Articles Referred Our Works

1900s

• Adrian Silvescu, Vasant Honavar, Temporal Boolean Network Models of Genetic Networks and Their Inference from Gene Expression Time Series, Complex Systems, 11, pp.1-18, 1997. [.pdf]
• L.Tanabe,U.Scherf,L.H.Smith,J.K.Lee,L.Hunter and J.N.Weinstein, MedMiner:An Internet Text-Mining Tool for Biomedical Information,with Application to Gene Expression Profiling, BioTechniques 27:1210-1217,December 1999.[.pdf]

2000

• E. J. Moler, M. L. Chow, and I. S. Mian, Analysis of molecular profile data using generative and discriminative methods, Physiol. Genomics 4, pp.109-126, 2000. [.pdf]
• E. J. Moler, D. C. Radisky and I. S. Mian, Integrating naive Bayes models and external knowledge to examine copper and iron homeostasis in Saccharomyces cerevisiae, Physiol. Genomics, Vol.4, No.2, pp.127-135, December 18, 2000. [.pdf], [.html]
• H. Genrich, R. Kuffner and K. Voss, Executable Petri Net Models for the Analysis of Metabolic Pathways, Proceedings of the workshop on Practical Use of High-level Petri Nets in 21st International Conference on Application and Theory of Petri Nets 2000 (ICATPN 2000), pp.1-14, Aarhus, Denmark, June 27, 2000. [.pdf]
• P. D'haeseleer, S. Liang and R. Somogyi, Genetic network inference: from co-expression clustering to reverse engineering, Bioinformatics, Vol.16, No.8, pp.707-726, 2000. [.pdf]
• P. D'haeseleer, Reconstructing Gene Networks from Large Scale Gene Expression Data, Ph.D. dissertation, University of New Mexico, December 2000. [.pdf]

2001

• Jiri Vohradsky, Neural Model of the Genetic Network, The Journal of Biological Chemistry, Vol.276, No.39, pp.36168-36173, September 28, 2001. [.pdf]
• J. A. Dickerson, Z. Cox*, E. Wurtele and A.W. Fulmer, Creating metabolic and regulatory network models using fuzzy cognitive maps, IFSA World Congress and 20th North American Fuzzy Information Processing Society (NAFIPS) International Conference, Vol.4, pp.2171-2176, Vancouver, British Columbia, July, 2001. [.pdf]
• M. Heiner, I. Koch and K. Voss, Analysis and Simulation of Steady States in Metabolic Pathways with Petri Nets, the 3rd Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools (CPN'01), pp.15-34, August 2001. [.pdf]
• Jean-Louis Giavitto, Olivier Michel and Franck Delaplace, Declarative simulation of dynamicals systems :the 81/2 programming language and its application to the simulation of genetic networks,Proceedings of IPCAT 2001(Workshop on Information Processing in Cellsand Tissues, Louvain),2001.[.pdf]
• Jeffrey T.Chang & Soumya Raychaudhuri, Towards Incorporating Scientific Literature into Biological Algorithms, Intelligent Systems in Molecular Biology,21 July 2001. [.pdf]
• D. Nicorici, Some Simulation of the Proteins-Genes Interactions, Seminar on Biocomputing, May 23, 2001. [.pdf]

