DNA9 1 Pages: 180-189
  • Peer Reviewed
• [Journal Article] Parallel translation of DNA clusters by VCSEL array trapping and temperature control with laser illumination (2003)
  • Author(s): Y. Ogura, T. Kawakami, F. Sumiyama, A. Suyama, J. Tanida
  • Journal Title: Proc. of DNA9 1 Pages: 19-27
  • Peer Reviewed
• [Journal Article] DNAコンピュータとその応用 (2003)
  • Author(s): 陶山明
  • Journal Title: ゲノム医学 3(2) Pages: 223-228
  • Peer Reviewed
• [Journal Article] DNAコンピュータ, 薄膜・表面物理セミナー「有機分子ナノテクノロジー」AP032326 (2003)
  • Author(s): 陶山明
  • Journal Title: 応用物理学会 1 Pages: 53-58
  • Peer Reviewed
• [Journal Article] 自律的に動作するin vivo DNAコンピュータ (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(11) Pages: 3
  • Peer Reviewed
• [Journal Article] DNAコンピュータで生命の謎を解く (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(8) Pages: 882-886
  • Peer Reviewed
• [Journal Article] 生命体は分子コンピュータである (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(5) Pages: 570-572
  • Peer Reviewed
• [Journal Article] 超並列DNAコンピュータの誕生 : エーデルマンの実験 (2003)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 22(1) Pages: 75-79
  • Peer Reviewed
• [Journal Article] The Fidelity of the Tag-Antitag System 2 : Reconciliation with the Stringency Picture (2003)
  • Author(s): John A. Rose, Masami Hagiya, Akira Suyama
  • Journal Title: Proceedings of the 2003 Congress on Evolutionary Computation (CEC'03) 1 Pages: 2740-2747
  • Peer Reviewed
• [Journal Article] A DNA-computing-based genetic program for in vitro protein evolution via constrained pseudomodule shuffling (2003)
  • Author(s): J. A. Rose, M. Takano, M. Hagiya, A. Suyama
  • Journal Title: Genetic Programming and Evolvable Machines 4 1 Pages: 139-152
  • Peer Reviewed
• [Journal Article] A PNA-mediated whiplash PCR-based program for in vitro protein evolution (2003)
  • Author(s): J. A. Rose, M. Takano, A. Suyama
  • Journal Title: LNCS 2568 Pages: 47-60
  • Peer Reviewed
• [Journal Article] Combining Droplet-Based Liquid Handling and On-Chip Capillary Electrophoresis With a New Sample Injection Method (2003)
  • Author(s): S. Kaneda, T. Fujii
  • Journal Title: Proc. ・TAS 2003 1 Pages: 1279-1282
  • Peer Reviewed
• [Journal Article] マイクロ生化学システムにおける表面技術 (2003)
  • Author(s): 金田祥平, 藤井輝夫
  • Journal Title: 表面技術 54 Pages: 319-314
  • Peer Reviewed
• [Journal Article] Small Volume Droplet-Based Liquid Handling Device for DNA Identification and Quantification by Electrophoretic Separation (2003)
  • Author(s): S. Kaneda, K. Ono, T. Yamamoto, T. Fujii
  • Journal Title: Proc Nanotech 2003 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] マイクロ生化学システムの新展開 (2003)
  • Author(s): 金田祥平, 小野航一, 藤井輝夫
  • Journal Title: 第9回創発システム・シンポジウム資料 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Hierarchical DNA Memory Based on Nested PCR (2003)
  • Author(s): S. Kashiwamura, M. Yamamoto, A. Kameda, T. Shiba, A. Ohuchi
  • Journal Title: DNA Computing (DNA8), LNCS 2568 Pages: 2568
  • Peer Reviewed
• [Journal Article] study of the Efficient Parameter Setting based on Mahalanobis-Taguchistrategy (2003)
  • Author(s): Masashi Nakatsugawa, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Two-step Search for DNA Seauence Design (2003)
  • Author(s): Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] State Transition Model Based on DNA Polymerization (2003)
  • Author(s): Keisuke Hashimoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Construction of DNA Hairpin-based RAM (2003)
