論文

• Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Qualitative analysis of gene regulatory networks by temporal logic, Theoretical Computer Science, Vol. 594, pp. 151-179, Aug. 2015.
• Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Modular analysis of gene networks by linear temporal logic, Journal of Integrative Bioinformatics, Vol. 10, No. 2, 216, 2013.  公式リンク  
  

国際会議発表 (査読有り)

• Takashi Tomita, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. A Formal Ontology of Interactions with Intensional Quantitative Semantics, Workshop on Computation: Theory and Practice (WCTP-2012), Theory and Practice of Computation, Proceedings in Information and Communications Technology, Vol. 7, pp. 13-33, June 2013.
• Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Modular analysis of gene networks by linear temporal logic, proceedings of 9th International Symposium on Integrative Bioinformatics, pp. 43-54, Mar. 2013.
• Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Qualitative analysis of gene regulatory networks using network motifs, proceedings of 4th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS2013), pp. 15-24, Feb. 2013.
• Sohei Ito, Takuma Ichinose, Masaya Shimakawa, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Modular analysis of gene networks using temporal logic (abstract), 5th Annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, program booklet, pp. 118-119, Nov. 2012.
• Sohei Ito, Takuma Ichinose, Naoko Izumi, Shigeki Hagihara, NAOKI YONEZAKI. Qualitative analysis of gene regulatory networks by approximation using network motifs, International Symposium on Integrative Bioinformatics 2011, Mar. 2011.
• Takashi Tomita, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Qualitative Inference Rules for Analysis of Biological Object Interactions, 9th International Conference on Bioinformatics, 9th International Conference on Bioinformatics, Abstracts, pp. 48, Sept. 2010.
• Sohei Ito, Naoko Izumi, Shigeki Hagihara, NAOKI YONEZAKI. Possible behavior analysis of Gene Regulatory Networks by Linear Temporal Logic, 9th International Conference on Bioinformatics, 9th International Conference on Bioinformatics, Abstracts, pp. 50, Sept. 2010.
• Sohei Ito, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Qualitative analysis of gene regulatory networks by satisfiability checking of Linear Temporal Logic, Proceedings of the 10th IEEE International Conference on Bioinformatics & Bioengineering, pp. 232-237, May 2010.
• Sohei Ito, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. Analysis of gene regulatory networks by checking satisfiability of Linear Temporal Logic, CBI-KSBSB Joint Conference, CBI-KSBSB Joint Conference, P12-143, pp. 216, Nov. 2009.
• Takashi Tomita, Naoko Izumi, Shigeki Hagihara, Naoki Yonezaki. 2-layered Formal Interaction Ontology among Biological Processes with Quantitative Semantics, CBI-KSBSB Joint Conference, CBI-KSBSB Joint Conference, P12-144, pp. 217, Nov. 2009.
• Naoko Izumi, Naoki Yonezaki. Formal system of interactions on biomedical ontology, Proceedings of the 19th European-Japanese conference on information modelling and knowledge basis, pp. 286-293, June 2009.
• Koji Tashima, Naoko Izumi, Naoki Yonezaki. A Quantitative Semantics of Formal Ontology of Drug Interactions, Proceedings of the 2008 International Conference on Bioinformatics & Computational Biology, BIOCOMP2008, Vol. II, pp. 760-766, July 2008.
• Naoko Izumi, Naoki Yonezaki. Mereology with class hierarchy for component structure, Proceedings of the IASTED International Conference Artificial Intelligence and Soft Computing, pp. 79--84, May 2001.
• Naoko Izumi, Naoki Yonezaki.. A logic of ontology for object oriented software component., Proc. of the 11th European-Japanese conference on Information Modelling and Knowledge Basis, pp. 74-87, May 2001.

国際会議発表 (査読なし・不明)

• Naoki Yonezaki, Naoko Izumi, Takumi Akiyama. Formal Ontology of Object Interaction, International Symposium on Large-scale Knowledge Resources (LKR2006), Proceedings of International Symposium on Large-scale Knowledge Resources (LKR2006), pp. 15-20, Mar. 2006.

国内会議発表 (査読なし・不明)

• 伊藤宗平, 泉直子, 萩原茂樹, 米崎直樹. 時間論理による仕様記述を用いた遺伝子ネットワークの定性的振る舞い解析, 情報処理学会第73回全国大会講演論文集, Vol. 1, pp. 231-232, Mar. 2011.
• 伊藤宗平, 泉 直子, 萩原茂樹, 米崎直樹. 時間論理LTLの充足可能性判定を用いた遺伝子ネットワークの解析, 日本ソフトウェア科学会第26回大会講演論文集, Sept. 2009.
• 冨田 尭, 泉 直子, 萩原茂樹, 米崎直樹. 量的関係を考慮した生体内の阻害・活性化機能の形式相互作用オントロジー, 日本ソフトウェア科学会第25回大会講演論文集, Sept. 2008.
• 秋山卓見, 泉直子, 萩原茂樹, 米崎直樹. 形式オントロジーに基づく遺伝子調節のための数値モデル, 情報処理学会研究報告, Vol. 2007, No. 21, pp. 71-78, Mar. 2007.
• 米崎直樹, 泉直子, 秋山卓見. 薬物相互作用の形式オントロジー, 日本ソフトウェア科学会第２２回大会講演論文集, Vol. cd-rom, Sept. 2005.
• 泉直子, 米崎直樹. オブジェクトの項表現を意味論の基礎とする論理体系としてのontologyとその表現力, 人工知能学会全国大会（第14回）論文集, Vol. 14, pp. 514-517, July 2000.
• 泉直子, 米崎直樹. ソフトウェア部品管理のためのクラス階層を持つオブジェクト項を導入したMeleology, 日本ソフトウェア科学会第16回大会論文集, pp. 181-184, Sept. 1999.

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