combAlign: A protein sequence comparison algorithm considering recombinations. - Katja Wegner; Stephan Jansen; Stefan Wuchty; Ralph Gauges; Ursula Kummer (Silico Biol., 2004)

Simulation of biochemical networks using COPASI: a complex pathway simulator. - Sven Sahle; Ralph Gauges; Jürgen Pahle; Natalia Simus; Ursula Kummer; Stefan Hoops; Christine Lee; Mudita Singhal; Liang Xu; Pedro Mendes 001 (WSC, 2006)

A model diagram layout extension for SBML. - Ralph Gauges; Ursula Rost; Sven Sahle; Katja Wegner (Bioinform., 2006)

COPASI - a COmplex PAthway SImulator. - Stefan Hoops; Sven Sahle; Ralph Gauges; Christine Lee; Jürgen Pahle; Natalia Simus; Mudita Singhal; Liang Xu; Pedro Mendes 001; Ursula Kummer (Bioinform., 2006)

SYCAMORE - a systems biology computational analysis and modeling research environment. - Andreas Weidemann; Stefan Richter 002; Matthias Stein; Sven Sahle; Ralph Gauges; Razif R. Gabdoulline; Irina Surovtsova; Nils Semmelrock; Bruno Besson; Isabel Rojas; Rebecca C. Wade; Ursula Kummer (Bioinform., 2008)

Standards and Tools for Model Exchange and Analysis in Systems Biology - Ralph Gauges (2011)

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core. - Ralph Gauges; Ursula Rost; Sven Sahle; Katja Wengler; Frank Thomas Bergmann (J. Integr. Bioinform., 2015)

SBML Level 3 package: Render, Version 1, Release 1. - Frank T. Bergmann; Sarah M. Keating; Ralph Gauges; Sven Sahle; Katja Wengler (J. Integr. Bioinform., 2018)