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.