Meiji Pharmaceutical University (Jan.2012-Dec.2022)
Meiji Pharmaceutical University (Jan.2012-Dec.2022)
Fukuchi, S., Noguchi, T., Ando, H., Homma, K.: "Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor", Mol. Biol. Evo., 40(1):mac272 (2022).
Homma, K., Anbo, H., Noguchi, T., Fukuchi, S.: "Both Intrinsically Disordered Regions and Structural Domains Evolve Rapidly in Immune-Related Mammalian Proteins", Int. J. Mol. Sci., 19(12), E3860 (2018).
Homma, K., Noguchi, T., Fukuchi, S.: "Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains", Nucleic Acids Res., 44(21), 10051-10061 (2016).
Fang, C., Noguchi, T., D., Yamana, H.: "Condensing position-specific scoring matrixs by the Kidera factors for ligand-binding site prediction", Int J Data Min Bioinform., 12(1), 70-84 (2015).
Goda, N., Shimizu, K., Kuwahara, Y., Tenno, T., Noguchi, T., Ikegami, T., Ota, M., Hiroaki, H.,: "A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR", Int. J. Mol. Sci., 16(7), 15743-15760 (2015).
Fang, C., Noguchi, T., D., Yamana, H.: "Simplified sequence-based method for ATP-binding prediction using contextual local evolutionary conservation", Algorithms Mol Biol., 9, 7 (2014). 
Fang, C., Noguchi, T., D., Yamana, H.: "Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites", J Bioinform Comput Biol., 12(5), 1440003 (2014).
Hirose, S. and Noguchi, T.: "ESPRESSO: a system for estimating protein expression and solubility in protein expression systems.", Proteomics, 13, 1444-1456 (2013). http://cblab.meiyaku.jp/ESPRESSO/
Fang, C., Noguchi, T., D., Yamana, H.: "SCPSSMpred: A General Sequence-based Method for Ligand-binding Site Prediction", IPSJ Transactions on Bioinformatics, 6, 35-42 (2013).
Fang, C., Noguchi, T., Tominaga, D., Yamana, H.: "MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation.", BMC Bioinformatics, Oct 4;14(1):300 (2013).
Fang, C., Yamana, H. and Noguchi, T.: "Sequence-Based Prediction of Molecular Recognition Features in Disordered Proteins", J. Med. and Bioeng., 2(2), June (2013).
菅野敦之、野口 保、山名早人:"セキュアな環境における副作用ファジー検索システムの構築"、第52回日本薬剤師会学術大会、Oct.(2019).
山田 弘、五十嵐芳暢、中津則之、山縣友紀、秋丸裕司、秋丸恵理佳、堀本勝久、福井一彦、江良択実、沼川忠広、松本志郎、植沢芳広、永井純子、野口 保："肝毒性インフォマティクスシステムの構築（AMEDプロジェクト）"、トーゴーの日シンポジウム2019、Oct.(2019).
山田 弘、五十嵐芳暢、中津則之、山縣友紀、秋丸裕司、秋丸恵理佳、堀本勝久、福井一彦、江良択実、沼川忠広、松本志郎、植沢芳広、永井純子、野口 保："肝毒性インフォマティクスシステムの構築（AMEDプロジェクト）"、第46回日本毒性学会学術年会、June(2019).
後藤亮大、廣瀬修一、野口 保:"タンパク質ディスオーダー領域における機能部位予測法の開発"、2017年度生命科学系学会合同年次大会、Dec. (2017).
野口 保："医薬品副作用解析システム実証実験"、JST CREST「ビッグデータ統合利活用の次世代基盤技術の創出・体系化」領域 ビッグデータ統合利用のためのセキュアなコンテンツ共有・流通基盤の構築 シンポジウム2016、March (2016).
廣瀬 修一、野口 保.: "タンパク質発現・可溶性予測システム（ESPRESSO）の改良", 第15回 日本蛋白質科学会年会 (2015).
Fang, C., Yamana, H. and Noguchi, T.: “Analyzing Conservation Patterns and Its Influence on Identifying Protein Functional Sites,” 4th International Conference on Bioinformatics and Computational Biology (BICoB), Las Vegas, USA, March (2014).
Noguchi, T., Shimizu, K., Kanai, S. and Hirose, S., " Development of software to support protein experiments", CBRC2013 , Tokyo, Japan, Sep. (2013).
Fang, C., Yamana, H. and Noguchi, T.: “Identifying Molecular Recognition Features in Disordered Proteins,” CBRC2013, Tokyo, Japan, Sep. (2013).
Fang, C., Yamana, H. and Noguchi, T.: “Identifying functional site of disordered proteins,” The 5th Forum on Data Engineering and Information Management (DEIM2013), Fukushima, Japan, March (2013).
