文字サイズ変更

Publications
since 2000

Publications

    in reverse chronological order

  • Miho Tagawa,Koh-ichiroh Shohda,Kenzo Fujimoto and Akira Suyama Stabilization of DNA nanostructures by photo-cross-linking: Soft Matter, 2011,7, 10931-10934
  • Yoko Sakai, Yoriko Mawatari, Kiyonari Yamasaki, Koh-ichiroh Shohda, and Akira Suyama Construction of AND gate for RTRACS with the capacity of extension to NAND gate. Lect. Notes Comput. Sc., 5877, 137-143 (2009).
  • Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama RNA oscillator: limit cycle oscillations based on artificial biochemical reactions New Generation Computing, vol.27, pp.107-127 (2009).
  • Miho Tagawa, Tadashi Ohtani, Koh-ichiroh Shohda, Kenzo Fujimoto, and Akira Suyama New photoligation method and strand phosphorylation to construct improved fully-addressed DNA scaffolds. Proceeding of The 6th Annual Conference on Foundations of Nanoscience: Self-assembled Architectures and Devices (FNANO09) .
  • Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama Design and numerical analysis of RNA oscillator Oral Presentation, Proceedings in Information and Communications Technology: Natural Computing, vol. 1, pp. 201-212 (2008).
  • Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama Experiments and simulation models of a basic computation element of an autonomous molecular computing system Phys. Rev. E, vol.78, article number 041921 (2008).
  • Tetsuro Kitajima, Masahiro Takinoue, Koh-ichiroh Shohda, and Akira Suyama Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics Lect. Notes Comput. Sc., vol.4848, pp.119-129 (2008).
  • John A. Rose, Russell J. Deaton, Masami Hagiya, and Akira Suyama Coupled equilibrium model of hybridization error for the DNA microarray and tag-antitag systems IEEE Transactions on Nanobioscience, 6 (1), 18-27 (2007).
  • Miho Tagawa, Koh-ichiroh Shohda, Kenzo Fujimoto, Tadashi Sugawara and Akira Suyama Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine Nucleic Acids Res, 35, (21), e140 (2007).
  • Masahiro Takinoue and Akira Suyama Hairpin DNA memory using molecular addressing Small, 2, 1244-1247 (2006).
  • Yusuke Ogura, Taro Beppu, Masahiro Takinoue, Akira Suyama, and Jun Tanida Control of DNA molecules on a microscopic bead using optical techniques for photonic DNA memory Lect. Notes Comput. Sc., 3892, 213-223 (2006)
  • Ken Komiya, Satsuki Yaegashi, Masami Hagiya, Akira Suyama, and John A. Rose Experimental validation for the statistical thermodynamic model for prediction of the behavior of autonomous molecular computers based on DNA hairpin formation Lect. Notes Comput. Sc., 4287, 428-438 (2006).
  • Koh-ichiroh Shohda, Daisuke Kiga, Masahiro Takinoue, Kageyama Yoshiyuki, Tadashi Sugawara, and Akira Suyama An autonomous molecular computing system in cell-sized liposome Proceedings of NanoBio-Tokyo 2006, 357-358 (2006).
  • Masahiro Takinoue, Daisuke Kiga, Koh-ichiroh Shohda, and Akira Suyama Bionano clock based on an autonomous biomolecular computing system Proceedings of NanoBio-Tokyo 2006, 361-362 (2006).
