logo PNP tri Home tri Site indexspace
leftintroductionpathwayspublicationslinkscontactsright
Publications
Papers
Poster abstracts
Books

Japanese articles

Home > Publications

spacerPublications

Papers

[1] Hiroshi Matsuno, Atsushi Doi, Masao Nagasaki, and Satoru Miyano, Hybrid Petri net representation of gene regulatory network, Pacific Symposium on Biocomputing 2000, pp.341-352, 2000. [.pdf]
[2] Hiroshi Matsuno, Atsushi Doi, Yuichi Hirata, and Satoru Miyano, XML documentation of biopathways and their simulations in Genomic Object Net, Genome Informatics, 12, pp.54-62, 2001. [.pdf]
[3] Hiroshi Matsuno, Ryutaro Murakami, Rie Yamane, Naoyuki Yamasaki, Sachie Fujita, Haruka Yoshimori, and Satoru Miyano, Boundary formation by Notch signaling in Drosophila multicellular systems: Experimental observations and a gene network modeling by Genomic Object Net, Pacific Symposium on Biocomputing 2003, pp.152-163, 2003. [.pdf]
[4] Hiroshi Matsuno, Yukiko Tanaka, Hitoshi Aoshima, Atsushi Doi, Mika Matsui, Satoru Miyano, Biopathways Representation and Simulation on Hybrid Functional Petri Net, In Silico Biology, 3(3), pp.389 - 404, 2003. [.html]
[5] Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, Genomic Object Net I: a platform for modeling and simulating biopathways, Applied Bioinformatics, 2(3), pp181-184, 2003. [abstract]
[6] Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno, Satoru Miyano, Genomic Object Net II: how to model biopathways with hybrid functional Petri net with extension, Applied Bioinformatics, 2(3), pp.185-188, 2003. [abstract]
[7] Mika Matsui, Sachie Fujita, Shunichi Suzuki, Hiroshi Matsuno, Satoru Miyano, Simulated Cell Division Processes of the Xenopus Cell Cycle Pathway by Genomic Object Net, Journal of Integrative Bioinformatics, 0001, Online Journal; http://journal.imbio.de/index.php?paper_id=3, 2004. [abstract] [.pdf]
[8] Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, A Versatile Petri Net Based Architecture for Modeling and Simulation of Complex Biological Processes, Genome Informatics, 15(1), pp.180-197, 2004. [.pdf]
[9] Atsushi Doi, Sachie Fujita, Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano, Constructing biological pathway models with hybrid functional Petri nets, In Silico Biology 4 (3), pp.271-291, 2004. [.html]
[10] Masao Nagasaki, Atushi Doi, Hiroshi Matsuno, and Satoru Miyano, Integrating biopathway databases for large-scale modeling and simulation, Conferences in Research and Practice in Information Technology, Vol.29 (Yi-Ping Phoebe Chen, Ed.) (The Second Asia Pacific Bioinformatics Conference 2004), pp.43-52, 2004.

[11] Sachie Fujita, Mika Matsui, Hiroshi Matsuno, Satoru Miyano, Modeling and simulation of fission yeast cell cycle on hybrid functional Petri net, IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences, E87-A(11), pp.2919-2928, 2004.
[12] Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano, A new regulatory interactions suggested by simulations for circadian genetic control mechanism in mammals, Proc. The 3rd Asia-Pacific Bioinformatics Conference, pp.171-180, Imperial College Press, 2005.
[13] Hironori Kitakaze, Hiroshi Matsuno, Nobuhiko Ikeda, Prediction of debacle points for robustness of biological pathways by using recurrent neural networks, Genome Informatics, 16(1), pp.192-202, 2005. [.pdf]
[14] Chen Li, Shunichi Suzuki, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, and Satoru Miyano, On modeling and analyzing signaling pathways with inhibitory interactions based on Petri net, Proc. The 2005 Internatinal Joint Conference of InCoB, AASBi and KSBI (BIOINFO2005), pp.348-353, 2005. [.pdf]
[15] Atsushi Doi, Masao Nagasaki, Hiroshi Matsuno and Satoru Miyano, Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net, In Silico Biology 6, 0001, 2006. [.html]