  • Author(s): Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] The Effect on a Bonding strength by the Freedom of Movement of a DNA Strand on a Solid Support in DNA Computing (2003)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of the 2003 International Technical Conference on Circuits/Systems, Computers and Communications 1 Pages: 1-5
  • Peer Reviewed
• [Journal Article] Evaluation and Benchmarking (2003)
  • Author(s): Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuehi
  • Journal Title: Proceedings of Workshop on Simulation Tools for Biomolecular Computing in 2003 Congress on Evolutionary Computation 1 Pages: 22-26
  • Peer Reviewed
• [Journal Article] 相互作用科学シリーズ生命複雑系からの計算パラダイム (2003)
  • Author(s): 大内東, 山本雅人, 川村秀憲, 柴肇一, 高柳俊明, 常闇愛晃, 遠藤聡志
  • Journal Title: 森北出版株式会社 1 Pages: 1-220
  • Peer Reviewed
• [Journal Article] The Effect of the Bulge Loop upon the Hybridization Process in DNA Computing (2003)
  • Author(s): Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: The 5th International Conference on Evolvable Systems : From Biology to Hardware LNCS 2606 Pages: 446-456
  • Peer Reviewed
• [Journal Article] Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation (2003)
  • Author(s): M. Ota, K. Kinoshita, K. Nishikawa
  • Journal Title: J. Mol. Biol. 327 Pages: 1053-1064
  • Peer Reviewed
• [Journal Article] Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 (2003)
  • Author(s): N. Handa, T. Terada, Y. Kamewari, H. Hamana, J. R. H. Tame, S. -Y. Park, K. Kinoshita, M. Ota, H. Nakamura, S. Kuramitsu, M. Shirouzu, S. Yokoyama
  • Journal Title: Protein Sci 12 Pages: 1621-1632
  • Peer Reviewed
• [Journal Article] Propagating beliefs in spin glass models (2003)
  • Author(s): Y. Kabashima
  • Journal Title: Phys. Soc. Jpn 72 Pages: 1645
  • Peer Reviewed
• [Journal Article] Average and reliability error exponents in low-density parity-check codes (2003)
  • Author(s): N. Skanzos, J. van Mourik, D. Saad, Y. Kabashima
  • Journal Title: J. Phys. A36 Pages: 11131
  • Peer Reviewed
• [Journal Article] A CDMA multiuser detection algorithm on the basis of belief propagation (2003)
  • Author(s): Y. Kabashima
  • Journal Title: J. Phys. A36 Pages: 11111
  • Peer Reviewed
• [Journal Article] Analysis of common attacks in public-key cryptosystems based on low-density parity-check codes (2003)
  • Author(s): N. Skanzos, D. Saad, Y. Kabashima
  • Journal Title: Phys. Rev. E68 Pages: 056125
  • Peer Reviewed
• [Journal Article] Thermodynamical Instenterpretation of Adaptive Walk on a Mt. Fuji-type Fitness Landscape : Einstein's Relation-like Formula holds in a Stochastic Evolution (2003)
  • Author(s): Aita T., Husimi Y.
  • Journal Title: J. Theor. Biol. 225 Pages: 215-228
  • Peer Reviewed
• [Journal Article] Computer Simulation of the Cellular Arrangement in Early Cleavage of the Nematode Caenorhabditis elegans (2003)
  • Author(s): Atsushi Kajita, Masayuki Yamamura, Yuji Kohara
  • Journal Title: Bioinformatics 19(6) Pages: 704-716
  • Peer Reviewed
• [Journal Article] GA-based Generic Method for Protein structure Comparison (2003)
  • Author(s): Park, S. J. *Yamamura, M.
  • Journal Title: Proc. 2003 Congress on Evolutionary Computation(CEC 2003) 1 Pages: 1528-1535
  • Peer Reviewed
• [Journal Article] Two-layer Protein Structure Comparison (2003)
  • Author(s): Sung-Joon Park, Masayuki Yamamura
  • Journal Title: Proc. 15th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2003) 1 Pages: 435-440
  • Peer Reviewed
• [Journal Article] Multi-Line Split DNA Synthesis : a combinatorial method to make a high quality peptide library (2003)
  • Author(s): Tabuchi I., Soramoto S., Ueno s., Husimi Y.