  • Miho Tagawa, Koh-ichiroh Shohda, Kenzo Fujimoto, and Akira Suyama Heat-resistant DNA arrays constructed by self-assembly Proceedings of NanoBio-Tokyo 2006, 383-384 (2006).
  • Masahiro Takinoue, Takashi Endoh, and Akira Suyama Amorphous hairpin DNA memory for assembling nanoparticles/biomacromolecules Foundations of Nanoscience 2006 ― Self-Assembled Architectures and Devices. John Reif, Ed., pp.140-141, Science Technica (2006).
  • Miho Tagawa, Koh-ichiroh Shohda, and Akira Suyama Programmable step-by-step assembly of DNA nano-triangles Foundations of Nanoscience 2006 ― Self-Assembled Architectures and Devices. John Reif, Ed., p.173, Science Technica (2006).
  • Akira Suyama Turing machine using RTRACS Preliminary proceedings of DNA 12, C. Mao, T. Yokomori, and B. Zhang, Eds., p. 422 (2006).
  • Takashi Endoh, Masahiro Takinoue, and Akira Suyama Large-capacity molecular memory using hairpin DNA immobilized on a substrate Preliminary proceedings of DNA 12, C. Mao, T. Yokomori, and B. Zhang, Eds., p. 421 (2006).
  • Daisuke Kiga, Koh-ichiroh Shoda, Masahiro Takinoue, and Akira Suyama Autonomous DNA computer in small vesicle Preliminary proceedings of DNA 12, C. Mao, T. Yokomori, and B. Zhang, Eds., p. 420 (2006).
  • Tetsuro Kitajima, Nasahiro Takinoue, and Akira Suyama Kinetic analysis of DNA hybridization Preliminary proceedings of DNA 12, C. Mao, T. Yokomori, and B. Zhang, Eds., p. 419 (2006).
  • Masahiro Takinoue, Daisuke Kiga, and Akira Suyama A numerical analysis of an autonomous molecular computing system, RTRACS Preliminary proceedings of DNA 12, C. Mao, T. Yokomori, and B. Zhang, Eds., p. 411 (2006).
  • Nao Nishida, Tetsuya Tanabe, Kento Hashido, Kouyuki Hirayasu, Miwa Takasu, Akira Suyama and Katsushi Tokunaga DigiTag assay for multiplex single nucleotide polymorphism typing with high success rate. Anal. Biochem., 346, 281-288 (2005).
  • H. Yoshida, T. Yokomori and A. Suyama A simple classifications of the volvocine algae by formal languages. Bulletin of Mathematical Biology, 67, 1339-1354 (2005).
  • Y. Ogura, T. Kawakami, F. Sumiyama, S. Irie, A. Suyama, and J. Tanida Methods for manipulating DNA molecules in a micrometer scale using optical techniques. Lect. Notes Comput. Sc., 3384, 258-267 (2005).
  • Y. Ogura, T. Beppu, M. Takinoue, A. Suyama, and J. Tanida Control of DNA molecules on a microscopic bead using optical techniques for photonic DNA memory. Preliminary proceedings of DNA 11, A. Carbone, M. Daley, L. Kari, I. McQuillan and N. Pierce, Eds., pp. 78-88 (2005).
  • O. Gotoh, Y. Sakai, Y. Mawatari, W. Gunji, Y. Murakami and A. Suyama Normalized molecular encoding method for quantitative gene expression profiling. Preliminary proceedings of DNA 11, A. Carbone, M. Daley, L. Kari, I. McQuillan and N. Pierce, Eds., p. 395 (2005).
  • D. Kiga, T. Mochida, M. Takinoue and A. Suyama Realization of RTRAC: Reverse transcription and Transcription-based Autonomous Computer. Preliminary proceedings of DNA 11, A. Carbone, M. Daley, L. Kari, I. McQuillan and N. Pierce, Eds., p. 397 (2005).