三上拓也、駒田康孝、野口 保、菅野敦之、山名早人: "医薬品副作用情報を用いた副作用検索システムの提案", 第157回DBS・第111回IFAT合同研究発表会(情報処理学会) (2013).
樋口裕哉、植沢芳広、菅裕亮、加賀谷肇、品田昌司、樋口和宏、川崎知己、野口保、田中博之.: "新規フェンセリン誘導体を用いたアセチルおよびブチリルコリンエステラーゼ選択的阻害活性の構造活性相関解析（２）", 第33回日本臨床薬理学会学術総会 (2012).
Hirose, S. and Noguchi T..: "Classification of soluble/ insoluble proteins with ESPRESSO", CBRC2012, 257-262 (2012).
花輪 孟、野口 保、廣瀬 修一.: "分子進化的観点から見た天然変性タンパク質の解析", 第12回 日本蛋白質科学会年会 (2012).
廣瀬 修一、野口 保.: "ESPRESSOによる可溶性および不溶性タンパク質の分類", 第12回 日本蛋白質科学会年会 (2012).
Fang, C., Noguchi, T and Yamana, H..: "Prediction of FAD Binding Residues with Combined Features from Primary Sequence", 2012 International Conference on Bioinformatics and Computational Biology, Kuala Lumpur, Malaysia (2012).
CBRC (Apr.2007-Dec.2011)
Hirose, S., Kawamura, Y., Mori, M., Yokota, K., Noguchi, T. and Goshima, N.: "Development and evaluation of data-driven designed tags (DDTs) for controlling protein solubility", New Biotechnol. 28:3, 255-231 (2011).
Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K.F., Yamamoto, Y., Yamaguchi, A., Kawashima, S., Chun, H.W., Aerts, J., Aranda, B., Barboza, L.H., Bonnal, R.JP., Bruskiewich, R., Bryne, J.C., Fern?ndez, J.M., Funahashi, A., Gordon, P.MK., Goto, N., Groscurth, A., Gutteridge, A., Holland, R., Kano, Y., Kawas, E.A., Kerhornou, A., Kibukawa, E., Kinjo, A.R., Kuhn, M., Lapp, H., Lehvaslaiho, H., Nakamura, H., Nakamura, Y., Nishizawa, T., Nobata, C., Noguchi, T., Oinn, T.M., Okamoto, S., Owen, S., Pafilis, E., Pocock, M., Prins, P., Ranzinger, R., Reisinger, F., Salwinski, L., Schreiber, M., Senger, M., Shigemoto, Y., Standley, D.M., Sugawara, H., Tashiro, T., Trelles, O., Vos, R.A., Wilkinson, M.D., York, W., Zmasek, C.M., Asai, K. and Takagi, T.: “The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium.” J Biomed Semantics, August 21, 1: 8 (2011).
Motono, C., Nakata, J., Koike, R., Shimizu, K., Shirota, M., Amemiya, T., Tomii, K., Nagano, N., Sakaya, N., Misoo, K., Sato, M., Kidera, A., Hiroaki, H., Shirai, T., Kinoshita, K., Noguchi, T. and Ota, M.: "SAHG, a comprehensive database of predicted structures of all human proteins", Nucreic Acid Research, 39:Database issue D487-D493 (2011).
Hirose, S., Yokota, K., Kuroda, Y., Wako, H., Endo, S., Kanai, S. and Noguchi, T.: "Prediction of protein motions from amino acid sequence and its application to protein-protein interaction", BMC Struct.Biol., Jul 13;10:20 (2010).
徳永 慎一, 関嶋 政和, 村岡洋一, 野口保: "確率的情報処理による生体分子の熱揺らぎ解析に関する研究", 2007-BIO-11, 275-280 (2007).
池田 潤一, 関嶋 政和, 村岡洋一, 野口保: "分子動力学法を用いたタンパク質・リガンドの相互作用解析", 2007-MPS-67, 143-146 (2007).
Shimizu, K., Hirose, S., Noguchi, T.: "POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.", Bioinformatics, 23(17), 2337-2338 (2007).
野口 保: "タンパク質disorder領域予測法の最前線", 生物物理, 47(4), 248-252, (2007).
Hirose, S., Shimizu, K., Kanai, S. and Noguchi, T.: "Prediction of Long Disorder Region Using Two-Step SVM", Bioinformatics, 23:16, 2046-2053 (2007).
関嶋 政和, 本田 真也, 野口 保: "超並列計算機を用いた生体分子解析 ─疾病関連蛋白質解析と世界最小蛋白質設計への応用─", 次世代スーパーコンピューティング・シンポジウム2007予稿集, 31-32 (2007)
Sekijima, M., Doi, A., Honda, S., Nogudhi, T., Shimizu, K., Akiyama, Y.: "Development of Free Energy Landscape Analysis System based on Parallel Molecular Dynamics Simulation", IPSJ Transactions on Bioinformatics, 48(17), 30-39 (2007).