  • Journal Title: BMC Biotech 4. 19 Pages: 1186
  • Peer Reviewed
• [Journal Article] In vitro virusと進化分子工学 (2003)
  • Author(s): 伏見譲, 田渕一郎
  • Journal Title: 蛋白質・核酸・酵素(特集 : 化学と生物学の接点がつくるNEWバイオテクノロジー) 48, (11) Pages: 1481-1487
  • Peer Reviewed
• [Journal Article] Intramolecular Fluorescent Resonance Energy Transfer (FRET)by BODIPY Chemical Modification of Cysteine-engineered Mutants of Green Fluorescent Protein (2003)
  • Author(s): Suzuki M., Ito Y., Savage H. E., Husimi Y., Douglas K. T.
  • Journal Title: Chem. Lett. 32 Pages: 306-307
  • Peer Reviewed
• [Journal Article] An in silico exploration of neutral network in protein sequence space (2003)
  • Author(s): Aita T., Ota M., *Husimi Y.
  • Journal Title: J. Theor. Biol. 221 Pages: 599-623
  • Peer Reviewed
• [Journal Article] グリッド環境に適した遺伝的アルゴリズムに関する考察とその実現 (2003)
  • Author(s): 染谷博司
  • Journal Title: 電気学会電子・情報・システム部門大会2003講演論文集 OS7-3 Pages: 435-439
  • Peer Reviewed
• [Journal Article] Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion (2003)
  • Author(s): Kobayashi T, Nureki 0, Ishitani R, Yaremchuk A, Tukalo M, Cusack S, Sakamoto K, Yokoyama S.
  • Journal Title: Nature Structural Biology 10 Pages: 425-432
  • Peer Reviewed
• [Journal Article] A Magic Pot : Self-assembly computation revisited (2002)
  • Author(s): T. Yokomori, Y. Sakakibara, S. Kobayashi
  • Journal Title: Lecture Notes in Computer Science 2300 Pages: 418-429
  • Peer Reviewed
• [Journal Article] On the computational power of Insertion-Deletion Systems (2002)
  • Author(s): A. Takahara, T. Yokomori
  • Journal Title: Proc. of DNA Based Computers (DNA8) 1 Pages: 139-150
  • Peer Reviewed
• [Journal Article] Molecular computing paradigm-toward freedom from Turing's charm (2002)
  • Author(s): Takashi Yokomori
  • Journal Title: Natural Computing 4 Pages: 333-390
  • Peer Reviewed
• [Journal Article] P-systems on Grraphs of restricted forms (2002)
  • Author(s): Gh. Paun, Y. Sakakibara, T. Yokomori
  • Journal Title: Publ. Math Debrecen 60 Pages: 635-660
  • Peer Reviewed
• [Journal Article] DNA Sequence Design Using Templates (2002)
  • Author(s): M. Arita, S. Kobayashi
  • Journal Title: New Generation Computing 20 Pages: 263-277
  • Peer Reviewed
• [Journal Article] On Template Method for DNA Sequence Design (2002)
  • Author(s): S. Kobayashi, T. Kondo, M. Arita
  • Journal Title: Proc・of DNA Based Computers (DNA8) 1 Pages: 115-124
  • Peer Reviewed
• [Journal Article] バルジ・内部ループを形成しないDNA配列セットの設計 (2002)
  • Author(s): 奥田講平, 小林聡
  • Journal Title: 情報処理学会研究報告 2002-MPS-42 Pages: 99-102
  • Peer Reviewed
• [Journal Article] A Pure Meta-Interpreter for Flat GHC, A Concurrent Constraint Language (2002)
  • Author(s): Kazunori Ueda
  • Journal Title: Computational Logic : Logic Programming and Beyond(A. C. Kakas, F. Sadri, Eds. ), LNAI, Springer-Verlag 2407 Pages: 138-161
  • Peer Reviewed
• [Journal Article] Programming with Logical Links : Design of the LMNtal language (2002)
  • Author(s): Kazunori Ueda, Norio Kato
  • Journal Title: Proc. 3rd Asian Workshop on Programming Languages and Systems (APLAS 2002) 1 Pages: 115-126
  • Peer Reviewed
• [Journal Article] Sequentiality Analysis for Concurrent Logic Programs (2002)
  • Author(s): Norio Kato, Kazunori Ueda
  • Journal Title: Proc. 6th World Multiconference on Systemics, Cybernetics and Informatics (SCI 2002) 11 Pages: 329-336
  • Peer Reviewed
• [Journal Article] Programming with Logical Links (2002)
  • Author(s): 上田和紀, 加藤紀夫