2002

• K. Nakai and J.-P. Vert, Genome informatics for data-driven biology, A report on the 12th international conference on genome informatics, Tokyo, Japan, December 17-19, 2001, Genome Biology, Vol.3, Issue 4, reports 4010.1-4010.3, 27 March 2002. [.pdf]
• Ming Chen, Andreas Freier, Jacob Köhler and Alexander Rüegg, The Biology Petri Net Markup Language, Proceedings of Promise'2002, Vol.21: pp.150-161. [.pdf]
• Hidde De Jong, Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology, Volume 9, Number 1, pp.67-103, 2002. [.pdf] [Abstract]
• R. Drath, Description of Hybrid Systems by Modified Petri Nets, Lecture Notes in Control and Information Science (LNCIS) Vol. 279, pp.1-15, 2002. [.Abstract]
• Kenta Nakai and Jean-Philippe Vert, Genome informatics for data-driven biology, Genome Biology 2002, 3(4):reports4010.1-4010.3. [Abstract], [.pdf], [.html]
• Mor Peleg, Iwei Yeh, and Russ B. Altman, Modeling biological processes using Workflow and Petri Net models, Bioinformatics, Vol.18, No.6, pp.825-837, June 2002.[.pdf] [Abstract]
• S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch and T. Dandekar, Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma Pneumoniae, BIOINFORMATICS, Vol. 18 no.2, pp.351-361, 2002. [.pdf] [Abstract]
• Ashish Tiwari, Patrick Lincoln, Automated Techniques for Stability Analysis of Delta-Notch Lateral Inhibition Mechanism. [.ps]
• A. Bockmayr and A. Courtois, Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems, Proceedings of the 18th International Conference on Logic Programming, Lecture Notes In Computer Science, Vol.2401, pp.85-99, Springer-Verlag London, UK, 2002, ISBN:3-540-43930-7. [.ps]
• E. P. van Someren, L. F. Wessels, E. Backer and M. J. Reinders, Genetic network modeling, Pharmacogenomics, Vol.3, No.4, pp.507-525, Ashley Publications Ltd, July 2002, ISSN:1462-2416. [.pdf]
• A. Gilman and A. P. Arkin, Genetic "code": representations and dynamical models of genetic components and networks, Annu. Rev. Genomics Hum. Genet., Vol.3, pp.341-369, September 2002. [.pdf]
• H. de Jong, Modeling and simulation of genetic regulatory systems: A literature review, Journal of Computational Biology, Vol.9, No.1, pp.67-103, 2002. [.pdf]
• Ming Chen, Modelling and Simulation of Metabolic Networks,Petri Nets Approach and Perspective in the proceeding of "ESM 2002,16th European Simulation Multiconference",2002,June 3-5,Darmstadt,Germany,441-444.[.pdf]
• Mor Peleg, Iwei Yeh, Russ B. Altman, Modelling biological processes using workflow and Petri Net models, BIOINFOMATICS,vol. 18, no.6, pp.825-837, 2002.[.pdf]
• Yun, Min Seon, Biopathway Reconstruction with New Clustering Algorithm, March, 9, 2002. [.ppt]
• Ming Chen, Andreas Freier, Petri Net Based Modeling and Simulation of Metabolic Networks in the Cell. [.pdf]
• Hakan Oktem, Ronald Pearson, Olli Yli-Harja, Daniel Nicorici, Karen Egiazarian, Jaakko Astola, A Computational Model for Simulating Continuous Time Boolean Networks, Workshop on Genomic Signal Processing and Statistics (GENSIPS), 2002. [.pdf]