Kimura, S., Sekijima, M., Takada, M., Nogudhi, T., Joe, K.: "Development of Molecular Dynamics Simulation based Flexible Docking System", Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007), 732-745 (2007).
Noguchi, T., Yamada, S., Shimizu, K. and Hirose, S.: "Protein disordered region and domain prediction by using POODLE-I and domain linker prediction methods", Proc. of CASP8, 33-34 (2008).
Hirose, S., Shimizu, K., Inoue, N., Kanai, S. and Noguchi, T.: "Disordered region prediction by integrating POODLE series", Proc. of CASP8, 14-15 (2008).
関嶋 政和, 土井 淳, 本田 真也, 野口 保, 清水 茂則, 秋山 泰: "大規模分子動力学シミュレーションによる自由エネルギー地形解析システムの開発", 情報処理学会研究報告, 2007(60), 63-70 (2007).
CBRC (Apr.2001-Mar.2007)
Sekijima, M., Doi, J., Noguchi, T., Akiyama, Y., Shimizu, S.: "Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L", Proceedings of the 25th IASTED International Conference on Parallel and Distributed Computing and Networks, 257-262 (2007).
Nagano, N., Noguchi, N., Akiyama, Y.: "Systematic Comparison of Catalytic Mechanisms of Hydrolysis and
Transfer Reactions Classified in the EzCatDB Database", PROTEINS: Structure, Function, and Bioinformatics,
66(1), 147-159 (2007).
Noguchi,T. and Akiyama,Y.: "PDB-REPRDB: a database of representative protein chains
from the Protein Data Bank (PDB) in 2003", Nucleic Acids Research, 31, 1, 492-493 (2003).
Onizuka,K., Noguchi,T., Akiyama,Y. and Matsuda,H.: "Using Data Compression for Multidimensional Distribution Analysis", IEEE Intelligent Systems, 17, 3, 48-54 (2002).
Noguchi,T., Ito,M., Matsuda,H., Akiyama,Y. and Nishikawa,K.:"Prediction of Protein Secondary Structure Using the Threading Algorithm and Local Sequence Similarity", Research Communications in Biochemistry, Cell & Molecular Biology, 5, 1&2, 115-131 (2001).
Noguchi,T., Matsuda,H. and Akiyama,Y.:"PDB-REPRDB: a database of representative
protein chains from the Protein Data Bank (PDB)", Nucleic Acids Research, 29, 1, 219-220 (2001).
山田 晃太郎, 山田 真介, 山名 早人, 野口 保: "タンパク質立体構造に基づく保存領域の自動抽出", 第6回日本蛋白質科学会年会プログラム・要旨集, 85 (2006).
廣瀬 修一, 清水 佳奈, 金井 理, 野口 保: "2ステップSVMによる長いdisorder領域予測システムの開発", 第6回日本蛋白質科学会年会プログラム・要旨集, 58 (2006).
富井 健太郎, 野口 保: "FORTEによるタンパク質の立体構造予測", バイオテクノロジージャーナル, 6(4), 428-431 (2006).
滝沢 雅俊, 山名 早人, 野口 保: "配列プロファイルを利用したドメインリンカー予測", 情報処理学会研究報告（バイオ情報学）, 41-47 (2006).
中澤 昌美, 高田 雅美, 横田 恭宣, 野口 保, 関嶋 政和, 城 和貴: "SVMを用いた生体分子への金属イオン結合部位予測システムの開発", 情報処理学会研究報告 - バイオ情報学, 2006(135), 157-164 (2006).
木村 紗知, 佐々木 愛美, 関嶋 政和, 高田 雅美, 野口 保, 城 和貴: "熱揺らぎを考慮したDockingシステム開発", 情報処理学会研究報告 - バイオ情報学, 2006(135), 119-126 (2006).
Noguchi, T., Takizawa, M., Inoue, N., Tomii, K.: "Prediction of disordered coil regions in proteins by fold recognition and secondary structure prediction., Proc. of CASP7, 32-33 (2006) .
Shimizu, K., Hirose, S., Inoue, N., Kanai, S., Noguchi, T.: "POODLE: predicting protein disorder using machine-learning approaches", Proc. of CASP7, 33-34 (2006).
Sekijima, M., Motono, C., Noguchi, T., Kaneko, K., Akiyama, Y.: "The Molecular Dynamics Simulations of the Conformational Transition of Prion Protein from its Cellular Form to the Anomalous Form using the Earth Simulator", Annual Report of the Earth Simulator Center 2004-2005 (2005).