tri Papers Top tri Top

Poster abstracts

[1] Atsusi Doi, Rainer Drath, Masao Nagasaki, and Satoru Miyano, Protein dynamics observation of lambda phage by hybrid Petri net, Genome Informatics 1999, pp.217-218, 1999. [.pdf]
[2] Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, Induction mechanism description of lambda phage by hybrid Petri net, Currents in Computational Molecular Biology (RECOMB2000), pp.26-27, 2000.
[3] Hiroshi Matsuno, Atsushi Doi, Rainer Drath, Satoru Miyano, Genomic Object Net: Object oriented representation of biological systems, Genome Informatics, 11, pp.229-230, 2000. [.html] [.pdf]
[4] Hiroshi Matsuno, Atsushi Doi, Rainer Drath, Satoru Miyano, Genomic Object Net: Hybrid Petri net for describing biological systems, Currents in Computational Molecular Biology 2001 (RECOMB2001), pp.233-234, 2001.
[5] Hiroshi Matsuno, Atsushi Doi, Sachie Fujita, Makiko Sasaki, Yuichi Hirata, Satoru Miyano, Genomic Object Net: XML Visualization of Simulation Results from Biological Modeling on Hybrid Functional Petri Net, Genome Informatics, 12, pp.239-240, 2001. [.html] [.pdf]
[6] Atsushi Doi, Rie Yamane, Naoyuki Yamasaki, Haruka Yoshimori, Ryutaro Murakami, Hiroshi Matsuno, Satoru Miyano, Simulation of the Pattern Formation in Multicellular Organism by Genomic Object Net, Genome Informatics, 12, pp.288-289, 2001. [.html] [.pdf]
[7] Mika Matsui, Atsushi Doi, Hiroshi Matsuno, Yuichi Hirata, Satoru Miyano, Biopathway Model Conversion from E-CELL to Genomic Object Net, Genome Informatics, 12, pp.290-291, 2001. [.html] [.pdf]
[8] Yuichi Hirata, Hiroshi Matsuno, Makiko Sasaki, Satoru Miyano, Genomic Object Net: Petri Net Enhancement for Multi-Cellular Processes, Genome Informatics, 12, pp.292-293, 2001. [.html] [.pdf]
[9] Mika Matsui, Atsushi Doi, Hiroshi Matsuno, Yuichi Hirata, and Satoru Miyano, Converting biopathway models of E-Cell to Genomic Object Net, Pacific Symposium on Biocomputing, poster abstract, pp.117, 2002.
[10] Hiroshi Matsuno, Yuichi Hirata, Atsushi Doi, and Satoru Miyano, Genomic Object Net: On-going report on biopathway modeling and simulation, Currents in Computational Molecular Biology 2002 (RECOMB2002), pp.132-133, 2002.
[11] Hiroshi Matsuno, Rie Yamane, Sachie Fujita, Naoyuki Yamasaki, Ryutaro Murakami, and Satoru Miyano, Modeling and visualization of the pattern formation in Drosophila melanogaster by Genomic Object Net, The 10th International Conference on Intelligent Systems for Morecular Biology, poster abstract, 46A, 2002. [abstract]
[12] Masao Nagasaki, Atsushi Doi, Makiko Sasaki, Christpher J. Savoie, Hiroshi Matsuno, and Satoru Miyano, Genomic Object Net (ver.1.0): A platform for biopathway modeling and simulation, European Conference on Computational Biology 2002, poster abstract, P112, 2002.
[13] Hiroshi Matsuno, Ryutaro Murakami, Rie Yamane, Naoyuki Yamazaki, Sachie Fujita, Haruka Yoshimori, Satoru Miyano, Experimental Observations and Simulations by Genomic Object Net of Notch Signaling in Drosophila Multicellular Systems, Genome Informatics, 13, pp.453-454, 2002. [.html] [.pdf]
[14] Toshinori Tanaka, Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano, Development of Genomic Object Net Builder for Supporting XML Design for Visualization, Genome Informatics, 13, pp.455-456, 2002. [.html] [.pdf]