  • Journal Title: 日本ソフトウェア科学会第19回大会論文集 1 Pages: 3A-1
  • Peer Reviewed
• [Journal Article] Kima : an Automated Error Correction System for Concurrent Logic Programs (2002)
  • Author(s): Yasuhiro Ajiro, Kazunori Ueda
  • Journal Title: Automated Software Engineering 9 Pages: 67-94
  • Peer Reviewed
• [Journal Article] Parallelization of a Local Search Method for the Generalized Assignment Problem (2002)
  • Author(s): M. Ishibashi, Y. Asahiro, M, Yamashita
  • Journal Title: Proc. of the Second Japanese-Sino Optimization Meeting (JSOM 2002) 1 Pages: 85
  • Peer Reviewed
• [Journal Article] On-Line Grid Packing with a Single Active Grid (2002)
  • Author(s): S. Fujita
  • Journal Title: Information Processing Letters 85, 4, 28 Pages: 199-204
  • Peer Reviewed
• [Journal Article] Location-Aware Buffering Schemes for Road Vehicle Communication Systems (2002)
  • Author(s): S. Tagashira, Y. Wang, s. Fujita
  • Journal Title: Proc. IASTED Int'l Conf. Networks, Parallel and Distributed Processing and Applications (NPDPA 2002) 1 Pages: 99-104
  • Peer Reviewed
• [Journal Article] 自己相似タイル貼り構成の計算例 (2002)
  • Author(s): 貞広泰造, 櫻井幸一
  • Journal Title: 数理解析研究所講究録, 数学解析の計算機上での理論的展開とその遂行可能性 1286 Pages: 119-130
  • Peer Reviewed
• [Journal Article] 有限遷移系の木表現式からの遷移図の自動作成 (2002)
  • Author(s): 井口修二, 溝口佳寛, 河原康雄
  • Journal Title: 応用数学合同研究集会報告集(2002/12) 1 Pages: 25-30
  • Peer Reviewed
• [Journal Article] Fair Circulation of a Token (2002)
  • Author(s): S. Ikeda, N. Okumoto, I. Kubo, M. Yamashita
  • Journal Title: IEEE Trans. Parallel and Distributed Systems 13(4) Pages: 367-372
  • Peer Reviewed
• [Journal Article] Uniform and Self-Stabilizing Fair Mutual Exclusion on Unidirectional Rings with Unfair Distributed Daemon (2002)
  • Author(s): H. Kakugawa, M. Yamashita
  • Journal Title: Journal of Parallel and Distributed Computing 62 Pages: 885-898
  • Peer Reviewed
• [Journal Article] Complexity analysis of the SATengine : DNA algorithms as probabilistic algorithms (2002)
  • Author(s): Masami Hagiya, John A. Rose, Ken Komiya, Kensaku Sakamoto
  • Journal Title: Theoretical Computer Science Vol. 287 Pages: 59-71
  • Peer Reviewed
• [Journal Article] Horn Clause Computation by Self-Assembly of DNA Molecules (2002)
  • Author(s): Hiroki Uejima, Masami Hagiya, Satoshi Kobayashi
  • Journal Title: DNA7 Lecture Notes in Computer Science Vol. 2340 Pages: 308-320
  • Peer Reviewed
• [Journal Article] Photo-Regulation of DNA-Triplex Formation by Azobenzene (2002)
  • Author(s): X. Liang, H. Asanuma, M. Komiyama
  • Journal Title: J. Am. Chem. Soc. 124 Pages: 1877-1883
  • Peer Reviewed
• [Journal Article] Photo-Regulation of Transcription Reaction by T7 RNA Polymerase by Tethering an Azobenzene in the Promoter (2002)
  • Author(s): H. Asanuma, D. Tamaru, A. Yamazawa, M. Liu, M. Komiyama
  • Journal Title: CHEMBIOCHEM 1 Pages: 786-789
  • Peer Reviewed
• [Journal Article] Photo-regulation of transcription by RNA polymerase with azobenzene-tethered promoter (2002)
  • Author(s): H. Asanuma, M. Liu, D. Tamaru, X. Liang, M. Komiyama
  • Journal Title: Nucleic Acids Res. Supple 2 1 Pages: 75-76
  • Peer Reviewed
• [Journal Article] H-Aggregation of Methyl Reds by the Hybridization of DNA-Dye conjugates (2002)
  • Author(s): H. Asanuma, R. Shirasuka, M. Komiyama
  • Journal Title: Chem. Lett. 1 Pages: 490-491
  • Peer Reviewed
• [Journal Article] Self-Organizing Formation Algorithm for Active Elements (2002)