2003

• Yves Deville, David Gilbert, Jacques van Helden, Shoshana Wodak, An Overview of Data Models for the Analysis of Biochemical Pathways, Briefings in Bioinformatics, 2003 4:3, pp.246-259, ISSN 1467-5463. [.pdf]
• Nathalie Chabrier, Francois Fages, Symbolic Model Checking of Biochemical Networks, Computational Methods in Systems Biology 2003, pp.149 - 162, February 24-26, 2003. [.ps]
• Burleigh, I., G. Suen, and C. Jacob., DNA in Action! A 3D Swarm-based Model of a Gene Regulatory System. Proceedings of the First Australian Conference on Artificial Life. Lecture Notes in Computer Science. Springer-Verlag: Berlin. 2003. [.pdf]
• Michel J.L. De Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano, Inferring Gene Reguratory Networks From Time-ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations, Pacific Symposium on Biocomputing 8:17-28, 2003. [.pdf]
• William H. Hsu, Roby Joehanes, Learning the Structure of Graphical Models of Gene Regulation from Microarray Data: Survey and Experiments, International Joint Conference on Artificial Intelligence (IJCAI) 2003. [.doc]
• Pat Langley, Dileep George, Kazumi Saito, Jeff Shrager, and Stephen Bay, Inducing Biologically Plausible Models from Temporal Expression Data, The Sixth International Conference on Discovery Science, 2003. [.ps]
• J.W. Pinney, D.R. Westhead and G.A. McConkey, Petri Net representations in systems biology, Biochemical Society Transactions 31, pp.1513-1515, 2003. [.pdf]
• V. Bassano and G. Bernot, Marked Regulatory Graphs : A formal Framework to Simulate Biological Regulatory networks with simple automata, in 4th IEEE International Workshop on Rapid System Prototyping (RSP'03), San Diego, California, pp.93-99, June 09-11, 2003. [.pdf]
• J. A. Dickerson, D. Berleant, Z. Cox, W. Qi, D. Ashlock, E. Wurtele and A.W. Fulmer, Creating Metabolic Network Models using Text Mining and Expert Knowledge, Computational Biology and Genome Informatics, World Scientific, pp.207-238, 2003, ISBN: 981-238-257-7. [.pdf]
• Y. Deville, D. Gilbert, J. van Helden and S. J. Wodak, An Overview of Data Models for the Analysis of Biochemical Pathways, Proceedings of the First International Workshop on Computational Methods in Systems Biology, Lecture Notes In Computer Science, Vol.2602, pp.174, Springer-Verlag London, UK, 2003, ISBN:3-540-00605-2. [.pdf]
• N. Chabrier-Rivier and F. Fages, The biochemical abstract machine BIOCHAM, Proceedings of the European Conference on Computational Biology (ECCB'03), pp.597-599, Paris, France, September, 2003. [.ps]
• C. Cotta, On the Evolutionary Inference of Temporal Boolean Networks, Lecture Notes in Computer Science, Vol.2686, pp.494-501, Springer-Verlag Berlin Heidelberg, 2003. [.pdf]
• D.Barleant,J.Ding,D.Nettleton, Corpus Properties of Protein Interaction Descriptions, unpublished 2003. [.pdf]
• Ming Chen, Ralf Hofestadt, Quantitative Petri Net Model of Gene Regulated Metabolic Networks in the Cell, in Silico Biology, vol.3, no.3, pp.347-365, 2003.
• Hiroshi Kitano, A graphical notation for biochemical networks, BIOSILICO, vol.1, no.5, pp.169-175, 2003. [.pdf]
• N. Dovgolevsky, CELL SIMULATION, Advanced Algorithms in Computational Biology (Course 236805), Seminar in Bioinformatics, May 12, 2003. [.ppt] [.doc]
• Francesco Bernardini, The Molecular X Machine Project, Transfer Report, December 2003. [.ps]
• M. McLean, Systems Biology and Data Organization (October 2003). [.doc]
• Andreas Constantinides, Mathematical Modeling of Gene Regulatory Networks Report: Product Form Solutions for Stochastic Petri Networks., EE6902, 05/10/2003. [.pdf]
• Francesco Bernardini, The Molecular X Machine Project Six Months Report, June 2003. [.ps]
• R. Machne, Modelling of Biochemical Reaction Networks: The MAP Kinase pathway, Seminar on Theoretical Biochemistry, March 17, 2003. [.pdf]
• A. M. Uhrmacher and D. Degenring, From Macro to Multi-Level Simulation and Beyond, Tutorial at the 4th International Conference on Systems Biology (ICSB 2003), St. Louis, USA, November 5?9, 2003. [.pdf]

