Publications of Mathias John

accepted

• Orianne Mazemondet, Mathias John, Stefan Leye, Arndt Rolfs and Adelinde Uhrmacher (accepted): Elucidating the sources of β-catenin dynamics in human neural progenitor cells - PLOS-One.

2011

• Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde Uhrmacher and Andrea Unger (2011): Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models - Formal Aspects of Computing, Online First.

2010 (to appear)

• Mathias John (2010 (to appear)): Reaction Constraints for the Pi-Calculus - A language for the stochastic and spatial modeling of cell-biological processes. - PhD thesis, Universität Rostock - PhD thesis, University of Rostock.

2010

• Eik Hoffmann, Sabrina Marion, Bibhuti Mishra, Mathias John, Ramona Kratzke, Syed Ahmad, Daniela Holzer, Paras Anand, Dieter Weiss, Gareth Griffiths and Sergei Kuznetsov (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):693-704.
• Carsten Maus, Mathias John, Stefan Rybacki and Adelinde M. Uhrmacher (2010): Towards Rule-Based Multi-Level Modeling - Poster, Edinburgh, UK, 11th International Conference on Systems Biology (ICSB).
• Stefan Leye, Mathias John and Adelinde M. Uhrmacher (2010): A Flexible Architecture for Performance Experiments with the pi-Calculus and its Extensions - In: 3rd International ICST Conference on Simulation Tools and Techniques, ICST, Malaga, Spain, ICST/IEEE.
• Mathias John, Cédric Lhoussaine, Joachim Niehren and Adelinde Uhrmacher (2010): The Attributed Pi-Calculus with Priorities - Transactions on Computational Systems Biology XII, 5945/2010:13-76.

2009

• Adelinde M. Uhrmacher, Mathias John, Orianne Mazemondet, Andrea Unger, Tareck Rharass, Benjamin M. Bader and Arndt Rolfs (2009): Computer Science Meets Cell Biology - GRK dIEM oSiRiS - Universität Rostock, Rostocker Informatik Berichte(32:77-90).
• Mathias John, Cédric Lhoussaine and Joachim Niehren (2009): Dynamic Compartments in the Imperative Pi-Calculus - In: CMSB 2009 - Computational Methods in Systems Biology, ed. by Pierpaolo Degano and Roberto Gorrieri, vol. 5688, pp. 235-250, Springer Verlag. LNCS.
• Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M. Uhrmacher and Arndt Rolfs (2009): Modeling the Cell Cycle Dependency of the Wnt/β-catenin Signaling Pathway in the Imperative π-Calculus - Poster, Bologna, Italy, Computational Methods in Systems Biology (CMSB).
• Andreas Schäfer and Mathias John (2009): Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems - In: APCCM, ed. by Markus Kirchberg and Sebastian Link, vol. 96, pp. 39-48, Australian Computer Society. CPRIT.
• Mathias John, Hans-Jörg Schulz, Heidrun Schumann, Adelinde M. Uhrmacher and Andrea Unger (2009): Interactive Poster: Exploring Time-Varying Hyper Graphs - Poster, Atlantic City, NJ, USA.
• Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M. Uhrmacher and Arndt Rolfs (2009): Integrating Diverse Reaction Types Into Stochastic Models - A Signaling Pathway Case Study in the Imperative Pi-Calculus - In: Proceedings of the Winter Simulation Conference, Austin, TX, USA, ed. by M. D. Rossetti, R. R. Hill, B. Johansson, A. Dunkin, R. G. Ingalls, pp. 932-943, IEEE Computer Society.