  • Author(s): K. Fujibayashi, S. Murata, K. Sugawara, M. Yamamura
  • Journal Title: Proc. 21^<st> IEEE Symposium on Reliable Distributed Systems 1 Pages: 416-421
  • Peer Reviewed
• [Journal Article] Enhanced nano-oxidation on a SC1-treated Si surface using atomic force microscopy (2002)
  • Author(s): W. C. Moon, T. Yoshinobu, H. Iwasaki
  • Journal Title: Jpn. J. Appl. Phys. 41 Pages: 4754-4-757
  • Peer Reviewed
• [Journal Article] AFM Fabrication of Oxide Patterns and Immobilization of Biomolecules on Si Surface (2002)
  • Author(s): T. Yoshinobu, J. Suzuki, W. C. Moon, H. Kurooka, H. Iwasaki
  • Journal Title: 53rd Annual Meeting of the International Society of Electrochemistry, EMNT2002 1 Pages: 3131-3135
  • Peer Reviewed
• [Journal Article] Towards DNA patterning on silicon surface--consideration on basic methods-- (2002)
  • Author(s): A. Nishikawa, H. Kurooka, S. Antoranz Contera, W. C. Moon, T. Yoshinobu, H. Iwasaki
  • Journal Title: Preliminary proceedings of DNA8 1 Pages: 334
  • Peer Reviewed
• [Journal Article] 分子計算の現状--DNA8の話題から (2002)
  • Author(s): 西川明男
  • Journal Title: Computer Today 第19巻5号 Pages: 17-21
  • Peer Reviewed
• [Journal Article] Programmable DNA computer with application to mathematical and biological problems (2002)
  • Author(s): A. Suyama
  • Journal Title: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers 1 Pages: 91
  • Peer Reviewed
• [Journal Article] Highly specific and Quantitative gene expression profiling based on DNA computing (2002)
  • Author(s): N. Nishida, M. Wakui, Y. Hatta-Ohashi, T. Tokunaga, A. Suyama
  • Journal Title: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers 1 Pages: 79
  • Peer Reviewed
• [Journal Article] Automated processing system for gene expression profiling based on DNA computing technologies (2002)
  • Author(s): N. Morimoto, M. Kiyohara, N. Sugiura, S. Karaki, T. Nakajima, T. Makino, N. Nishida, A. Suyama
  • Journal Title: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers 1 Pages: 331
  • Peer Reviewed
• [Journal Article] Solving a 10-variable 43-clause instance of 3-SAT problems on DNA computer automatically executing a basic instruction set (2002)
  • Author(s): T. Nakajima, Y. Sakai, A. Suyama
  • Journal Title: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers 1 Pages: 332
  • Peer Reviewed
• [Journal Article] ハイブリッドDNAコンピュータのハードウェア (2002)
  • Author(s): 陶山明
  • Journal Title: 電気学会誌 122(3) Pages: 160-163
  • Peer Reviewed
• [Journal Article] DNAコンピュータの現状と将来 (2002)
  • Author(s): 陶山明
  • Journal Title: Computer Today 109 Pages: 11-16
  • Peer Reviewed
• [Journal Article] 実用化されはじめたDNAコンピューター (2002)
  • Author(s): 陶山明
  • Journal Title: 日経サイエンス 5月号 Pages: 114
  • Peer Reviewed
• [Journal Article] 分子生物学の教科書に隠されていたDNAコンピュータ. (2002)
  • Author(s): 陶山明
  • Journal Title: 細胞工学 21(11) Pages: 1346-1349
  • Peer Reviewed
• [Journal Article] An Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer (2002)
  • Author(s): J. A. Rose, E. J. Deaton, M. Hagiya, A. Suyama
  • Journal Title: Physical Review E Vol. 65, No. 2-1 Pages: 1-13
  • Peer Reviewed
• [Journal Article] The Fidelity of the Tag-Antitag System, DNA Computing (2002)
  • Author(s): John A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama
  • Journal Title: DNA7, LNCS 2340 Pages: 138-149
  • Peer Reviewed
• [Journal Article] PNA-mediated Whiplash PCR, DNA Computing (2002)
  • Author(s): John. A. Rose, Russell J. Deaton, Masami Hagiya, Akira Suyama
