(Declaration: Copyrights of the following papers are owned by the respective journals!) *These authors equally contributed to this work ===== 学術論文誌　Journal papers ===== - **__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**//) - 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] - 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] - Nagasaki M, Saito A, **__Li C__**, Jeong E, Miyano S, Systematic reconstruction of TRANSPATH data into Cell System Markup Language, //BMC Syst Biol.//, 23;2(1):53, 2008 Jun. [[http://www.biomedcentral.com/1752-0509/2/53|{{[PDF]}}]] (//**IF:4.06**// (2010.7)) - **__Li C__**, Suzuki S, Ge QW, Nakata M, Matsuno H, Miyano S, Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets, //Journal of Bioinformatics and Computational Biology (JBCB),//**4**(5), 1119-1140, 2006. [[http://www.worldscinet.com/cgi-bin/details.cgi?id=pii:S021972000600234X&type=html|{{[PDF]}}]] - **__Li C__**, Ge QW, Nakata M, Matsuno H, Miyano S, Modelling and Simulation of Signal Transductions in an Apoptosis Pathway by Using Timed Petri Nets, //Journal of Biosciences,// **32**(1), January, 113-127, 2007. [[http://www.ias.ac.in/jbiosci/jan2007/113.pdf|{{[PDF]}}]] (//**IF:1.703**// (2008)) - Matsuno H, **__Li C__**, Miyano S, Petri Net Based Descriptions for Systematic Understandings of Biological Pathways, //IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences, //**89-A**(11), 3166-3174, 2006. [[http://ietfec.oxfordjournals.org/cgi/content/refs/E89-A/11/3166|{{[PDF]}}]] - Ge QW, **__Li C__**, Nakata M, A New Proposal to Two-Processor Scheduling Problem for SWITCH-less Program Nets, //IEICE Trans. Fundamentals of Electronics, Communications and Computer Sciences, //**E87-A**(11), 2859-2867, 2004. [[http://search.ieice.org/bin/summary.php?id=e87-a_11_2859&category=A&year=2004&lang=E&abst=|{{[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]}}]] ===== 査読付き国際会議　Refereed proceedings (peer reviewed) ===== - 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__***, 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, 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). - **__Li C__**, Suzuki S, Ge QW, Nakata M, Matsuno H, Miyano S, On Modeling and Analyzing Signaling Pathways with Inhibitory Interactions Based on Petri Net, // Proceedings of the 2005 International Joint Conference of Income, AASBi and KSBI,//348-353, 2005 (//**Best Paper Award**//).{{li2005_bioinfo_.pdf|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.