| 2013 | VMCAI | Knockout Prediction for Reaction Networks with Partial Kinetic Information. | Mathias John, Mirabelle Nebut, Joachim Niehren |
| 2011 | ESOP | Biochemical Reaction Rules with Constraints. | Mathias John, Cdric Lhoussaine, Joachim Niehren, Cristian Versari |
| 2009 | APCCM | Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems. | Andreas Schfer, Mathias John |
| 2009 | WSC | Integrating Diverse Reaction Types into Stochastic Models - A Signaling Pathway Case Study in the Imperative pi-Calculus. | Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M. Uhrmacher, Arndt Rolfs |
| 2008 | VDA | Visual and analytical extensions for the table lens. | Mathias John, Christian Tominski, Heidrun Schumann |
| 2007 | WSC | Combining micro and macro-modeling in DEVS for computational biology. | Adelinde M. Uhrmacher, Roland Ewald, Mathias John, Carsten Maus, Matthias Jeschke, Susanne Biermann |
| 2007 | WSC | Visual support for modeling and simulation of cell biological systems. | Andrea Unger, Susanne Biermann, Mathias John, Adelinde M. Uhrmacher, Heidrun Schumann |