Sekijima, M., Motono, C., Akiyama, Y., Kaneko, K., Noguchi, T.: "Dynamics Differences among Species of Prion Protein: Molecular Dynamics Simulation of Mouse, Dog, Cat, Pig, Sheep, Cattle, and Human", Protein Science, 14(suppl1), 264 (2005).
野口 保: "タンパク質構造変化部位データベースの構築", 第5回日本蛋白質科学会年会プログラム・要旨集, 24 (2005).
Sekijima, M., Motono, C., Noguchi, T., Kaneko, K., Akiyama, Y.:
"Conformational transition of Prion Protein from its cellular form to the fibril form
investigated by molecular dynamics simulations", Biophysical Journal, 88(1), 36 (2005).
Noguchi,T., Hirose,S., Shimizu,K. and Tomii,K.:"Prediction of disordered coil regions in proteins by threading and secondary structure prediction”, Proc. of CASP6, A-34-35 (2004).
Shimizu,K., Hirose,S. and Noguchi,T.:"Predicting protein disordered regions using SVMs”,Proc. of CASP6, A-35-36 (2004).
Sekijima,M., Motono,C., Noguchi,T, Kaneko,K. and Akiyama, Y.:”Structural Changes in flexible region of the Prion Protein induced by P102L Substitution: Investigation through Molecular Dynamics Simulations”, PROTEIN SCIENCE , 13, suppl. 1, 170 (2004).
Tomii,K., Ota,M., Noguchi,T. and Akiyama,Y.: "PILOT: a Fold Recognition Server Based on PSI-BLAST, IMPALA and LIBra-Rotamer", Proc. of CASP5,A-122(2002)
Tomii,K., Hirokawa,T., Noguchi,T., Suenaga,A. and Akiyama,Y.: "Integrating a New Fold Recognition Method with an Exhaustive Molecular Modeling System: FORTE1 and FOLTE-SUITE", Proc. of CASP5, A-37-38(2002).
野口 保: "PDB代表タンパク質チェイン決定システム -タンパク質立体構造研究への応用-",
AIST Today, 2(6), 15 (2002).
関嶋 政和, 土井 淳, 本田 真也, 野口 保, 清水 茂則, 秋山 泰: "大規模分子動力学シミュレーションによる自由エネルギー地形 解析システムの開発", 情報処理学会研究報告, 2007(60), 63-70 (2007).
関嶋 政和, 本野 千恵, 秋山 泰, 野口 保: "プリオンタンパク質の自由エネルギー地形解析", 第7会・`白質科学会年会, 仙台, 2007年5月26日.
清水 佳奈、廣瀬 修一、野口 保: "POODLE-S,W：タンパク質のディスオーダー予測のためのwebアプリケーション", 第7会蛋白質科学会年会, 仙台, 2007年5月26日.
Shimizu, K., Hirose, S., Noguchi, T.: "POODLE-W: Predicting disordered proteins by using spectral graph transducer", 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, 23nd Jul., 2007.
関嶋 政和, 本野 千恵, 秋山 泰, 野口 保: "Free Energy Landscape Analysis of Prion Protein", Biophysical Journal, 209a (2007).
滝沢雅俊, 山名早人, 野口保:”配列プロファイルを利用したドメインリンカー予測", 情報処理学会研究報告 (2006).
Hirose,S., Shimizu,K., Kanai,S. and Noguchi,T.:”Prediction of Long Disorder Region Using Two-Step SVM “, GIW2005, Yokohama (2005).
Sekijima,M., Motono,C., Noguchi,T., Kaneko,K. and Akiyama,Y.: “The Molecular Dynamics Simulations of the Conformational Transition of Prion Protein from its Cellular Form to the Anomalous Form using the Earth Simulator”, Annual Report of the Earth Simulator Center 2004-2005, (2005). 野口 保: "タンパク質構造変化部位データベースの構築 “, 第５回日本蛋白質科学会年会, 博多 (2005).
Noguchi, T.: "Detection of conformational changes in the membrane proteins by using PDB-REPRDB", GIW 2004 (The 15th International Conference on Genome Informatics), Tokyo, 13th Dec., 2004.
池谷 鉄兵, 伊藤 隆, 清水 謙多郎, 野口 保: "NOESY-HSQCスペクトルのback-calculation", 第26回分子生物情報研究会(SIG-MBI), 横浜, 2004年12月13日.
Sekijima,M., Motono,C., Noguchi,T., Kaneko,K. and Akiyama, Y.:”Molecular Dynamics Simulation of Wild-Type and Mutant Human Prion Protein: Effect of Pro102Leu”, 1st Pacific-Rim International Conference on Protein Science, Yokohama (2004).
