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publication_list [2011/03/25 15:37] mlabadm [Journal papers and refereed proceedings (peer reviewed):] |
publication_list [2012/12/23 17:24] (current) mlabadm [Journal papers and refereed proceedings (peer reviewed):] |
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- | - **__Li C__***, Nagasaki M*, Hock Koh C, Miyano S,Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with hybrid functional Petri net with extension, //Mol. Biosyst.//, DOI:10.1039/C0MB00253D, 2011. (//**IF:3.859**//) (//**Selected as Molecular BioSystems HOT Article**//) [http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/C0MB00253D] | + | |
- | - Hock Koh C, Nagasaki M, Saito A, **__Li C__**, Wong L, Miyano S, MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models, Bioinformatics, 2011 (accepted). [http://www.ncbi.nlm.nih.gov/pubmed/21208986] | + | - Nagasaki M, Fujita A, Sekiya Y, Saito A, Ikeda E, **__Li C__**, Miyano S, XiP: a computational environment to create, extend and share workflows, // Bioinformatics//, Bioinformatics. 2013 Jan 1;29(1):137-9. (//**IF:5.468**//) |
- | - Miwa Y, Murakami Y, Ge QW, **__Li C__**, Matsuno H, Miyano S, Delay time determination for the timed Petri net model of a signaling pathway based on its structural information, // IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences//, **E93-A**(12), 2717-2729, 2010. [http://search.ieice.org/bin/summary.php?id=e93-a_12_2717] | + | - Chen L, Kawabuchi M, Ge QW, Nakata M, **__Li C__**, Tonou H, Kamiyama N, Shimata K, A proposal of block division for task graphs, // Proc. of the 26th International Technical Conference on Circuits/Systems, Computers and Communications ITC-CSCC 2011//, pp.15--18, June 19-22, Geyongju, Korea, 2011. |
- | - **__Li C__***, Nagasaki M*, Saito A and Miyano S, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, //BMC Syst Biol.//, **4**:39, 2010 Apr. [http://www.biomedcentral.com/1752-0509/4/39/] (//**IF:4.06**// (2010.7) | + | - **__Li C__***, Kuroyanagi K, Nagasaki M, Miyano S, Parameter estimation of biological pathways using data assimilation and model checking, //Proceedings of the 2nd International Workshop on Biological Processes & Petri Nets (BioPPN2011)//, Newcastle upon Tyne, UK, June 2011, online: http://ceur-ws.org/Vol-724 pp.53-70. |
- | - Miwa Y*, **__Li C__***, Ge QW, Matsuno H and Miyano S, On Determining Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules, //In Silico Biol.//, **10**, 0004, 2010. [http://www.bioinfo.de/isb/2010/10/0004/] | + | - **__Li C__***, Nagasaki M*, Hock Koh C, Miyano S, Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with hybrid functional Petri net with extension, //Mol. Biosyst.//, **7**(5), 1576–1592, 2011. (//**IF:3.859**//) [http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/C0MB00253D] (//**Selected as Molecular BioSystems HOT Article**//) |
- | - Nagasaki M, Saito A, Jeong E, **__Li C__**, Kojima K, Ikeda E, Miyano S, Cell Illustrator 4.0: A computational platform for systems biology, //In Silico Biol.//, **10**, 0002, 2010. [http://www.bioinfo.de/isb/2010/10/0002/] | + | - Hock Koh C, Nagasaki M, Saito A, **__Li C__**, Wong L, Miyano S, MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models, Bioinformatics, 27(5):734-5, 2011. (//**IF:4.926**//) http://www.ncbi.nlm.nih.gov/pubmed/21208986 |
- | - **__Li C__***, Nagasaki M*, Ueno K, Miyano S, Simulation-based Model Checking Approach to Cell Fate Determination During Caenorhabditis elegans Vulval Development by Hybrid Functional Petri Net with Extension, // BMC Syst Biol.//, **3**:42, 2009 Apr. [http://www.biomedcentral.com/1752-0509/3/42] (//**IF:4.06**// (2010.7)) | + | - Miwa Y, Murakami Y, Ge QW, **__Li C__**, Matsuno H, Miyano S, Delay time determination for the timed Petri net model of a signaling pathway based on its structural information, // IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences//, **E93-A**(12), 2717-2729, 2010. http://search.ieice.org/bin/summary.php?id=e93-a_12_2717 |
+ | - **__Li C__***, Nagasaki M*, Saito A and Miyano S, Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram, //BMC Syst Biol.//, **4**:39, 2010 Apr. http://www.biomedcentral.com/1752-0509/4/39/ (//**IF:4.06**//) (2010.7) | ||