  • M. Takinoue, Y. Hatano, Y. Endoh and A. Suyama Amorphous DNA memory constructed with hairpin DNA immobilized on a soliud surface. Preliminary proceedings of DNA 11, A. Carbone, M. Daley, L. Kari, I. McQuillan and N. Pierce, Eds., p. 410 (2005).
  • M. Tagawa, D. Kiga, T. Yoshinobu, H. Iwasaki, and A. Suyama Programmable step-by-step assembly of DNA nanostructures. Foundations of Nanoscience 2005 ― Self-Assembled Architectures and Devices. John Reif, Ed., p.192, Science Technica (2005).
  • 陶山明 DNAエンコード技術を用いた発現解析 蛋白質核酸酵素, 50 (16), 2300 (2005).
  • 陶山明 細胞の中で働くコンピュータ (前編) BIONICS 7月号, 58-60 (2005).
  • 陶山明 細胞の中で働くコンピュータ (後編) BIONICS 8月号, 54-56 (2005).
  • Masahiro Takinoue, Akira Suyama "Molecular reactions for a molecular memory based on hairpin DNA" Chem-Bio Informatics Journal, 4, 93-100 (2004).
  • Omagari K, Yoshimura H, Takano M, Hao D, Ohmori M, Sarai A, Suyama A. "Systematic single base-pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803" FEBS Lett., 563, 55-58 (2004)
  • Hironori K. Nakamura, Masaki Sasai, Mitsunori Takano "Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model" PROTEINS: Structure, Function, and Genetics, vol. 55, 99-106 (2004)
  • J. A. Rose and A. Suyama, "Physical Modeling of Biomolecular Computers: Models, limitations, and experimental validation." Natural Computing, 3, 411-426 (2004).
  • J. A. Rose, R. J. Deaton, and A. Suyama "Statistical thermodynamic analysis and design of DNA-based Computers." Natural Computing, 3, 443-459 (2004).
  • N. Nitta and A. Suyama "Autonomous biomolecular computer modeled after retroviral replication." Lect. Notes Comput. Sc., 2943, 203-212 (2004).
  • Y. Ogura, T. Kawakami, F. Sumiyama, A. Suyama, and J. Tanida "Parallel translation of DNA clusters by VCSEL array trapping and temperature control with laser illumination." Lect. Notes Comput. Sc., 2943, 10-18 (2004).
  • Y. Ogura, T. Kawakami, F. Sumiyama, S. Irie, A. Suyama, and J. Tanida "Methods for manipulating DNA molecules in a micrometer scale using optical techniques." Preliminary proceedings of DNA 10, C. Ferretti, G. Mauri, and C. Zandron, Eds., pp.365-374 (2004).
  • M. Takinoue and A. Suyama "Development of a molecular memory using hairpin DNA." Preliminary proceedings of DNA 10, C. Ferretti, G. Mauri, and C. Zandron, Eds., p.436 (2004).
  • 陶山明 (分担執筆) "DNAコンピュータの現状と将来" 臨時別冊・数理科学 SGCライブラリ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-(萩谷昌己・編著), 129-135 (2004).
  • 陶山明 "DNAコンピュータとナノテクノロジー" 細胞工学, 23 (2), 241-246 (2004).
  • 陶山明 "バイオコンピュータ・DNAデバイス" 新訂版・表面科学の基礎と応用, 日本表面科学会編, pp.1365-1367, エヌ・ティー・エス (2004).
  • J. A. Rose, 陶山明 "DNA二重らせんの安定性を解く―その理論と応用" 東京大学バイオインフォマティクス集中講義, 高木利久監修, pp.60-67, 羊土社 (2004).
  • N. Nitta and A. Suyama "Autonomous biomolecular computer modeled after retroviral replication." Proc. of DNA9, 180-189 (2003).
  • J. A. Rose, M. Takano, M. Hagiya, and A. Suyama "A DNA-computing-based genetic program for in vitro protein evolution via constrained pseudomodule shuffling." Genetic Programming and Evolvable Machines, 4, 139-152 (2003).
  • M. Takano, H. K. Nakamura, K. Nagayama, and A. Suyama "Investigating a link between all-atom model simulation and the Ising-based theory on the helix--coil transition. II. Nonstationary properties." J. Chem. Phys., 118, 10312-10322 (2003).
