Combining micro and macro-modeling in DEVS for computational biology. - Adelinde M. Uhrmacher; Roland Ewald; Mathias John; Carsten Maus; Matthias Jeschke; Susanne Biermann (WSC, 2007)

Visual support for modeling and simulation of cell biological systems. - Andrea Unger; Susanne Biermann; Mathias John; Adelinde M. Uhrmacher; Heidrun Schumann (WSC, 2007)

A Spatial Extension to the pi Calculus. - Mathias John; Roland Ewald; Adelinde M. Uhrmacher (FBTC@CONCUR, 2007)

The Attributed Pi Calculus. - Mathias John; Cédric Lhoussaine; Joachim Niehren; Adelinde M. Uhrmacher (CMSB, 2008)

One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II. - Adelinde M. Uhrmacher; Jan Himmelspach; Matthias Jeschke; Mathias John; Stefan Leye; Carsten Maus; Mathias Röhl; Roland Ewald (FMSB, 2008)

Die Modellierung von Raum und Struktur in molekularbiologischen Systemen. - Mathias John (Modellierung, 2008)

Hierarchical Modeling for Computational Biology. - Carsten Maus; Mathias John; Mathias Röhl; Adelinde M. Uhrmacher (SFM, 2008)

Visual Analysis of Bipartite Biological Networks. - Hans-Jörg Schulz; Mathias John; Andrea Unger; Heidrun Schumann (VCBM, 2008)

Visual and analytical extensions for the table lens. - Mathias John; Christian Tominski; Heidrun Schumann (Visualization and Data Analysis, 2008)

Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Systems. - Andreas Schäfer 001; Mathias John (APCCM, 2009)

Dynamic Compartments in the Imperative pi-Calculus. - Mathias John; Cédric Lhoussaine; Joachim Niehren (CMSB, 2009)

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 (WSC, 2009)

A flexible architecture for performance experiments with the pi-Calculus and its extensions. - Stefan Leye; Mathias John; Adelinde M. Uhrmacher (SimuTools, 2010)

The Attributed Pi-Calculus with Priorities. - Mathias John; Cédric Lhoussaine; Joachim Niehren; Adelinde M. Uhrmacher (Trans. Comp. Sys. Biology, 2010)

Reaction constraints for the pi-calculus: a language for the stochastic and spatial modeling of cell-biological processes. - Mathias John (Logos-Verlag, 2010)

Biochemical Reaction Rules with Constraints. - Mathias John; Cédric Lhoussaine; Joachim Niehren; Cristian Versari (ESOP, 2011)

Knockout Prediction for Reaction Networks with Partial Kinetic Information. - Mathias John; Mirabelle Nebut; Joachim Niehren (VMCAI, 2013)

Constructing and visualizing chemical reaction networks from pi-calculus models. - Mathias John; Hans-Jörg Schulz; Heidrun Schumann; Adelinde M. Uhrmacher; Andrea Unger (Formal Aspects Comput., 2013)

Qualitative Reasoning for Reaction Networks with Partial Kinetic Information. - Joachim Niehren; Mathias John; Cristian Versari; François Coutte; Philippe Jacques (CMSB, 2015)

Predicting changes of reaction networks with partial kinetic information. - Joachim Niehren; Cristian Versari; Mathias John; François Coutte; Philippe Jacques (Biosyst., 2016)