2004

• A. Regev, E. M. Panina, W. Silverman, L. Cardelli and E. Shapiro, BioAmbients: An abstraction for biological compartments, Theoretical Computer Science, Vol.325, pp.141-167, 2004. [.pdf]
• C. Talcott, S. Eker, M. Knapp, P. Lincoln and K. Laderoute, Pathway logic modeling of protein functional domains in signal transduction, Pac Symp Biocomput, pp.568-580, 2004. [.pdf]
• J. Mandel, N. Palfreyman, J. Lopez and W. Dubitzky, Representing Bioinformatic Causality, Briefings in Bioinformatics, Vol.5, No.3, pp.270-283, Henry Stewart Publications, 2004. [.pdf]
• P. Sendi, J Al Maiwenn and M. Battegay, Optimising the performance of an outpatient setting, Swiss Med Wkly, Vol.134, pp.44?49, 2004. [.pdf]
• R. Backofen, M. Badea, A. Burger, F. Fages, P. Lambrix, W. Nutt, M. Schroeder, S. Soliman and S. Will, State-of-the-art in Bioinformatics, REWERSE Deliverable A2-D1, 2004. [.pdf]
• C. Chaouiya, L. Mendoza, E. Remy, P. Ruet and D. Thieffry, From logical regulatory graphs to standard Petri nets: dynamical roles and functionality of feedback circuits, Concurrent Models in Molecular Biology, Electronic Notes in Computer Science, Elsevier, 2004. [.ps]
• O. Shaw, A. Koelmans, L. J. Steggles and A. Wipat, Applying Petri Nets to Systems Biology using XML Technologies, Proceedings of the workshop on the Definition, Implementation and Application of a Standard Interchange Format for Petri Nets, Satellite event of the 25th International Conference on Application and Theory of Petri Nets 2004 (ICATPN 2004), pp.11-25, Bologna, Italy, June 26, 2004, [.pdf] , Technical report University of Newcastle, CS-TR: 827, Newcastle University Library, March 2004. [Abstract] [.pdf]
• D. G. Clarke, D. F. de Oliveira Costa and F. Arbab, Modelling coordination in biological systems, CWI Report SEN-R0415, September 30, 2004. [.pdf]
• C. Jacob and I. Burleign, Agent-based Models of Biomolecular Systems, the 2nd International E. Coli Alliance (IECA) Conference on Systems Biology Information, Banff, Canada, June 19, 2004. [.pdf]
• J. Mandel and N. Palfreyman, A Pen-and-Paper Notation for Teaching Biosciences, Proceedings of the International Symposium on Knowledge Exploration in Life Science Informatics 2004 (KELSI 2004), pp.84-95, Milan, Italy, November 25-26, 2004, Lecture Notes in Computer Science (LNCS), Lecture Notes in Artificial Intelligence (LNAI), Vol.3303, pp.1-8, Springer Berlin Heidelberg New York, 2004, ISBN:3-540-23927-8. [.pdf]
• C. Chaouiya, E. Remy, P. Ruet and D. Thieffry, Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets, Proceedings of the 25th International Conference on Application and Theory of Petri Nets 2004 (ICATPN 2004), Bologna, Italy, June 21?25, 2004, Lecture Notes in Computer Science (LNCS), Vol.3099, pp.137-156, Springer-Verlag GmbH, 2004, ISBN:3-540-22236-7. [.ps] [Abstract]
• C. Priami1 and P. Quaglia1, Modelling the dynamics of biosystems, Briefings in Bioinformatics, Vol.5, No.3, pp.259-269, Henry Stewart Publications, September 2004.
• I. Koch, M. Schuler and M. Heiner, STEPP - Search Tool for Exploration of Petri net Paths: A new tool for Petri net-based path analysis in biochemical networks, In Silico Biology, Vol.5, No.2, pp.129-137, IOS Press, 2005. [.html]
