====== Publication List =====

(Declaration: Copyrights of the following papers are owned by the respective journals!)

*These authors equally contributed to this work
===== Journal papers and refereed proceedings (peer reviewed): =====



  -  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**//) 
  -  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.
  -  **__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
  -  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). 
  -  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]}}]]
  -  **__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, 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]}}]]
  -  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. 
=====     International Conference Talks, Posters and Software Demonstrations: =====


  -  [Poster] __**Li C**__, Nagasaki M, Saito A, Miyano S, Time-dependent key element analysis with active state transition diagram: a high-level Petri net approach, //Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010)//, X072, John B. Hynes Convention Center in Boston, MA, USA, July 11-13, 2010.
  -  [Poster] __**Li C**__, Nagasaki M, Saito A, Miyano S, Active State Transition Diagram Analysis from Time Course Simulation Data: an HFPNe Approach, //Proceedings of the 20th International Conference on Genome Informatics (GIW2009)//, P087, 2009.
  -  [SoftDemo] Nagasaki M, Ueno K, Ikeda E, __**Li C**__, Kojima K, Saito A, Miyano S, Cell Illustrator Online 4.0: A Platform for Systems Biology, //Proceedings of the 20th International Conference on Genome Informatics (GIW2009)//, S005, 2009.
  -  [Talk/SoftDemo] __**C. Li**__, M. Nagasaki, A. Saito and S. Miyano, Simulation-based Model Checking Approach for Cell Fate Specification - Using Cell Illustrator Online: A Computational Platform for Systems Biology -, //2009 International Workshop on Computational and Integrative Biology a satellite meeting of the International Conference of Integrative Biology (CIB'2009)//, Sep. 18-20, 2009. Hangzhou, China.
  - [Poster] 長崎正朗、沼田和幸、鄭恩娥、__**李晨**__、植野和子、池田恵美、小島要、斉藤あゆむ、宮野悟、セルイラストレータオンラインとダイナミックシグナル伝達データベースへのTranspathの再構築、//BMB2008 Biochemistry and Molecular Biology//,3P-1034, 2008.
  - [Poster] M. Nagasaki, A. Saito, __**C. Li**__, K. Numata, E. Jeong and S. Miyano, Systematic Reorganization of TRANSPATH Database to Cell System Markup Language, S04, //Proceedings of the 2008 Annual Conference of Japanese Society for Bioinformatics//, 2008.
  - [Poster] K. Hioka, Y. Miwa, __**C. Li**__, Q.W. Ge, H. Matsuno and S. Miyano, An Algorithm Determining Delay Times in a Mark Graph for Smooth Signal Flowing, //Proceedings of the 19th International Conference on Genome Informatics (GIW2008)//, S31, 2008.
  - [Talk/Poster] __**C. Li**__, M. Nagasaki, K. Ueno and S. Miyano, Formal Validation of Quantitative Models of Cell Fate Specification During C. elegans Vulval Development by Simulation-based Model Checking Approach, // Proceedings of the 2008 Annual Conference of Japanese Society for Bioinformatics//, P060/T15, 2008 (Selected as oral presentation).
  - [Poster] __**C. Li**__, M. Nagasaki, K. Ueno and S. Miyano, Vulval Development Modeling Using Hybrid Functional Petri Net with extension and its Simulation-based Formal Model Validation, // Proceedings of the 19th International Conference on Genome Informatics (GIW2008)//, S09, 2008.
  - [Talk/SoftDemo] M. Nagasaki, E. Jeong, K. Ueno, E. Ikeda, __**C. Li**__, K. Kojima, A. Saito and S. Miyano, Cell Illustrator 3.5 and Cell System Ontology 3.0, // Proc. of the 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007),// Software Demonstrations 02 & Oral presentation 05, 2007.   [[PDF:http://www.csml.org/download/publication/S2_Nagasaki.pdf|{{[PDF]}}]]
  - [Poster] __**C. Li**__, Q.W. Ge, H. Matsuno and S. Miyano, On Timed Petri Nets Based Modeling and Simulation of Signaling Pathways, // Proc. of the 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi2007),// Poster 032, 2007.
  - [Poster] E. Jeong, M. Nagasaki, __**C. Li**__, K. Ueno, E. Ikeda, K. Kojima, A. Saito and S. Miyano, Cell System Markup Language 3.0 and its Platform Cell Illustrator 4.0 for Systematic Translation of Cell System, // Proc. of the 7th International Workshop on Advanced Genomics New Horizon//, Poster 045, 2007.  
  -  [Poster] __**C. Li**__, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, Petri Net Based Modeling and Time-Related Simulation of Signaling Pathways Demonstrated for Apoptosis, //Proc. of the Seventh Annual International Workshop on Bioinformatics and Systems Biology//, Poster 030, 2007. 
  -  [Poster] __**C. Li**__, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, Structural Representation of Signaling Pathway Based on Petri Net, // Proc. of 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB)//, Poster C023, 2007.  
  -  [Poster] __**C. Li**__, S. Suzuki, Y. Takeuchi, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, Petri Net Based Modeling of Signaling Pathways Including Inhibitory Function, // Proceedings of the 16th International Conference on Genome Informatics,// p115, 2005.
  - [Poster] __**C. Li**__, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, A New Petri Net Modeling Method for Signaling Pathways with a Focus on Enzyme, //Proceedings of the 15th International Conference on Genome Informatics//, Poster abstract, P004, 2004.  
  -  [Talk/Poster] __**C. Li**__, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, A New Petri Net Based Modeling Method For Signaling Pathways With a Focus on Enzymes, Student Satellite Symposium, //Proceedings of the 3rd Asia-Pacific Bioinformatics Conference,// 2005. 