野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)による膜タンパク質構造変化部位の抽出", 第3回産総研 生命情報科学人材養成コース シンポジウム「未来を拓く バイオインフォマティクス」, 東京, 2004年10月1日.
Sekijima, M., Motono, C., Noguchi, T., Kaneko, K., Akiyama, Y.: "Structural Changes in flexible region of the Prion Protein induced by P102L Substitution: Investigation through Molecular Dynamics Simulations", 18th Annual Symposium of the The Protein Society, San Diego, CA, USA, 17th Aug., 2004.
野口 保: "Detection of conformational changes in the membrane proteins by using a database of representative protein chains from the PDB (PDB-REPRDB)", 科学研究費補助金特定領域研究「膜インタフェイス」 第２回公開シンポジウム, 大阪府吹田市, 2004年8月4日.
Sekijima,M., Motono,C., Noguchi,T., Kaneko,K. and Akiyama, Y.:”The Molecular Dynamics Simulations of the Conformational Transition of Prion Protein from its Cellular Form to the Anomalous Form using the Earth Simulator “, Annual Report of the Earth Simulator Center April 2003 - March 2004, 171-174 (2004).
野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)によるタンパク質構造変化部位の抽出", 平成15年度ライフサイエンス分野融合会議・生命工学部会バイオテクノロジ−研究会 合同研究発表会・講演会, 産業技術総合研究所, つくば, 2004年2月3日.
村上 恵, 野口 保: "タンパク質代表チェイン決定システム（PDB-REPRDB)", 平成15年度ライフサイエンス分野融合会議・生命工学部会バイオテクノロジ−研究会 合同研究発表会・講演会, 産業技術総合研究所, つくば, 2004年2月3日.
村上 恵, 野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)の改良", 第2回 産総研生命情報科学人材養成コース シンポジウム「バイオインフォマティクス 未来への挑戦−お台場から世界に向けて−」, 東京, 2003年10月3日.
野口 保: "PDB代表タンパク質チェイン決定システム（PDB-REPRDB)", 第233回CBI学会研究講演会, 東京, 2003年7月2日.
野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)による膜タンパク質立体構造の分類"、 第３回日本蛋白質科学会年会、札幌、74（2003）.
富井 健太郎, 太田 元規, 野口 保, 秋山 泰: "1D-3Dプロファイル融合とthreading potentialによる鋳型構造スクリーニング", 平成14年度ライフサイエンス分野融合会議・生命工学・秤・oイオテクノロジ−研究会 合同研究発表会・講演会, 産業技術総合研究所, つくば, 2003年2月24日.
野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)の改良", 平成14年度ライフサイエンス分野融合会議・ 生命工学部会バイオテクノロジ−研究会 合同研究発表会・講演会, 産業技術総合研究所, つくば, 2003年2月24日.
Tomii,K., Ota,M., Noguchi,T., Akiyama,Y.: "Construction of a fold recognition server PILOT based on PSI-BLAST, IMPALA and LIBRA-rotamer｡､Pacific Symposium on Biocomputing "｡､Kaua'i, U.S.A.｡､133-133(2003.1.5)
Noguchi, T., Akiyama, Y.: "PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)", AIST international symposium 2002 -Bioinformatics in the Post-Genome Era-, Tokyo, 8th Nov., 2002.
Tomii, K., Ota, M., Noguchi, T., Akiyama, Y.: "Constructing a protein structure prediction server PILOT", AIST international symposium 2002 -Bioinformatics in the Post-Genome Era-, Tokyo, 8th Nov., 2002.
野口 保: "PDB代表タンパク質チェイン決定システム(PDB-REPRDB)", 産総研 生命情報科学人材養成コース 設立1周年記念シンポジウム「21世紀生命情報科学の飛翔ーお台場から世界に向けてー」, 東京, 2002年10月4日.
富井 健太郎, 太田 元規, 野口 保, 秋山 泰: "タンパク質立体構造予測サーバーPILOTの構築", 産総研生命情報科学人材養成コース 設立1周年記念シンポジウム「21世紀生命情報科学の飛翔ーお台場から世界に向けてー」, 東京, 2002年10月4日.
太田 元規, 富・・健太郎, 野口 保, 津田 宏治, 浅井 潔, 秋山 泰: "配列プロフィールサーチ， 構造-配列適合性関数と非線形判別法を利用したタンパク質の構造認識法", 第2回日本蛋白質科学会年会, 名古屋国際会議場, 2002年6月14日.
野口 保, 富井 健太郎, 高橋 明子, 秋山 泰, 太田 元規: "FOREST(タンパク質立体構造認識手法ベンチマーク用標準プラットフォーム)" , 平成13年度ライフサイエンス分野融合会議・生命工学部会バイオテクノロジ−研究会 合同研究発表会・講演会, 産業技術総合研究所, つくば, 2002年2月8日.