[15] Masafumi Nakano, Hironori Kitakaze, Hiroshi Matsuno, Satoru Miyano, XML Pathway File Conversion between Genomic Object Net and SBML, Genome Informatics, 13, pp.457-458, 2002. [.html] [.pdf]
[16] Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Eri Torikai, Hiroshi Matsuno, Satoru Miyano, BPE:Biopathway executer for large-scale modeling and simulation, Genome Informatics, 14, pp.296-297, 2003. [.pdf]
[17] Mika Matsui, Sachie Fujita, Shunichi Suzuki, Hiroshi Matsuno, Satoru Miyano, Xenopus cell cycle pathway for simulating cell division processes by Genomic Object Net, Genome Informatics, 14, pp.615-616, 2003. [.pdf]
[18] Rie Yamane, Junko Umezaki, Hiroshi Matsuno, Ryutaro Murakami, Naoyuki Yamasaki, Satoru Miyano, Simulation of Drosophila boundary cell formation in forced-expression on Notch-deltaE, Genome Informatics, 14, pp.617-618, 2003. [.pdf]
[19] Tomokazu Kono, Ryuhei Noda, Hironori Kitakaze, Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, Distributed client-server system architecture for high performance simulations on Genomic Object Net, Genome Informatics, 14, pp.619-620, 2003. [.pdf]
[20] Hironori Kitakaze, Ryuhei Noda, Hiroshi Matsuno, Nobuhiko Ikeda, Satoru Miyano, Prediction of debacle parts for robustness in a cell by using recurrent neural networks, The Fifteenth International Conference on Genome Informatics, poster abstract, P001, 2004. [.pdf]
[21] Mao Yamaji, Hideo Iwasaki, Hiroshi Matsuno, Satoru Miyano, Modeling and simulation of cyanobacterial circadian clock mechanism by hybrid functional Petri net, The Fifteenth International Conference on Genome Informatics, poster abstract, P002, 2004. [.pdf]
[22] Yasushi Fujii, Yasuki Okitsu, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi T. Inouye, A new regulatory interactions suggested by simulations for circadian genetic control mechanism in mammals, The Fifteenth International Conference on Genome Informatics, poster abstract, P003, 2004. [.pdf]
[23] Chen Li, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano, A new Petri net modeling method for signaling pathways with a focus on enzyme, The Fifteenth International Conference on Genome Informatics, poster abstract, P004, 2004. [.pdf]
[24] Toshinori Tanaka, Katsuyuki Harada, Hironori Kitakaze, Junkichi Yamanaka, Hiroshi Matsuno, Satoru Miyano, Tools for Supporting Computational Experiments on Genomic Object Net, The Sixteenth International Conference on Genome Informatics, poster abstract, S11, 2005.
[25] Ryo Okada, Chigusa Miyakawa, Manabu Sugii, Hiroshi Matsuno, Satoru Miyano, Machine Learning Prediction of Amino Acid Sequence Characterization in Protein N-Myristoylation, The Sixteenth International Conference on Genome Informatics, poster abstract, P096, 2005.
[26] Yumi Harada, Natsumi Mito, Yasushi Fujii, Hiroshi Matsuno, Satoru Miyano, Shin-Ichi Inouye, Simulation of Light-Induced Phase Response in Mammals with Hybrid Function Petri Net, The Sixteenth International Conference on Genome Informatics, poster abstract, P111, 2005.
[27] Chen Li, Shunichi Suzuki, Yoko Takeuchi, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano, Petri Net Based Modeling of Signaling Pathways Including Inhibitory Function, The Sixteenth International Conference on Genome Informatics, poster abstract, P115, 2005.