  • Journal Title: DNA7, LNCS 2340 Pages: 104-116
  • Peer Reviewed
• [Journal Article] A DNA-based in vitro Genetic Program (2002)
  • Author(s): J. A. Rose, M. Hagiya, R. J. Deaton, A. Suyama
  • Journal Title: J. Biol. Phys. 28 Pages: 493-498
  • Peer Reviewed
• [Journal Article] A PNA-mediated whiplash PCR-based program for in vitro protein evolution (2002)
  • Author(s): J. A. Rose, M. Takano, A. Suyama
  • Journal Title: Preliminary Proc. of The Eighth International Meeting on DNA Based Computers 1 Pages: 5-18
  • Peer Reviewed
• [Journal Article] PDMS glass hybrid microreactor array with embedded temperature controldevice. Application to cell-free protein synthesis (2002)
  • Author(s): Takatoki Yamamoto, Teruo Fujii, Takahiko Nojima
  • Journal Title: Lab on a Chip 2 Pages: 197-202
  • Peer Reviewed
• [Journal Article] Towards a High Reliability of the PCR Amplification Process in DNA Computing (2002)
  • Author(s): Masashi Nakatsugawa, Satoshi Kashiwamura, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: International Journal of Computational Intelligence and Applications Vol. 2, No. 4 Pages: 423-432
  • Peer Reviewed
• [Journal Article] Local Search by Concentration Controlled DNA Computing (2002)
  • Author(s): Masahito Yamamoto, Atsushi Kameda, Nobuo Matsuura, Toshikazu Shiba, Yumi Kawazoe, Azuma Ohuchi
  • Journal Title: International Journal of Computational Intelligence and Applications Vol. 2, No. 4 Pages: 447-455
  • Peer Reviewed
• [Journal Article] A Security System for Personal Genome Information at DNA level (2002)
  • Author(s): Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of IEEE Computer Society Bioinfomation Conference 1 Pages: 314-320
  • Peer Reviewed
• [Journal Article] An Analysis of Computational Efficiency of DNA Computing (2002)
  • Author(s): Atsushi Kameda, Nobuo Matsuura, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Unconventional Models of Computation, Lecture Notes in Computer Science 2509 Pages: 2509
  • Peer Reviewed
• [Journal Article] A Separation Method for DNA Computing Based on Concentration Control (2002)
  • Author(s): Masahito Yamamoto, Atsushi kameda, Nobuo Matsuura, Toshikazu Shiba, Yumi Kawazoe, Azuma Ohuchi
  • Journal Title: New Generation Computing 20 Pages: 251-261
  • Peer Reviewed
• [Journal Article] Towards Optimization of PCR Protocol in DNA Computing (2002)
  • Author(s): Satoshi Kashiwamura, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA7), LNCS 2340 Pages: 14-22
  • Peer Reviewed
• [Journal Article] Developing Support System for Sequence Design in DNA Computing (2002)
  • Author(s): Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: The 7th International Meeting on DNA Computing, LNCS 2340 Pages: 129-137
  • Peer Reviewed
• [Journal Article] Solutions of Shortest Path Problems by Concentration Control (2002)
  • Author(s): Masahito Yamamoto, Nobuo Matsuura, Toshikazu Shiba, Yumi Kawazoe, Azuma Ohuchi
  • Journal Title: DNA Computing (DNA7), LNCS 2340 Pages: 203-212
  • Peer Reviewed
• [Journal Article] Towards a General Purpose Sequence Design System in DNA Computing (2002)
  • Author(s): Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Proceedings of 2002 Congress on Evolutionary Computation 1 Pages: 73-78
  • Peer Reviewed
• [Journal Article] Simulation Analysis of Hybridization Process for DNA Computing with Concentration Control (2002)