野口 保, 富井 健太郎, 太田 元規, 秋山 泰:"FOREST: Fold Recognition Stadium", 文部科学省科学研究費 ・ﾁ定領域研究Ｃ「ゲノム情報科学」『ゲノム情報科学の新展開』公開シンポジウム, 57 (2002). 2002年1月12日
RWCP (Apr.1997-Mar.2001)
Noguchi,T., Onizuka,K., Ando,M., Matsuda,H. and Akiyama,Y.: "Quick Selection of Representative Protein Chain Sets Based on Customizable Requirements", Bioinformatics, 16, 520-526 (2000). [D-99-135]
Saito,M., Misoo,K., Shizawa,Y., Marukawa,K., Akiyama,Y., Noguchi,T. and Onizuka,K.:
"Parallelization and Performance Evaluation of MD Program AMBER and Barnes-Hut Tree Code",
Transactions of IPSJ, 40, 5, 2142-2151 (1999). [in Japanese]
[]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Biological- and Chemical- Parallel Applications on a PC Cluster", Proc. of the International Symposium on High Performance Computing (ISHPC'99) (Lecture Notes on Computer Sciences. Springer-Verlag), 220-233 (1999). [D-98-195]
Ando,M., Akiyama,Y., Onizuka,K. and Noguchi,T.:
"ESCAPE: Parallel Tree Search System for Conformational Analysis of
Peptides", Proc. of the 1999 International Conference on Parallel and
Distributed Processing Techniques and Applications, 3, 1537-1543 (1999).
[D-98-193]
Onizuka,K., Noguchi,T., Ando,M. and Akiyama,Y.:
"A compressed representation of multiple-dimensional distribution by
linear base-transformation, and its application to the residue-pair relative
distribution of proteins",
Transactions of IPSJ, 40, No.SIG2 (TOM1), 105-116 (1999). [in Japanese]
[D-98-135]
Totoki,Y., Akiyama,Y., Onizuka,K., Noguchi,T., Saito,M. and Ando,M.:
"Multiple Protein Sequence Alignment using Parallel Iterative
Algorithm and A* Algorithm",Transactions of IPSJ, 40,
No.SIG9 (TOM2), 138-149 (1999). [in Japanese]
[D-98-128]
Noguchi,T., Akiyama,Y., Onizuka,K. and Ando,M.: "The classification of protein structures based on the sequential and structural similarity, and the database of representative protein chains (PDB-REPRDB)", Transactions of IPSJ, 40, No.SIG2 (TOM1), 117-128 (1999). [in Japanese] [D-98-103]
Ando,M., Akiyama,Y., Onizuka,K. and Noguchi,T.:
"Parallel Tree Search-based Protein Conformation Analysis System
Implemented on a Massively Parallel Computer", Transactions of IPSJ,
40, No.SIG2 (TOM1), 91-104 (1999). [in Japanese]
[D-98-102]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Parallel Protein Information Analysis (PAPIA) system running on a 64-node PC Cluster", Proc. of the 9th Genome Informatics Workshop , 131-140(1998). [D-98-088]
Saito,M., Misoo,K., Shizawa,Y., Marukawa,K., Akiyama,Y., Noguchi,T. and Onizuka,K.:
"Parallelization and Performance Evaluation of MD Program AMBER and Barnes-Hut Tree Code",
Proc. of the Joint Symposium on Parallel Processing 1998 (JSPP'98), 231-238 (1998). [in Japanese]
[D-97-174]
Onizuka,K., Noguchi,T. and Akiyama,Y.:
"Parallel PDB Data Retriever 'PDB Diving Booster'"
in High Performance Computing (Polychronopoulos, et.al Eds.),
Lecture Notes in Computer Science 1336, Springer, 389-396 (1997).
[D-97-067]
Akiyama,Y., Misoo,K., Omura,Y., Matsumoto,H., Saito,M., Noguchi,T. and Onizuka,K.:
"Parallelization of Space Plasma Particle Simulation"
in High Performance Computing (Polychronopoulos, et.al Eds.),
Lecture Notes in Computer Science 1336, Springer, 281-292 (1997).
[D-97-063]
Noguchi,T., Onizuka,K., Akiyama,Y. and Saito,M.:
"PDB-REPRDB: A Database of Representative Protein Chains in PDB
(Protein Data Bank)", Proc. of the fifth Int'l Conf. on Intelligent
Systems for Molecular Biology, 214-217, AAAI Press (1997).