tri Poster abstracts Top tri Top

Books

[1] Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano, Computational Modeling of Biological Processes with Petri Net-Based Architecture, Bioinformatics Technologies (Yi-Ping Phoebe Chen (Ed.)), pp.179-242, Springer, 2005.
[2] Seiya Imoto, Hiroshi Matsuno, and Satoru Miyano, Gene Networks: Estimation, Modeling and Simulation, Computational Systems Biology (A. Kriete and Roland Eils (Ed)), pp.205-228, Elsevier, 2005.

tri Books Top tri Top

Japanese articles

[1] 松野浩嗣、宮野悟、バーチャルセル構築のためのプラットフォーム〜ハイブリッドオブジェクトネットによる遺伝子制御シミュレーション〜、bit, Vol. 32, No.8, pp.22-31, 共立出版、2000.
[2] 松野浩嗣、土井淳、和田信明、宮野悟、ハイブリッドペトリネットによるλファージの誘発と逆調節機構の表現、第13回回路とシステム(軽井沢) ワークショップ論文集、pp.263-268, 2000.
[3] 松野浩嗣、宮野悟、ゲノムデータからの知識発見と遺伝子オブジェクトのシミュレーション、電子情報通信学会誌、Vol.84, No.5, pp.356-358, 2001.
[4] 松野浩嗣、Rainer Drath, 宮野悟(分担)、遺伝子制御ネットワークのハイブリッドペトリネットによるシミュレーション、「システムバイオロジーの展開(北野宏明編)」、pp.165-176, シュプリンガー・フェアラーク東京、2001.
[5] 藤田祥恵、土井淳、松野浩嗣、宮野悟、ハイブリッド関数ペトリネットによる大腸菌のlacオペロンと解糖系の遺伝子ネットワークのモデル化とシミュレーション、第15回回路とシステム(軽井沢)ワークショップ論文集、pp.601-606, 2002.
[6] 松野浩嗣、宮野悟、バイオシミュレーションツール Genomic Object Net〜生命システムをわかりやすくモデル化・視覚化できる〜、実験医学、Vol.20, No.13(2002年9月号), pp.1873-1878, 2002.
[7] 松野浩嗣、宮野悟、パスウエイをデジタル化する、蛋白質核酸酵素、Vol.47, No.15 (2002年12月号), pp.2062-2070, 2002.
[8] 長崎正朗、土井淳、松野浩嗣、宮野悟、バイオパスウエイモデリングとシミュレーションを実現するためのシステム-Genomic Object Net-、人工知能学会誌、Vol.18, No.1, pp.8-13, 2003.
[9] 土井淳、田中由紀子、長崎正朗、青島均、松野浩嗣、宮野悟、アポトーシスシグナル伝達経路のGenomic Object Netによるモデル化とシミュレーション、第16回回路とシステム(軽井沢)ワークショップ論文集、pp.261-266, 2003.
[10] 土井淳、長崎正朗、松野浩嗣、宮野悟、細胞反応のシミュレーション、わかる実験医学シリーズ「バイオインフォマティクスがわかる」(菅原秀明編集)、pp.81-84, 羊土社、2003.
[11] 藤田祥恵,松井美香,松野浩嗣,宮野悟,ハイブリッド関数ペトリネットによる分裂酵母細胞周期のモデル化とシミュレーション,電子情報通信学会技術研究報告,CST2003-42, pp.1-6, 2004.
[12] 土井淳,長崎正朗,松野浩嗣,宮野悟,Genomic Object Netによるパスウエイの表現とシミュレーション,ゲノミクス・プロテオミクスの新展開 〜生物情報の解析と応用〜(今中忠之編), pp.930-937, エヌ・ティー・エス, 2004.
[13] 土井淳,長崎正朗,松野浩嗣,宮野悟,生命パスウエイのモデル化・可視化技術と創薬研究への応用,月刊薬事, Vol.46, No.7, pp.1265-1272, 2004.

tri Japanese articles Top tri Top