+ | - Miwa Y*, **__Li C__***, Ge QW, Matsuno H and Miyano S, On Determining Delay Time of Transitions for Petri Net Based Signaling Pathways by Introducing Stochastic Decision Rules, //In Silico Biol.//, **10**, 0004, 2010. http://www.bioinfo.de/isb/2010/10/0004/ | ||
+ | - Nagasaki M, Saito A, Jeong E, **__Li C__**, Kojima K, Ikeda E, Miyano S, Cell Illustrator 4.0: A computational platform for systems biology, //In Silico Biol.//, **10**, 0002, 2010. http://www.bioinfo.de/isb/2010/10/0002/ | ||
+ | - **__Li C__***, Nagasaki M*, Ueno K, Miyano S, Simulation-based Model Checking Approach to Cell Fate Determination During Caenorhabditis elegans Vulval Development by Hybrid Functional Petri Net with Extension, // BMC Syst Biol.//, **3**:42, 2009 Apr. (//**IF:4.06**// (2010.7)) http://www.biomedcentral.com/1752-0509/3/42 | ||
- Miwa Y, Hioka K, **__Li C__**, Matsuno H, Miyano S, Delay Time Estimation for Petri Net Models of Signaling Pathways Based on Experimental Data, //Proc. of The 23rd International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2008)//, 297-300, 2008. | - Miwa Y, Hioka K, **__Li C__**, Matsuno H, Miyano S, Delay Time Estimation for Petri Net Models of Signaling Pathways Based on Experimental Data, //Proc. of The 23rd International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2008)//, 297-300, 2008. | ||
- Hioka K, Miwa Y, **__Li C__**, Ge QW, Matsuno H, Miyano S, An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data, //Bionetics 2008,// Hyogo, Japan, November 25-28, 2008 (Invited Paper). | - Hioka K, Miwa Y, **__Li C__**, Ge QW, Matsuno H, Miyano S, An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data, //Bionetics 2008,// Hyogo, Japan, November 25-28, 2008 (Invited Paper). | ||
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- Ge QW, **__Li C__**, Nakata M, Performance Evaluation of a Two-Processor Scheduling Method for Acyclic SWITCH-less Program Nets, // IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences, //**E88-A**(6), 1502-1506, 2005. [[http://ietfec.oxfordjournals.org/cgi/content/abstract/E88-A/6/1502|{{[PDF]}}]] | - Ge QW, **__Li C__**, Nakata M, Performance Evaluation of a Two-Processor Scheduling Method for Acyclic SWITCH-less Program Nets, // IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences, //**E88-A**(6), 1502-1506, 2005. [[http://ietfec.oxfordjournals.org/cgi/content/abstract/E88-A/6/1502|{{[PDF]}}]] | ||
- Ge QW, **__Li C__**, Nakata M, On Evaluation of a New Priority List for Two-Processor Scheduling Problems of Program Nets, //Proc. of the 2004 International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC2004),// 7E3L-2-1-7E3L-2-4, 2004. | - Ge QW, **__Li C__**, Nakata M, On Evaluation of a New Priority List for Two-Processor Scheduling Problems of Program Nets, //Proc. of the 2004 International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC2004),// 7E3L-2-1-7E3L-2-4, 2004. | ||
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===== International Conference Talks, Posters and Software Demonstrations: ===== | ===== International Conference Talks, Posters and Software Demonstrations: ===== | ||
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===== Domestic Conference Papers: ===== | ===== Domestic Conference Papers: ===== | ||
+ | - 東京大学医科学研究所研究成果発表会, "オーダーメード解析プラットフォーム:CSMLパイプラインとセルイラストレータオンライン", 長崎正朗,斉藤あゆむ,__**李晨**__,植野和子,関谷弥生,池田恵美,島村徹平,山口類,藤田アンドレ,新井田厚司,小島要,井元清哉,宮野悟 2010.5.31-6.1. | ||
- Y. Miwa, __**C. Li**__, Q.W. Ge and H. Matsuno, A Method to Determine Firing Times of Transitions for Timed Petri Nets by Introducing Stochastic Decision Rules, //Technical Report of IEICE.//, vol.109, no.300, pp.71-76, 2009-11-27. | - Y. Miwa, __**C. Li**__, Q.W. Ge and H. Matsuno, A Method to Determine Firing Times of Transitions for Timed Petri Nets by Introducing Stochastic Decision Rules, //Technical Report of IEICE.//, vol.109, no.300, pp.71-76, 2009-11-27. | ||
- 東京大学生命科学研究ネットワークシンポジウム2008, "生命体パスウェイシミュレーションモデルのためのデータ手法およびソフトウェアの開発", (山口類*, 長崎正朗, 吉田亮, 井元清哉, 山内麻衣, 斉藤あゆむ, 中村和幸, 島村徹平, 鄭恩娥, __**李晨**__, 植野和子, 池田恵美, 関谷弥生, 小島要, 玉田嘉紀, 藤田アンドレ, 樋口知之, 後藤典子, 宮野悟) 2008.9. | - 東京大学生命科学研究ネットワークシンポジウム2008, "生命体パスウェイシミュレーションモデルのためのデータ手法およびソフトウェアの開発", (山口類*, 長崎正朗, 吉田亮, 井元清哉, 山内麻衣, 斉藤あゆむ, 中村和幸, 島村徹平, 鄭恩娥, __**李晨**__, 植野和子, 池田恵美, 関谷弥生, 小島要, 玉田嘉紀, 藤田アンドレ, 樋口知之, 後藤典子, 宮野悟) 2008.9. |