• M. Curti, P. Degano, C. Priami and C. T. Baldari, Modelling Biochemical Pathways Through Enhanced π-Calculus, Theoretical Computer Science, Vol.325, No.1, pp.111-140, Elsevier, 2004. [.pdf]
• A. Regev and E. Shapiro, The π-calculus as an abstraction for biomolecular systems, Modelling in Molecular Biology, pp.219-266, Natural Computing Series, Springer, 2004, ISBN:3-540-40799-5. [.pdf]
• N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages and V. Schachter, Modeling and Querying Biomolecular Interaction Networks, Theoretical Computer Science, Vol.325, No.1, pp.25-44, September 2004. [.pdf]
• P. Langley, J. Shrager, N. Asgharbeygi, S. Bay and A. Pohorille, Inducing explanatory process models from biological time series, Proceedings of the Ninth Workshop on Intelligent Data Analysis and Data Mining, pp.85-90, Stanford, CA, 2004. [.ps]
• S. M. Welch, Z. Dong, J. L. Roe and S. Das, Modeling gene networks controlling transition to flowering in Arabidopis, Proceedings of the 4th International Crop Science Congress (ICSC2004), Brisbane, Australia, Sep 26 - Oct 1, 2004, ISBN:1-920842-20-9. [.pdf]
• F. Fages, S. Soliman and N. Chabrier-Rivier, Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry, Vol.4, No.2, pp.64-73, October 2004. [.pdf]
• S. Biermann, L. Uhrmacher and H. Schumann, Supporting Multi-level Models in Systems Biology by Visual Methods, Proceedings of the 18th European Simulation Multiconference (ESM'04), Magdeburg, Germany, June 2004. [.pdf]
• Thomas Runge, Qualitative path analysis of metabolic pathways using Petri Nets for generic modelling,institute of Computer Science,report03/04,pp.1-26,August 2004.[.pdf]
• Nicola Cannata,Flavio Corradiru,Emanuela Merelli,Alessandro Ricci, An Agent-oriented Conceptual Framework for Biological Systems Simulation,NETTAB Workshop on Models and Metaphors from Biology to Bioinformatics Tools,Sept.2004.[.pdf]
• 皿井伸明,天野晃,松岡達,松田哲也,野間昭典,生物学的視点に基づくオブジェクト指向生体機能シミュレーション,シミュレーション,vol.23,No.1,p.4-13, 2004.[.pdf]
• Tsuyoshi Koga, Kazuhiro Aoyama, PRODUCT BEHAVIOR AND TOPOLOGICAL STRUCTURE DESIGN SYSTEM BY STEP-BY-STEP DECOMPOSITION,Proceedings of DETC’04 ASME 2004 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference,pp.1-13,2004.[.pdf]
• Frank Doyle and Douglas Lauffenburger, NETWORK INFERENCE,WTEC Panel Report on International Research and Developmentin Systems Biology,chapter3,pp.19-27,2004.[.pdf]
• C. Reinke, Haskell-Coloured Petri Nets, Implementation and Applications (work-in-progress) IFL’04, Lubeck, Germany, 10 September 2004. [.ppt]
• F. Fages, Constraint-based Model Checking of Non-deterministic Hybrid Systems: A First Experiment in Systems Biology, Workshop on Constraint Programming and Constriants for Verification CP+CV'04 associated to ETAPS'04, March 2004. [.ppt]
• Tan Chee Meng, Sandeep Somani, Pawan Dhar, Modelling and Simulation of Biological Systems with Stochasticity, 2004. [.pdf]
• I. Koch and M. Heiner, Qualitative biochemical pathway analysis using Petri nets, CNRS, Structural & Genomic Information Lab., Marseille, February 2004, 49 p. [.pdf]
• C. Chaouiya, E. Remy and D. Thieffry, From logical regulatory graphs to Petri Nets to SBML, The Ninth Workshop on Software Platforms for Systems Biology, Heidelberg, Germany, October 14-15, 2004. [.pdf]