2008

• Hans-Jörg Schulz, Mathias John, Andrea Unger and Heidrun Schumann (2008): Interactive Poster: Table-based Visualization and Interaction for Bipartite Graphs - Poster, Columbus, USA, IEEE Information Visualization.
• Mathias John (2008): Die Modellierung von Raum und Struktur in molekularbiologischen Systemen - In: Modellierung, pp. 221-224.
• Carsten Maus, Mathias John, Mathias Röhl and Adelinde M Uhrmacher (2008): Hierarchical Modeling for Computational Biology - In: SFM 2008, Formal Methods for Computational Systems Biology, ed. by Marco Bernardo, Pierpaolo Degano and Gianluigi Zavattaro, pp. 81-124, Springer, Berlin Heidelberg.
• Mathias John, Christian Tominski and Heidrun Schumann (2008): Visual and Analytical Extensions for the Table Lens - In: Visualization and Data Analysis 2008, ed. by Börner, Katy; Gröhn, Matti T.; Park, Jinah; Roberts, Jonathan C., vol. 6809.
• Mathias John, Roland Ewald and Adelinde M. Uhrmacher (2008): A Spatial Extension to the Pi Calculus - In: Electronic Notes in Theoretical Computer Science, vol. 194(3), pp. 133-148.
• Adelinde M. Uhrmacher, Jan Himmelspach, Matthias Jeschke, Mathias John, Stefan Leye, Carsten Maus, Mathias Röhl and Roland Ewald (2008): One Modeling Formalism & Simulator is not enough! - A Perspective for Computational Biology Based on JAMES II - In: Proceedings of the 1st FMSB Workshop, ed. by Jasmin Fisher, pp. 123-138, Cambridge, UK, Springer. Lecture Notes of Computer Science, LNBI subseries.
• Hans-Jörg Schulz, Mathias John, Andrea Unger and Heidrun Schumann (2008): Visual Analysis of Bipartite Biological Networks - In: Proceedings of the Eurographics Workshop on Visual Computing for Biomedicine 2008, Delft, Netherlands, ed. by Charl Botha, Gordon Kindlmann, Wiro Niessen and Bernhard Preim, pp. 135-142, The Eurographics Association.
• Mathias John, Cédric Lhoussaine, Joachim Niehren and Adelinde Uhrmacher (2008): The Attributed Pi Calculus - In: Computational Methods in Systems Biology, International Conference CMSB 2008, ed. by Monika Heiner, Adelinde M. Uhrmacher, vol. 5307, pp. 83-102, Springer Verlag. LNBI.

2007

• Andrea Unger, Susanne Biermann, Mathias John, Adelinde Uhrmacher and Heidrun Schumann (2007): Visual Support for Modeling and Simulation of Cell Biological Systems - Poster, Washington, D.C., USA, Winter Simulation Conference.
• Dagmar Köhn and Mathias John (2007): The Pi Markup Language - Toward Pi-Model Exchange and Reuse - Poster, Long Beach, California (US), Online Proceedings of the Eighth International Conference on Systems Biology.
• Carsten Maus, Mathias John and Adelinde M. Uhrmacher (2007): A Multi-Level and Multi-Formalism Approach for Model Composition in Systems Biology - Poster, Edinburgh (GB), Computational Methods in Systems Biology (CMSB).
• Mathias John, Dagmar Köhn and Robert Waltemath (2007): The Pi Markup Language - A First Approach to Make Pi Exchangable - Poster, Edinburgh, CMSB.
• Mathias John (2007): Spatial Modeling of Molecular Biological Systems - Miscellaneous publication, Dagstuhl.
• Adelinde M Uhrmacher, Roland Ewald, Mathias John, Carsten Maus, Matthias Jeschke and Susanne Biermann (2007): Combining Micro and Macro-Modeling in DEVS for Computational Biology - In: WSC '07: Proceedings of the 39th conference on Winter simulation, pp. 871-880, IEEE Press.
• Stefan Leye, Matthias Jeschke and Mathias John (2007): The SpacePi simulator - Poster, Edinburgh, Computational Methods in systems Biology.

2006

• Mathias John, Christian Tominski and Heidrun Schumann (2006): Interactive Poster: Two-Tone Pseudo Coloring for Multiple Variables - Poster, Baltimore, USA, IEEE Symposium on Information Visualization (InfoVis '06).

Contained Smart Bibliography Lists:

Co-authors by Jan Himmelspach — last modified 2010-08-05 08:16