 



=====    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.
  - 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.  
  - 三輪良雅, 樋岡幹司,  __**李晨**__, 葛崎偉, 松野浩嗣, 宮野悟, 実験データに基づくシグナル伝達経路ペトリネットモデルの遅延時間推定手法, 平成20年度電気・情報関連学会中国支部連合大会 (in Japanese), pp.99-100, 鳥取大学,  2008.
  - 樋岡幹司, 三輪良雅, __**李晨**__, 葛崎偉, 松野浩嗣, 宮野悟, 時間ペトリネットによるシグナル伝達経路モデルの反応時間決定のアルゴリズムの提案, 平成20年度電気・情報関連学会中国支部連合大会 (in Japanese), pp.101-102, 鳥取大学,  2008.
  - 樋岡幹司, __**李晨**__, 松野浩嗣, 宮野悟, 実験データに基づいたペトリネット分割によるシグナル伝達経路パラメータの推定方法の提案, 平成19年度電気・情報関連学会中国支部連合大会講演論文集, pp.127-128, 2007. 
  - S. Suzuki, __**C. Li**__, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, Structural Representation of a Signaling Pathway by T-invariants, //Technical Report of IEICE// (in Japanese), CAS2005-62, CST2005-31, 7-12, 2005-11. 
  -  __**C. Li**__, S. Suzuki, Q.W. Ge, M. Nakata, H. Matsuno and S. Miyano, A New Proposal of Petri Net Based Formulation for Analyzing Signaling Pathways,//Technical Report of IEICE.,// CST2004-39, 1-8, 2005-01.  
  -  __**C. Li**__, Q.W. Ge and M. Nakata, A Proposal of New Priority List on Two-Processor Scheduling of Program Nets, //Technical Report of IEICE.,// CAS2003-88, CST2003-31, 23-28, 2003-11. 
  -  __**C. Li**__, Q.W. Ge and M. Nakata, Two-Processor Scheduling for the SWITCH-less Program Nets Whose AND-nodes Possess Two Input Edges, //Technical Report of IEICE. //(in Japanese), 2002.