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Publications

Publications

MA Blätke, A Bräutigam (2019). Evolution of C4 photosynthesis predicted by constraint-based modelling. eLife. DOI: 10.7554/eLife.49305
MA Blätke (2018). BioModelKit – An integrative framework for multi-scale biomodel-engineering. Journal of Integrative Bioinformatics 15 (3). DOI: 10.1515/jib-2018-0021
MA Blätke, C Rohr (2018). BioModelKit: Spatial modelling of complex multiscale molecular biosystems based on modular models. Fundamenta Informaticae 160 (1-2), 221-254. DOI: 10.3233/FI-2018-1682
MA Blätke (2017). Biomodelkit - A framework for modular biomodel-engineering. (PhD Thesis) Otto-von-Guericke-Universität Magdeburg. URL: PDF
MA Blätke, C Rohr (2015). A coloured Petri net approach for spatial Biomodel engineering-based on the modular model composition framework Biomodelkit. In Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2015), CEUR-WS.org. CEUR Workshop Proceedings (1373), 37-54. URL: PDF
MA Blätke, M Heiner, W Marwan (2015). Biomodel engineering with Petri nets. In Algebraic and Discrete Mathematical Methods for Modern Biology, (R Robeva, Ed.), Elsevier Inc., pages 141–193. DOI: 10.1016/B978-0-12-801213-0.00007-1
MA Blätke, C Rohr, M Heiner and W Marwan (2014). A Petri net based framework for biomodel engineering. In Large-Scale Networks in Engineering and Life Sciences, (Benner, P, Findeisen, R, Flockerzi, D, Reichl, U and Sundmacher, K, Eds.). Springer, Birkhäuser Mathematics (317–366). DOI: 10.1007/978-3-319-08437-4_6
F Liu, MA Blätke, M Heiner and M Yang (2014). Modelling and simulating reaction–diffusion systems using coloured Petri nets. Computers in Biology and Medicine (53), 297–308. DOI: 10.1016/j.compbiomed.2014.07.004
MA Blätke, A Dittrich, C Rohr, M Heiner, F Schaper and W Marwan (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(6)), 1290-1307. DOI: 10.1039/C3MB25593J
MA Blätke, A Dittrich, M Heiner, F Schaper and W Marwan (2012). JAK-STAT signalling as example for a database-supported modular modelling concept. In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI (7605), 362–365. DOI: 10.1007/978-3-642-33636-2_21
MA Blätke, M Heiner and W Marwan (2012). Predicting phenotype from genotype through automatically composed Petri nets. In Proc. 10th International Conference on Computational Methods in Systems Biology (CMSB 2012), London, Springer, LNCS/LNBI (7605), 87–106. DOI: 10.1007/978-3-642-33636-2_7
W Marwan, MA Blätke (2012). A module-based approach to biomodel engineering with Petri nets. Proceedings of the Winter Simulation Conference (297),1-12. URL: webpage
MA Blätke, W Marwan (2012). A database-supported modular modelling platform for systems and synthetic biology. Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2012), satellite event of Petri Nets 2012. CEUR Workshop Proceedings (852), 18-19. URL: PDF
MA Blätke, M Heiner, W Marwan (2011). Petri nets in systems biology. (Technical Report) Otto-von-Guericke University Magdeburg. URL: PDF
MA Blätke, S Meyer, W Marwan (2011). Pain signaling - A case study of the modular Petri net modeling concept with prospect to a protein-oriented modeling platform. Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2011), satellite event of Petri Nets 2011. CEUR Workshop Proceedings (724), 117-134. URL: PDF
MA Blätke, S Meyer, C Stein, W Marwan (2010). Petri Net Modeling via a modular and hierarchical approach applied to nociception. Proc. Int. Workshop on Biological Processes & Petri Nets (BioPPN 2010), satellite event of Petri Nets 2010. 131-143. URL: PDF
MA Blätke (2010): Petri-Netz Modellierung mittels eines modularen and hierarchischen Ansatzes mit Anwendung auf nozizeptive Signalkomponenten. (Diploma Thesis). Otto-von-Guericke University Magdeburg.
MA Blätke, W Marwan (2010). Modular and hierarchical modelling concept for large biological Petri nets applied to nociception. Proc. 17th German Workshop on Algorithms and Tools for Petri Nets. CEUR Workshop Proceedings (643), 42-50. URL: PDF