2005

• J. P. Vert and Y. Yamanishi, Supervised graph inference, Proceedings of Neural Information Processing Systems (NIPS2004), Vancouver and Whistler, British Columbia, Canada, December 14-16, 2004, Advances in Neural Information Processing Systems 17, pp.1433-1440, The MIT Press, July 2005, ISBN:0-262-19534-8. [.pdf]
• L. Popova-Zeugmann, M. Heiner and I. Koch, Time Petri Nets for Modelling and Analysis of Biochemical Networks, Fundamenta Informaticae, Vol.67, pp.149-162, 2005. [.pdf]
• S. Ramsey, D. Orrell and H. Bolouri, Dizzy: Stochastic simulation of large-scale genetic regulatory networks, Journal of Bioinformatics and Computational Biology, Vol.3, No.2, pp.415-436, 2005. [.pdf]
• M. Calder, V. Vyshemirsky, D. Gilbert and R. Orton, Analysis of Signalling Pathways using the Prism Model Checker, Proceedings of Computational Methods in Systems Biology (CMSB 2005), Edinburgh, Scotland, April 3-5, 2005. [.pdf]
• J. Nummela and B. A. Julstrom, Evolving petri nets to represent metabolic pathways, Proceedings of the 2005 conference on Genetic and Evolutionary Computation (GECCO 2005), Washington DC, USA, June 25-29, 2005, Genetic And Evolutionary Computation Conference, pp.2133-2139, ACM Press, New York, USA, 2005, ISBN:1-59593-010-8. [.ps]
• S. Biermann, Y. Gu, H. Schumann and L. Uhrmacher, Information Visualization in Systems Biology, Rostocker Informatik-Berichte, Heft 29, Universitat Rostock, Fakultat fur Informatik und Elektrotechnik, 2005, ISSN 0233-0784. [.pdf]
• A. Freier, R. Hofestaedt and T. Toepel, Investigating the Effective Range of Agents by Using Integrative Modelling, Handbook of Toxicogenomics, pp.233-251, Wiley-VCH, 2005, Print ISBN:3-527-30342-1, Online ISBN:3-527-60371-9.
• David L.Dill,Memil A.Knapp,Pamela Gage,Carolyn Tlcott,Keith Laderoute, The Pathalyzer: a Tool for Analysis of Signal,The First Annual Recomb Satellite Workshop on Systems Biology,2005.[.pdf]
• Cynthia Stokes and Adam Arkin, MODELING AND NETWORK ORGANIZATION,Assessment of International Research and Development in Systems Biology,WTEC Panel Report on International Research and Development in Systems Biology,pp.29-51,October,2005.[.pdf]
• Mitsuru Kato, Masao Nagasaki, Atsushi Doi and Satoru Miyano, Automatic Drawing of Networks Using Cross Cost and Subcomponent Data,Genome Informatics 16(2): 22-31 (2005). [.pdf]
• Mor Peleg, PhD, Daniel Rubin, MD, MSc and Russ B. Altman, MD, PhD , Using Petri Net Tools to Study Properties and Dynamics of Biological Systems, Journal of the American Medical Informatics Association 12(2):181-199, 2005. [.pdf]
• Ross D. King, Simon M. Garrett and George M. Coghill, On the use of qualitative reasoning to simulate and identify metabolic pathways, BININFOMATICS, Vol.21, no.9, pp.2017-2026, 2005. [.pdf]
• F. Fages, The Biochemical Abstract Machine BIOCHAM, Talk at IRISA, March 2005. [.ppt]
• P. Milazzo, Probabilistic Modelling and Verification of Biological Systems, Ph.D. Thesis Proposal, January 26, 2005. [.pdf]
• L. Cardelli, Biological Systems as Reactive Systems, Cambridge Anatomy Department, July 5, 2005. [.pdf]
• N. Shah, Formal Methods for Genomic Data Integration, Ph.D. dissertation, Pennsylvania State University, August 2005. [.pdf ]
• F. d’Alche-Buc and V. Schachter, Modeling and identification of biological networks, Proceedings of the International Symposium on Applied Stochastic Models and Data Analysis (ASMDA 2005), Brest, France, May 17-20, 2005. [.pdf]

