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John, Mathias and Schulz, Hans-Jörg and Schumann, Heidrun and Uhrmacher, Adelinde M. and Unger, Andrea (2013) Constructing and visualizing chemical reaction networks from pi-calculus models. Formal Aspects of Computing, 25 (5), pp. 723-742. ISSN 0934-5043.
Mazemondet, Orianne and John, Mathias and Leye, Stefan and Rolfs, Arndt and Uhrmacher, Adelinde M. (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS ONE, 7 (8), e42792. ISSN 1932-6203.
John, Mathias (2011) Reaction Constraints for the Pi-Calculus. A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes. Logos Verlag Berlin. ISBN 978-3-8325-2725-9.
Hoffmann, Eik and Marion, Sabrina and Mishra, Bibhuti Bhusan and John, Mathias and Kratzke, Ramona and Ahmad, Syed Furquan and Holzer, Daniela and Anand, Paras Kumar and Weiss, Dieter G. and Griffiths, Gareth and Kuznetsov, Sergei A. (2010) Initial receptor–ligand interactions modulate gene expression and phagosomal properties during both early and late stages of phagocytosis. European Journal of Cell Biology, 89 (9), pp. 693-704. ISSN 01719335.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim and Uhrmacher, Adelinde M. (2010) The Attributed Pi-Calculus with Priorities. Transactions on Computational Systems Biology 12, pp. 13-76.
John, Mathias (2010) Reaction Constraints for the Pi-Calculus - A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes. PhD thesis, Institute of Computer Science, University of Rostock.
Maus, Carsten and John, Mathias and Rybacki, Stefan and Uhrmacher, Adelinde M. (2010) Towards Rule-Based Multi-Level Modeling. In: 11th International Conference on Systems Biology (ICSB 2010), 10-15 Oct 2010, Edinburgh, UK. Poster.
Leye, Stefan and John, Mathias and Uhrmacher, Adelinde M. (2010) A flexible architecture for performance experiments with the pi-Calculus and its extensions. In: 3rd International Conference on Simulation Tools and Techniques (SIMUTOOLS 2010), 15-19 Mar 2010, Torremolinos, Malaga, Spain. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, 35:1-35:10.
Uhrmacher, Adelinde M. and John, Mathias and Mazemondet, Orianne and Unger, Andrea and Rharass, Tareck and Bader, Benjamin and Rolfs, Arndt (2009) Computer Science Meets Cell Biology - GRK dIEM oSiRiS. University of Rostock.
Schäfer, Andreas and John, Mathias (2009) Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Sstems. In: APCCM '09 Proceedings of the Sixth Asia-Pacific Conference on Conceptual Modeling, January 01, Wellington, New Zealand. Proceedings,, pp. 39-48.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim (2009) Dynamic Compartments in the Imperative π-Calculus. In: CMSB 2009: 7th International Conference on Computational Methods in Systems Biology, August 31 - September 1, Bologna, Italy. Proceedings,, pp. 235-250.
Mazemondet, Orianne and John, Mathias and Maus, Carsten and Uhrmacher, Adelinde M. and Rolfs, Arndt (2009) Integrating Diverse Reaction Types into Stochastic Models - A Signaling Pathway Case Study in the Imperative π-Calculus. In: Winter Simulation Conference, WSC 2009, December 13-16, Austin, TX, USA. Proceedings,, pp. 932-943.
John, Mathias and Schulz, Hans-Jörg and Schumann, Heidrun and Uhrmacher, Adelinde M. and Unger, Andrea (2009) Interactive Poster: Exploring Time-Varying Hypergraphs. In: InfoVis 2009, October 11-16, Atlantic City, NJ, USA. Poster.
Mazemondet, Orianne and John, Mathias and Maus, Carsten and Uhrmacher, Adelinde M. and Rolfs, Arndt (2009) Modeling the Cell Cycle Dependency of the Wnt/β-catenin Signaling Pathway in the Imperative π-Calculus. In: CMSB 2009: 7th International Conference on Computational Methods in Systems Biology, August 31 - September 1, Bologna, Italy. Poster.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim and Uhrmacher, Adelinde M. (2008) The Attributed Pi Calculus. In: 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, October 12-15, Rostock, Germany. Proceedings,, pp. 83-102.
John, Mathias (2008) Die Modellierung von Raum und Struktur in molekularbiologischen Systemen. In: Modellierung 2008, March 12-14, Berlin, Germany. Proceedings,, pp. 221-224.
Maus, Carsten and John, Mathias and Röhl, Mathias and Uhrmacher, Adelinde M. (2008) Hierarchical Modeling for Computational Biology. In: Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, Advanced Lectures, June 2-7, Bertinoro, Italy. Proceedings,, pp. 81-124.
Schulz, Hans-Jörg and John, Mathias and Unger, Andrea and Schumann, Heidrun (2008) Interactive Poster: Table-based Visualization and Interaction for Bipartite Graphs. In: VisWeek 2008, October 19-24, Columbus, Ohio, USA. Poster.
Uhrmacher, Adelinde M. and Himmelspach, Jan and Jeschke, Matthias and John, Mathias and Leye, Stefan and Maus, Carsten and Röhl, Mathias and Ewald, Roland (2008) One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II. In: 1st International Workshop Formal Methods in Systems Biology, FMSB 2008, June 4-5, Cambridge, UK. Proceedings,, pp. 123-138.
John, Mathias and Ewald, Roland and Uhrmacher, Adelinde M. (2008) A Spatial Extension to the π Calculus. Electr. Notes Theor. Comput. Sci., 194 (3), pp. 133-148.
John, Mathias and Tominski, Christian and Schumann, Heidrun (2008) Visual and analytical extensions for the table lens. In: Conference on Visualization and Data Analysis 2008, January 28-31, San Jose, CA, USA.
Uhrmacher, Adelinde M. and Ewald, Roland and John, Mathias and Maus, Carsten and Jeschke, Matthias and Biermann, Susanne (2007) Combining micro and macro-modeling in DEVS for computational biology. In: Proceedings of the Winter Simulation Conference, WSC 2007, Washington, DC, USA, December 9-12, 2007. Proceedings,, pp. 871-880.
Unger, Andrea and Biermann, Susanne and John, Mathias and Uhrmacher, Adelinde M. and Schumann, Heidrun (2007) Visual support for modeling and simulation of cell biological systems. In: Proceedings of the Winter Simulation Conference, WSC 2007, Washington, DC, USA, December 9-12, 2007. Proceedings,, p. 2378.
