Computational Methods

 

• Blätke, M.A., Heiner, M. and Marwan, W. 2015. BioModel Engineering with Petri Nets. In: Algebraic and Discrete Mathematical Methods for Modern Biology (Ed. Robeva), Academic Press, Burlington, pp. 141-192.
• Soldatova, L.N., Nadis, D., King, R.D, Basu, P.S., Haddi, E., Baumle, V., Saunders, N.J., Marwan, W. and Rudkin, B.B. 2014. EXACT2: the semantics of biomedical protocols. BMC Bioinformatics 15, Suppl 14: S5.
• Blätke, M.A., Rohr, C., Heiner, M. and Marwan, W. 2014. A Petri-Net-Based Framework for Biomodel Engineering. In: Large-Scale Networks in Engineering and Life Sciences (Ed. Benner et al). Springer International Publishing, pp. 317-366.
• Liu, F., Blätke, M.A., Heiner, M. and Yang., M. 2014. Modelling and simulating reaction diffusion systems using coloured Petri nets. Computers in biology and medicine 53, 297-308.
• Favre, C.F., Marwan, W. and Wagler, A. K. 2014. Integrating prior knowledge in automatic network reconstruction. Proc. of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2014, CEUR-WS.org, CEUR Workshop Proceedings, volume 1159, pages 145-59.
• Durzinsky, M., Marwan, W. and Wagler, A. 2013. Reconstruction of extended Petri nets from time-series data by using logical control functions. Journal of Mathematical Biology 66, 203-223.
• Marwan, W., Rohr, C. and Heiner, M. 2012. Petri Nets in Snoopy: A Unifying Framework for the Graphical Display, Computational Modelling, and Simulation of Bacterial Regulatory Networks. In: Methods in Molecular Biology (Ed. Van Helden et al), Springer, 804/2012, pp. 409-437.
• Blätke, M.A., Dittrich, A., Rohr, C., Heiner, M. and Marwan, W. 2013. JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology. Molecular BioSystems 9, 1290-1307.
• Marwan, W. and Blätke, M.A. 2012. A Module-based Approach to Biomodel Engineering with Petri Nets. In: Proceedings of the 2012 Winter Simulation Conference (Ed. Laroque et al), WSC 2012 Berlin, IEEE, pp. 3383-3394.
• Blätke, M.A., Heiner, M. and Marwan, W. 2012. Predicting Phenotype from Genotype through Automatically Composed Petri Nets. In: Computational Methods in Systems Biology (Ed. Gilbert et al) Springer, London. LNCS volume 7605, pp. 87-106.
• Blätke, M.A., Dittrich, A., Heiner, M., Schaper, F. and Marwan, W. 2012. JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept. In: Computational Methods in Systems Biology (Ed. Gilbert et al), Springer, London. LNCS volume 7605, pp. 362-365.
• Blätke, M.A., Dittrich, A., Rohr, C., Heiner, M., Schaper, F. and Marwan, W. 2012. JAK/STAT signalling - an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems- and synthetic biology. arXiv:1206.0959 [q-bio.MN]
• Blätke, M.A., Marwan, W. 2012. A database-supported modular modelling platform for systems and synthetic biology. Proc. of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2012, CEUR Workshop Proceedings 852, 18-19.
• Durzinsky, M., Marwan, W., Ostrowski, M., Schaub, T. and Wagler, A. 2011. Automatic network reconstruction using ASP. Theory and Practice of Logic Programming 11, 749-766.
• Blätke, M.A., Meyer, S. and Marwan, W. 2011. A database-supported modular modelling platform for systems and synthetic biology. Proceedings of the 3rd International Workshop on Biological Processes & Petri Nets (BioPPN), satellite event of Petri Nets 2011, CEUR Workshop Proceedings 724, 117-134.
• Blätke, M.A. 2011. Pain Signaling - A Case Study of the Modular Petri Net Modeling Concept with Prospect to a Protein-Oriented Modeling Platform. In: Formal Methods in Molecular Biology (Ed. Breitling et al), Report from Dagstuhl Seminar 11151, 46-47.
• Durzinsky, M., Wagler, A. and Marwan, W. 2011. Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks. BMC Systems Biology 5, 113.  
• Blätke, M.A. and Marwan,W. 2010. Modular and hierarchical modelling concept for large biological Petri nets applied to nociception. 17th German Workshop on Algorithms and Tools for Petri Nets, CEUR Workshop Proceedings 643(4).
• Blätke, M.A., Meyer, S., Stein, C. and Marwan, W. 2010. Petri net modeling via a modular and hierarchical approach applied to nociception. International Workshop on Biological Processes & Petri Nets (BioPPN), Braga, Protugal 2010 Proceedings, ISBN: 978-972-8692-53-7.
• Rohr C., Marwan, W. and Heiner, M..2010. Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinformatics, 26,7:974-975.
• Heiner, M., Lehrack, S., Gilbert, D. and Marwan, W. 2009. Extended Stochastic Petri Nets for Model-based Design of Wetlab Experiments. In: RJ Back Computational models for cell processes. Transactions on Computational Systems Biology (Ed. Petre, Priami), Springer 5750/2009, 138-163.
• Durzinsky, M., Wagler,A., Weismantel, R. and Marwan, W. 2008. Automatic reconstruction of molecular and genetic networks from discrete time series data. BioSystems 93, 181-190.
• Marwan, W., Wagler, A. and Weismantel, R. 2008. A mathematical approach to solve the network reconstruction problem. Math. Meth. Oper. Res. 67, 117-132.