  • J. A. Rose, M. Takano, and A. Suyama "A PNA-mediated whiplash PCR-based program for in vitro protein evolution." LNCS Vol. 2568, 47-60 (2003).
  • Y. Ogura, T. Kawakami, F. Sumiyama, A. Suyama, and J. Tanida "Parallel translation of DNA clusters by VCSEL array trapping and temperature control with laser illumination." Proc. of DNA9, 19-27 (2003).
  • J. A. Rose, M. Hagiya, and A. Suyama "The fidelity of the tag-antitag system 2: Identifying the regime of stringency." Proc. of The 2003 Congress on Evolutionary Computation Vol. 4, R. Sarker et al., Eds., pp. 2740-2747, IEEE Press (2003).
  • 陶山明 "DNAコンピュータとその応用" ゲノム医学, 3 (2), 223-228 (2003).
  • 陶山明 "自律的に動作するin vivo DNAコンピュータ" 細胞工学, 22 (11), 1244-1249 (2003).
  • 陶山明 "DNAコンピュータで生命の謎を解く" 細胞工学, 22 (8), 882-886 (2003).
  • 陶山明 "生命体は分子コンピュータである" 細胞工学, 22 (5), 570-572 (2003).
  • 陶山明 "汎用型DNAコンピュータを目指して" 細胞工学, 22 (3), 348-352 (2003).
  • 陶山明 "超並列DNAコンピュータの誕生:エーデルマンの実験" 細胞工学, 22 (1), 75-79 (2003).
  • 陶山明 "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, pp.53-58, 応用物理学会 (2003).
  • J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama "Equilibrium Analysis of the Efficiency of an Autonomous Molecular Computer." Phys. Review E, 65, Article 02910, 1-13 (2002). also published in Virtual Journal of Biological Physics 3, Issue 3 (2002).
  • J. A. Rose, M. Hagiya, R. J. Deaton, and A. Suyama "A DNA-based in vitro Genetic Program." J. Biol. Phys., 28, 493-498 (2002).
  • J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama "PNA-mediated Whiplash PCR." LNCS Vol. 2340, 104-117 (2002).
  • J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama "The Fidelity of the Tag-Antitag System." LNCS Vol. 2340, 138-149 (2002).
  • M. Takano, K. Nagayama, and A. Suyama "How the all-atom simulation and the Ising-based theory reconcile with each other on the helix-coil transition." J. Biol. Phys., 28, 155-161 (2002).
  • M. Takano, K. Nagayama, and A. Suyama "Investigating a link between all-atom model simulation ans the Ising-based theory on the helix coil transition: Equilibrium statistical mechanics." J. Chem. Phys., 116, 2219-2228 (2002).
  • A. Suyama "Programmable DNA computer with application to mathematical and biological problems." Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 91 (2002).
  • N. Nishida, M. Wakui, Y. Hatta-Ohashi, T. Tokunaga, and A. Suyama "Highly specific and quantitative gene expression profiling based on DNA computing." Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 79 (2002).
  • J. A. Rose, M. Takano, and A. Suyama "A PNA-mediated whiplash PCR-based program for in vitro protein evolution." Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, pp. 5-18 (2002).
  • N. Morimoto, M. Kiyohara, N. Sugiura, S. Karaki, T. Nakajima, T. Makino, N. Nishida, and A. Suyama "Automated processing system for gene expression profiling based on DNA computing technologies." T. Nakajima, Y. Sakai, and A. Suyama "Solving a 10-variable 43-clause instance of 3-SAT problems on DNA computer automatically executing a basic instruction set." Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 332 (2002).Preliminary Proc. of The Eighth International Meeting on DNA Based Computers, p. 331 (2002).