2006

• Carolyn Talcott, SYMBOLIC MODELING OF SIGNAL TRANSDUCTION IN PATHWAY LOGIC,Proceedings of the 2006 Winter Simulation Conference,L.F.Perrone,F.P.Wieland,J.Liu,B.G.Lawson,D.M.Nicol,and R.M.Fujimoto,eds.[.pdf]
• Joseph Makin, Srini Narayanan, and Roopa Ramamoorthi, Hybrid System Modeling of Human Blood Clotting,2005 Technology Breakthrough Competition,pp.1-17,August 28,2006.[.pdf]
• Roberto Barbuti, Andrea Maggiolo-Schettini,Paolo Milazzo, and Angelo Troina, Bisimulation Congruences in the Calculus of Looping Sequences 3rd Int,Colloquium on Theoretical Aspects of Computing (ICTAC'06),Springer LNCS 4281, pp. 93-107, Tunis, Tunisia, November 2006.[.pdf]
• Daniel Scheibler, Ein Aerkzeug zum Entwerfen und Simulieren kontinuierlicher Petrinetze, master-theses of Brandenburg university of technology cottbus, Januar 2006. [.pdf]
• Anna Gambin A1, Sıawomir Lasota A1, Michaı Rutkowski A1 , Analyzing Stationary States of Gene Regulatory Network Using Petri Nets,In Silico Biology, Volume 6, Number 1-2 /pp.93 - 109, 2006.
• Andrea Sackmann, Monika Heiner, and Ina Koch, Application of Petri net based analysis techniques to signal transduction pathways, BMC Bioinformatics 2006, 7:482 (2 November 2006). [.pdf]
• Muffy Calder, Vladislav Vyshemiesky, David Gilbert, Richard Orton, Analysis of Signalling Pathways Using Continuous Time Markov Chains, Lecture Notes in Computer Science 4220:pp. 44-67, 2006. [.pdf]
• Claudio Eccher and Corrado Priami, Design and implementation of a tool for translating SBML into the biochemical stoshastic π-calculus, Bioinformatics 22(24): 3075-3081, 2006.
• L. J. Steggles, R. Banks and A. Wipat, COMPUTING SCINENCE: Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets, Newcastle University, TECHNICAL REPORT SERIES, No. CS-TR-962, 2006.[.pdf]
• Andrea Sackmann, Monika Heiner and Ina Koch, Application of Petri net based analysis techniques to signal transduction pathways, BMO Bioinfomaticspp. 1-17, 2006.
• DEREK A. RUTHS, LUAY NAKHLEH, M. SRIRAM IYENGAR, SHRIKANTH A.G. REDDY, and PRAHLAD T. RAM, Hypothesis Generation in Signaling Networks, JOURNAL OF COMPUTATIONAL BIOLOGY, vol 13, pp. 1546-1557, 2006. [.pdf]
• Shinya Tasaki, Masao Nagasaki, Masaaki Oyama, Hiroko Hata, Kazuko Ueno, Ryo Yoshida, Tomoyuki Higuchi, Sumio Sugano, Satoru Miyano, Modeling and Estimation of Dynamic EGFR Pathway by Data Assimilation Approach Using Time Series Proteomic Data, Genome Infomatics, 17(2):226-238, 2006. [.pdf]
• Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, and Janine Guespin, Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in Human Early Haematopoiesis, Pacific Symposium on Biocomputing 11:427-438, 2006. [.pdf]
• Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Angelo Troina, A Calculus of Looping Sequences for Modelling Microbiological Systems, Fundamenta Infomaticae, volume 72, No. 1-3, pp. 21-35, 2006. [.pdf]
• Jun Li, Liang Wang, Yoshifumi Hashimoto, Chen-Yu Tsao, Thomas K Wood, James J Valdes, Evanghelos Zafiriou and William E Bentley, A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways, Molecular Systems Biology (Mol), pp.2-67, 2006. [.pdf]