[P-96-065]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "An opened Internet calculation service using a 64-node PC cluster - the Parallel Protein Information Analysis (PAPIA) system -", IPSJ SIG Notes, 99-OS-81-11, 59-64 (1999). [in Japanese] [D-99-013]
Noguchi,T.: "Protein secondary structure predictions and structural alignments for CASP3 targets", RWC Technical Report (RWC TR-98009) (1998). [in Japanese] [TR98-009]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Parallel Protein Information Analysis (PAPIA) system.", Proc. of the 1998 RWC Symposium (RWC TR-98001), Real World Computing Partnership, 123-128 (1998). [TR-98001]
Onizuka,K., Noguchi,T., Ando,M. and Akiyama,Y.:
"A compressed representation of multiple-dimensional distribution by linear base transformation, and its application to protein 3D structure recognition",
IPSJ SIG Notes, 98-MPS-22-13, 75-80 (1998). [in Japanese]
[D-98-134]
Onizuka,K., Noguchi,T., Ando,M. and Akiyama,Y.:
"A compressed representation of multiple-dimensional distribution by linear base transformation,
and it's application to residue-pair-relative-distribution of proteins",
IPSJ SIG Notes, 98-MPS-21-5, 37-42 (1998). [in Japanese]
[D-98-109]
Noguchi,T., Akiyama,Y., Onizuka,K. and Ando,M.:
"The classification of protein structures based on the sequential and structural
similarity, and the database of representative protein chains (PDB-REPRDB)",
IPSJ SIG Notes, 98-MPS-21-6, 31-36 (1998). [in Japanese]
[D-98-104]
Ando,M., Akiyama,Y., Onizuka,K. and Noguchi,T.:
"Parallel Tree Search-based Protein Conformation Analysis System
Implemented on a Massively Parallel Computer", IPSJ SIG Notes,
98-MPS-21-5, 25-30 (1998). [in Japanese]
[D-98-101]
Ando,M., Akiyama,Y., Onizuka,K. and Noguchi,T.:
"Parallel Tree Search-based Protein Conformation Analysis System",
IPSJ SIG Notes, 98-HPC-72-8, 43-48 (1998). [in Japanese]
[D-98-071]
Onizuka,K., Akiyama,Y., Noguchi,T. and Saito,M.: "PAPIA System An Integrated Parallel Environment for Protein Structure Analysis", RWC Technical Report (RWC TR-97007) (1997). [TR-97-007]
Akiyama,Y., Onizuka,K., Noguchi,T., Ando,M. and Saito,M.:
"Parallel Protein Information Analysis (PAPIA) system implemented on RWC PC cluster II",
IPSJ SIG Notes, 97-HPC-70-6, 31-36 (1998). [in Japanese]
[D-97-160]
Totoki,Y., Akiyama,Y., Onizuka,K., Noguchi,T., Saito,M. and Ando,M.:
"Employing A* Algorithm in Parallel Multiple Protein Sequence Alignment",
IPSJ SIG Notes, 97-MPS-16-4, 19-24 (1997). [in Japanese]
[D-97-110]
Onizuka,K., Noguchi,T., Saito,M. and Akiyama,Y.:
"An Integrated Parallel System for Protein Structure Analysis",
IPSJ SIG Notes, 97-HPC-68-8, 45-50 (1997). [in Japanese]
[D-97-092]
Noguchi,T., Akiyama,Y., Onizuka,K., Saito,M., Ando,M. and Shizawa,Y.:
"Parallelization of the automatic determination system for
representative protein chains of the Protein Data Bank (PDB)",
IPSJ SIG Notes, 97-HPC-67-6, 31-36 (1997). [in Japanese]
[D-97-054]
Totoki,Y., Akiyama,Y., Noguchi,T., Onizuka,K., Saito,M. and Ando,M.:
"Multiple Alignment using A* Algorithm and Parallel Iterative Algorithm",
IPSJ SIG Notes, 97-HPC-67-7, 37-42 (1997). [in Japanese]
[D-97-053]
Akiyama,Y., Misoo,K., Omura,Y., Matsumoto,H.,Saito,M., Noguchi,T. and Onizuka,K.:
"Parallelization of Space Plasma Particle Simulation",
IPSJ SIG Notes, 97-HPC-66-1, 1-6 (1997). [in Japanese]
[D-97-011]
Akiyama,Y., Onizuka,K., Noguchi,T., Horton,P. and Ando,M.: "RWCP High-Performance Computing for Structural Biology", The 7th meeting of Software Infrastructure Forum (1999). [D-99-081]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Development of the PAPIA system on a large-scale PC cluster", The 180th meeting on Chemistry, Biology, and Informatics (1999). [D-99-064]
Noguchi,T., Onizuka,K. and Akiyama,Y.: "PDB-REPRDB: An Interactive Database of Representative Protein Chains from the Protein Data Bank(PDB)", The Seventh International Conference on Intelligent Systems for Molecular Biology (1999). [D-99-063]
Onizuka,K., Noguchi,T. and Akiyama,Y.: "The Mini-threading by Multi-dimensional Mean Force Potentials", The Seventh International Conference on Intelligent Systems for Molecular Biology (1999). [D-99-061]
Ando,M., Akiyama,Y., Onizuka,K. and Noguchi,T.:
"ESCAPE: Parallel Tree Search System for Conformational Analysis of Peptides",
the 2nd International Workshop on Advanced Genomics (1999).
