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

A new dynamical layout algorithm for complex biochemical reaction networks. - Katja Wegner; Ursula Kummer (BMC Bioinform., 2005)

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

The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks. - Katja Wegner; Johannes F. Knabe; Mark Robinson; Attila Egri-Nagy; Maria J. Schilstra; Chrystopher L. Nehaniv (BMC Syst. Biol., 2007)