  • Author(s): Masahito Yamamoto, Atsushi Kameda, Nobuo Matsuura, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Proceedings of 2002 Congress on Evolutionary Computation 1 Pages: 85-90
  • Peer Reviewed
• [Journal Article] Design of a PCR Protocol for Improving Reliability of PCR in DNA Computing (2002)
  • Author(s): Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Proceedings of 2002 Congress on Evolutionary Computation 1 Pages: 91-96
  • Peer Reviewed
• [Journal Article] Improvement of the Reliability of Experiments in DNA Computing (2002)
  • Author(s): Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Preliminary Proceedings of 8th International Meeting on DNA Based on Computings 1 Pages: 333
  • Peer Reviewed
• [Journal Article] Constructions of Security System for Information Encoded by DNA (2002)
  • Author(s): Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto, Azuma Ohuchi
  • Journal Title: Proceedings of 8th International Meeting on DNA Based on Computings 1 Pages: 337-337
  • Peer Reviewed
• [Journal Article] Hierarchical DNA Memory based on Nested PCR (2002)
  • Author(s): Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba, Azuma Ohuchi
  • Journal Title: Proceedings of 8th International Meeting on DNA Based Computers 1 Pages: 231-240
  • Peer Reviewed
• [Journal Article] 解説 DNAコンピューテイングパラダイム-その原理と工学応用への課題 (2002)
  • Author(s): 山本雅人, 柴肇二,大内東
  • Journal Title: システム/制御/情報 5 Pages: 260-268
  • Peer Reviewed
• [Journal Article] Optimization of Noisy Fitness Functions by means of Genetic Algorithms using History. of Search with Test of Estimation (2002)
  • Author(s): Yasuhito Sano, Hajime Kita
  • Journal Title: Proc. CEC2002 1 Pages: 360-365
  • Peer Reviewed
• [Journal Article] 探索履歴を利用した遺伝的アルゴリズムによる不確実関数の最適化 (2002)
  • Author(s): 佐野泰仁, 喜多一
  • Journal Title: 電気学会論文誌 Vol. 122-C, No. 6 Pages: 1001-1008
  • Peer Reviewed
• [Journal Article] GTOP : a database of protein structures predicted from genome sequences (2002)
  • Author(s): T. Kawabata, S. Fukuchi, K. Honmma, M. Ota, J. Araki, T. Ito, N. Ichiyoshi, K. Nishikawa
  • Journal Title: Nucleic Acids Res. 30 Pages: 294-298
  • Peer Reviewed
• [Journal Article] A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome (2002)
  • Author(s): K. Homma, S. Fukuchi, T. Kawabata, M. Ota, K. Nishikawa
  • Journal Title: Gene 294 Pages: 25-33
  • Peer Reviewed
• [Journal Article] Identification of amino acids involved in protein structural uniqueness : Implication for de novo protein design (2002)
  • Author(s): Y. Isogai, M. Ota, A. Ishii, M. Ishida, K. Nishikawa
  • Journal Title: Protein Vol. 15, No. 7 Pages: 555-560
  • Peer Reviewed
• [Journal Article] A statistical-mechanical approach to CDMA multiuser detection : propagating beliefs in a densely connected graph (2002)
  • Author(s): Yoshiyuki Kabashima
  • Journal Title: cond-mat/0210535 A36 Pages: 11111-11121
  • Peer Reviewed
• [Journal Article] Robust Evolutionary Algorithms with Toroidal Search Space Conversion for Function Optimization (2002)
  • Author(s): Hiroshi Someya, Masayuki Yamamura
  • Journal Title: In Proceedings of the Genetic and Evolutionary Computation Conference 2002 (GECCO-2002) 1 Pages: 553-560
  • Peer Reviewed
• [Journal Article] 探索オペレータの機能分担を考慮した進化型計算による関数最適化 (2002)
  • Author(s): 染谷博司, 山村雅幸
  • Journal Title: 電気学会論文誌C Vol. 122-C, No. 3 Pages: 363-373
  • Peer Reviewed
• [Journal Article] Design of Various High Quality Random Libraries for in vitro Protein Evolution (2002)
  • Author(s): Soramoto, S., Ueno, S., Tabuchi, I., Husimi, Y.