[D-99-002]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Development of Parallel Protein Information Analysis (PAPIA) system", "Classification, prediction, and design of protein structure" meeting (1999). [D-98-178]
Noguchi,T., Ito,M., Akiyama,Y. and Nishikawa,K.:
"Improvement of protein secondary structure prediction using the 3D-1D compatibility algorithm", The 5th Workshop on "Principles of Protein Architecture" (1998).
[D-98-125]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Development of Biological- and Chemical- Applications on a 64-node PC Cluster", Int'l Workshop on Innovative Architectures for Future Generation High-Performance Processors and Systems (IWIA'98) (1998). [D-98-097]
Akiyama,Y., Onizuka,K., Noguchi,T. and Ando,M.: "Parallel Protein Information Analysis (PAPIA) system on RWC PC Cluster", ACM Int'l Conf. on Supercomputing (ICS'98), Melbourne (1998). [D-98-073]
Akiyama,Y., Misoo,K., Omura,Y., Matsumoto,H., Noguchi,T. and Onizuka,K.: "Parallelization of Space Plasma Particle Simulator KEMPO1", Proc. of the Joint Symposium on Parallel Processing (JSPP)'98, 161 (1998). [in Japanese] [D-98-013]
Akiyama,Y., Onizuka,K., Noguchi,T., Ando,M. and Saito,M.: "Parallel Protein Information Analysis (PAPIA) system on RWC PC Cluster", Workshop on Global and Cluster Computing (WGCC'98), Tsukuba (1998). []
Onizuka,K., Noguchi,T., Saito,M. and Akiyama,Y.:
"An integrated protein structure analysis system PAPIA",
The 4th Workshop on "Principles of Protein Architecture" (1997).
[D-97-115]
Noguchi,T., Onizuka,K., Akiyama,Y. and Saito,M.: "PDB-REPRDB: A database of representative protein chains in PDB based on both sequential and structural similarity", The 4th Workshop on "Principles of Protein Architecture" (1997). [D-97-105]
Yutaka Akiyama, Kentaro Onizuka, Tamotsu Noguchi, and Makoto Ando: "Parallel Protein Information Analysis (PAPIA) system", The 5th Workshop on "Principles of Protein Architecture" (1998). [D-98-124]
Kentaro Onizuka, Tamotsu Noguchi, and Yutaka Akiyama: "Parallel PDB Data Retriever 'PDB Diving Booster'", the fifth Int'l Conf. on Intelligent Systems for Molecular Biology (1997). [D-96-064]
Others (Apr.1984-Mar.1997)
Imanishi,A., Ishii,T., Kato,S., Miyachi,T., Nakamura,A., Takeuchi,Y., Ukai,K., Baba,K., Morita,Y., Sumi,Y., Noguchi,T., Ohmori,T., Shimura,N., Takahashi,K., Wada,Y. and Kurita,K.: "Measurement of Large-Angle Cross-Section for Coherent Pion Photoproduction on Deuteron", Il Nuovo Cimento, 100A, 5, 735-755 (1988).
Ishii,T., Egawa,K., Imanishi,A., Kato,S., Takeuchi,Y., Ukai,K., Yoshioka,M., Noguchi,T., Ohmori,T., Shimura,N., Takahashi,K. and Wada,Y.: "Differential Cross Section for Proton Compton Scattering at Incident Photon Energies between 900 MeV and 1050 MeV", Nuclear Physics, B254, 458-474 (1985)
Imanishi,A., Ishii,T., Kato,S., Miyachi,T., Nakamura,A., Takeuchi,Y., Ukai,K., Noguchi,T., Ohmori,T., Shimura,N., Takahashi,K., Baba,K., Morita,Y., Sumi,Y., Wada,Y. and Kurita,K.: "Neutral-Pion Photoproduction on Deuteron", Physical Review Letters, 54, 23, 2497-2500 (1985).
Wada,Y., Egawa,K., Imanishi,A., Ishii,T., Kato,S., Ukai,K., Naito,F., Nara,H., Noguchi,T. and Takahashi,K.: "Proton Compton Scattering at Backward Angles in the Energy Range from 400 MeV to 1050 MeV", Nuclear Physics, B247, 313-338 (1984).
Last updated:23 Jan. 2016
