Towards Whole Cell "in Silico" Models for Cellular Systems: Model Set-up and Model Validation. - Andreas Kremling; Katja Bettenbrock; Sophia Fischer; Martin Ginkel; Thomas Sauter; Ernst Dieter Gilles (POSTA, 2003)

Modular Modeling of Cellular Systems with ProMoT/Diva. - Martin Ginkel; Andreas Kremling; Torsten Nutsch; R. Rehner; Ernst Dieter Gilles (Bioinform., 2003)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. - Steffen Klamt; Jörg Stelling; Martin Ginkel; Ernst Dieter Gilles (Bioinform., 2003)

A model library for membrane reactors implemented in the process modelling tool PROMoT. - Michael Mangold; Martin Ginkel; Ernst Dieter Gilles (Comput. Chem. Eng., 2004)

Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems). - Andreas Kremling; Steffen Klamt; Martin Ginkel; Ernst Dieter Gilles (it Inf. Technol., 2004)

Visual setup of logical models of signaling and regulatory networks with ProMoT. - Julio Saez-Rodriguez; Sebastian Mirschel; Rebecca Hemenway; Steffen Klamt; Ernst Dieter Gilles; Martin Ginkel (BMC Bioinform., 2006)

Numerical analysis of higher order singularities in chemical process models. - Mykhaylo Krasnyk; Martin Ginkel; Michael Mangold; Achim Kienle (Comput. Chem. Eng., 2007)

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules. - Julio Saez-Rodriguez; Stefan Gayer; Martin Ginkel; Ernst Dieter Gilles (ECCB, 2008)

PROMOT: modular modeling for systems biology. - Sebastian Mirschel; Katrin Steinmetz; Michael Rempel; Martin Ginkel; Ernst Dieter Gilles (Bioinform., 2009)

SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. - Lucian Paul Smith; Michael Hucka; Stefan Hoops; Andrew Finney; Martin Ginkel; Chris J. Myers; Ion I. Moraru; Wolfram Liebermeister (J. Integr. Bioinform., 2015)