  • 陶山明 "ハイブリッドDNAコンピュータのハードウェア." 電気学会誌, 122 (3), 160-163 (2002).
  • 陶山明 "分子生物学の教科書に隠されていたDNAコンピュータ." 細胞工学, 21 (11), 1346-1349 (2002).
  • 陶山明 "DNAコンピュータの現状と将来." Computer Today No. 109, 11-16 (2002).
  • 陶山明 "実用化されはじめたDNAコンピューター." 日経サイエンス 5月号, 114 (2002).
  • Y. Suzuki, H. Taira, T. Tsunoda, J. Mizushima-Sugano, J. Sese, H. Hata, T. Ota, T. Isogai, T. Tanaka, S. Morishita, K. Okubo, Y. Sakaki, Y. Nakamura, A. Suyama, and S. Sugano. "Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites." EMBO reports, 21, 388-393 (2001).
  • Y. Suzuki, T. Tsunoda, J. Sese, H. Taira, J. Mizushima-Sugano, H. Hata, T. Ota, T. Isogai, T. Tanaka, Y. Nakamura, A. Suyama, Y. Sakaki, S. Morishita, K. Okubo, and S. Sugano "Identification and characterization of the potential promoter regions of 1031 kinds of human genes." Genome Research, 11, 677-684 (2001).
  • J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama "The Fidelity of the Universal DNA Chip." Currents in Computational Molecular Biology 2001 (N. El-Manrouk, T. Lengauer, D. Sankoff, Eds.), pp. 163-164, Les Publications CRM, Montreal, Canada (2001).
  • N. Nishida, M. Wakui, K. Tokunaga, and A. Suyama "Highly specific and quantitative gene expression profiling based on DNA computing." Genome Informatics, 12, 259-260 (2001).
  • 陶山明 (第4章:実験的アプローチ 分担執筆) "DNAコンピュータ (萩谷昌己, 横森貴 共編)," 培風館, 222頁 (2001).
  • 牧野徹, 中島隆夫, 陶山明 "遺伝情報解析とDNAコンピュータ." 応用物理学会誌, 70 (12), 1436-1441 (2001).
  • 西田奈央, 陶山明 "DNAコンピューティングによる遺伝子解析." 遺伝子医学, 5 (4), 107-110 (2001).
  • 陶山明 "分子コンピュータの実験." 別冊・数理科学「生命情報科学の拡がり」, 82-88 (2001).
  • 小林聡, 榊原康文, 陶山明, 横森貴 "分子コンピュータ ―その理論と実験." 別冊・数理科学「生命情報科学の拡がり」, 62-72 (2001).
  • 陶山明 "生物情報を利用した計算機:DNAコンピュータ." 応用物理学会スクールA「情報科学と生命科学にみる応用物理の芽」テキスト pp. 15-29, (2001).
  • Y. Suzuki, D. Ishihara, M. Sasaki, H. Nakagawa, H. Hata, T. Tsunoda, M. Watanabe, T. Komatsu, T. Ota, T. Isogai, A. Suyama, and S. Sugano "Statistical analysis of the 5' untranslated region of human mRNA using "oligo-capped" cDNA libraries." Genomics, 64, 286-297 (2000).
  • H. Yoshida and A. Suyama "Solution to 3-SAT by breadth first search." DIMACS Vol. 54, 9-22, (2000).
  • Y. Sakakibara and A. Suyama "Intelligent DNA chips: Logical operation of gene expression profiles on DNA computers." Genome Informatics 11, 33-42 (2000).
  • 中島隆夫, 酒井洋子, 陶山明 "DNAコンピュータのハードウェアの開発." 新しい計算パラダイムシンポジウム2000論文集 情報処理学会シンポジウムシリーズVol. 2000, 51-58 (2000).
  • 吉田寛, 陶山明 "ほぼ自己相似な構造体を用いた計算について." 新しい計算パラダイムシンポジウム2000論文集 情報処理学会シンポジウムシリーズ Vol. 2000, 87-90 (2000).
  • J. A. Rose, A. Suyama, M. Hagiya, R. J. Deaton "An antisense antidote for whiplash PCR." 新しい計算パラダイムシンポジウム2000論文集 情報処理学会シンポジウムシリーズ Vol. 2000, 101-108 (2000).
  • 陶山明 "DNAコンピュータの実現 ―NP完全問題の解法からゲノム解析まで―." 新しい計算パラダイム報告集, 情報処理学会, 27-34 (2000).
  • 陶山明 "分子コンピュータの実験." 数理科学 No.445, 27-31 (2000).

Contact Information

〒 153-8902

東京都 目黒区 駒場 3-8-1 東京大学

大学院 総合文化 研究科 16号館 3階

327A号室(陶山居室)

TEL/FAX: 03-5454-6528

328(実験室) 329 (計算機室)

TEL: 03-5454-6529