Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. - Raimo Franke; Melanie Müller; Nicole Wundrack; Ernst Dieter Gilles; Steffen Klamt; Thilo Kähne; Michael Naumann (BMC Syst. Biol., 2008)

From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study. - Raimo Franke; Fabian J. Theis; Steffen Klamt (J. Integr. Bioinform., 2010)

Alignment of time-resolved data from high throughput experiments. - Nada Abidi; Raimo Franke; Peter Findeisen; Frank Klawonn (J. Bioinform. Comput. Biol., 2016)

CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics. - Tobias Depke; Raimo Franke; Mark Brönstrup (Bioinform., 2019)