Interpreting peptide mass spectra by VEMS. - Rune Matthiesen; M. Lundsgaard; Karen G. Welinder; G. Bauw (Bioinform., 2003)

Integration of gel-based proteome data with pProRep. - Kris Laukens; Rune Matthiesen; Filip Lemière; Eddy Esmans; Harry Van Onckelen; Ole Nørregaard Jensen; Erwin Witters (Bioinform., 2006)

Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. - Michael Hackenberg; Rune Matthiesen (Bioinform., 2008)

ContDist: a tool for the analysis of quantitative gene and promoter properties. - Michael Hackenberg; Gorka Lasso; Rune Matthiesen (BMC Bioinform., 2009)

PAnalyzer: A software tool for protein inference in shotgun proteomics. - Gorka Prieto; Kerman Aloria; Nerea Osinalde; Asier Fullaondo; Jesus M. Arizmendi; Rune Matthiesen (BMC Bioinform., 2012)

CHAPTER 6. Identification and Localization of Post-Translational Modifications by High-Resolution Mass Spectrometry. - Rune Matthiesen; Ana Sofia Carvalho (Proteome Informatics, 2016)