  • Journal Title: Genome Informatics 13 Pages: 527-528
  • Peer Reviewed
• [Journal Article] Evolutionary molecular engineering and the evolvability of biopolymers (2002)
  • Author(s): Husimi, Y.
  • Journal Title: 7th International Symposium on Bio-Nanoelectronics : Creation of Nano-Micro structures in Bioscience & Technology 7 Pages: 14-28
  • Peer Reviewed
• [Journal Article] Construction of block shuffled libraries of DNA for evolutionary protein engineering : Y-ligation based block shuffling (2002)
  • Author(s): Kitamura, K., Kinoshita Y., Narasaki, Nemoto, N., Husimi, Y., Nishigaki, K.
  • Journal Title: Protein Engineering 15 Pages: 843-853
  • Peer Reviewed
• [Journal Article] An efficient ligation in the making of in vitro virus for in vitro protein evolution (2002)
  • Author(s): Tabuchi I., Soramoto S., Suzuki M., Nemoto, N., Husimi, Y.
  • Journal Title: Biological Proc On-Line 4 Pages: 49-54
  • Peer Reviewed
• [Journal Article] Correlated Flexible Molecular Coding and Molecular Evolvability (2002)
  • Author(s): Husimi Y., Aita T., Tabuchi I.
  • Journal Title: J. Biol. Phys. 28 Pages: 499-507
  • Peer Reviewed
• [Journal Article] Surveying a Local Fitness Landscape of a Protein with Epistatic Sites for the study of Directed Evolution (2002)
  • Author(s): Aita T., Hamamatsu N., Nomiyama Y., Uchiyama, N., Shibanaka, Y., Husimi, Y.
  • Journal Title: Biopolymers 64 Pages: 95-105
  • Peer Reviewed
• [Journal Article] An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-tree system (2002)
  • Author(s): Kiga, D., Sakamoto, K., Kodama, K., Kigawa, T., Matsuda, T., Yabuki, T., Shirouzu, M., Harada, Y., Nakayama, H., Takio, K., Hasegawa, Y., Endo, Y., Hirao, I., Yokoyama, S.
  • Journal Title: Proc. Natl. Acad. Sci. USA 99 Pages: 9715-9720
  • Peer Reviewed
• [Journal Article] Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells (2002)
  • Author(s): Sakamoto, K., Hayashi, A., Sakamoto, A., Kiga, D., Nakayama, H., Soma, A., Kobayashi, T., Kitabatake, M., Takio, I, Saito, K., Shirouzu, M., Hirao, I., Yokoyama, S.
  • Journal Title: Nucleic Acids Research 30 Pages: 4692-4699
  • Peer Reviewed
• [Journal Article] How to pack directed acyclic graphs into small blocks
  • Author(s): Y. Asahiro, T. Furukawa, K. Ikegami, E. Miyano
  • Journal Title: Proc. 6th International Conference on Algorithms and Complexity(ClAC 2006), Lecture Notes in Computer Science 3998 2006 Pages: 272-283
  • Peer Reviewed
• [Book] 岩波科学ライブラリ (2007)
  • Author(s): 西川明男, 萩谷昌己
  • Publisher: 『DNAマシン----分子が動く, 計算する』
• [Book] 12^<th> International Meeting on DNA Computing, DNA12, Lecture Notes in Computer Science (2006)
  • Author(s): Chengde Mao, Takashi Yokomori
  • Total Pages: 440
  • Publisher: Springer-Verlag
• [Book] 進化・情報・かたち-"生命知"のパースペクティブ, 4-2 生物の形-システムの生成と進化の観点から (2006)
  • Author(s): 村田 智(分担執筆)
  • Total Pages: 156-170
  • Publisher: 培風館
• [Patent(Industrial Property Rights)] Apparatus and method for fabricating Nanoconstruct (2006)
  • Inventor(s): 村田智, 染井康太郎
  • Industrial Property Rights Holder: 東京工業大学
  • Industrial Property Number: PCT(国際出願)JP2006/311237
  • Filing Date: 2006-12-17
  • Overseas