2007

• William J Bosl, Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery, BMC Systems Biology 2007, volume 1, pp.1-13, 2007. [.pdf]
• Tra Thi Vu and Jiri Vohradsky, Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae, Nucleic Acids Research,Vol. 35, No. 1 pp. 279-287, 2007. [.pdf]
• PETER J. BENTLEY, Systemic computation: A model of interacting systems with natural characteristics, The International Journal of Parallel, Emergent and Distributed Systems,Vol. 22, No. 2, pp.103-121, 2007. [.pdf]
• Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato and Satoru Miyano, An efficient grid layout algorithm for biological networks utilizing various biological attributes, BMC Bioinfomatics, volume 8, issue 1, pp.1-76, 2007.[.pdf]
• L. Jason Steggles, Richard Banks , Oliver Shaw and Anil Wipat, Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach, BIOINFOMATICS, Vol.23. no.3, pp.336-343, 2007.
• Nicola Neretti, Daniel Remondini, Marc Tatar, John M Sedivy, Michela Pierini, Dawn Mazzatti, Jonathan Powell, Claudio Franceschi and Gastrone C Castellani, Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation, BMC (Bioinfomatics 2007), volume.8, Supply.1, pp.1-14, 2007.[.pdf]
• Wayne Materi and David S. Wishart, Computational systems biology in cancer; modelling methods and applications: Gene Regulation and Systems Biology, pp.91-110, 2007. [.pdf]
• Simon Hardy and Pierre N. Robillard, Petri net-based methods for the analysis of the dynamics signal propagation in signaling pathways: Bioinfomatics, volume 24, issue 2, pp.209-217, 2007.
• Andrea Sackmann, Dorota Formanowicz, Potr Formanowicz, Ina Koch, Jacek Blazewicz, An analysis of Petri net based model of the human body iron homeostasis process, Computational Biology and Chemistry, vol.31, no.1, pp.1-10, 2007.[.pdf]
• Thomas Schlitt, Alvis Brazma, Current approaches to gene regulatory network modelling, Bioinfomatics, vol.8, supply.6, 2007. [.pdf]
• Anastasia Yartseva, Hanna Klaudel, Raymond Debillers, François Képès, Incemental and unifying modelling formalism for biological interaction networks, Bioinfomatics, vol.8, 2007. [.pdf]
• Vincent Danos, Jean Krivine, Formal Molecular Biology Done in CCS-R, Thoretical Comuputer Science, vol.180, no.3, pp.31-49, 2007. [.pdf]
• Carlos Gomez-Uribe, George C. Verghese, Leonid A. Mirny, Oparating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering, COMPUTATIONAL BIOLOGY, vol.3, no. 12, 2007. [.pdf]
• Francesco Bernardini, Marian Gheorghe, Natalio Krasnogor, Quorum sensing P systems, Theoretical Computer Science, vol.371, issue. 1-2, pp.20-33, 2007. [.pdf]

2008

• Stephen Gilmore, Jane Hillston, Performance evaluation comes to life: quantitative methods applied to biological systems: ACM SIGMETRICS Performance Evaluation Review, volume 35, issue 4, pp.3-13, 2008.
• Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch, Modularization of biochemical networks based classification of petri net t-invariants: BMC Bioinfomatics, volume 9, issue 90, 2008.

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  Power point slides

  • 濱口清治, 応用ネットワーク工学 (7). [.ppt] (in Japanese)

  ---

  Others

  • Patrik D'haeseleer, Reconstructing Gene href="http://www.cs.unm.edu/~forrest/dissertations-and-proposals/patrik.pdf">[.pdf]
  • Tan Chee Meng, Sandeep Somani, Pawan Dhar, Modelling and Simulation of Biological Systems with Stochasticity. [.pdf]