compomics-utilities: an open-source Java library for computational proteomics. - Harald Barsnes; Marc Vaudel; Niklaas Colaert; Kenny Helsens; Albert Sickmann; Frode S. Berven; Lennart Martens (BMC Bioinform., 2011)

iTRAQ Data Interpretation. - Marc Vaudel; Julia Maria Burkhart; René Peiman Zahedi; Lennart Martens; Albert Sickmann (Quantitative Methods in Proteomics, 2012)

Chapter 8. MS2-Based Quantitation. - Marc Vaudel (Proteome Informatics, 2016)

PeptideMapper: efficient and versatile amino acid sequence and tag mapping. - Dominik Kopczynski; Harald Barsnes; Pål R. Njølstad; Albert Sickmann; Marc Vaudel; Robert Ahrends (Bioinform., 2017)

BioContainers: an open-source and community-driven framework for software standardization. - Felipe da Veiga Leprevost; Björn A. Grüning; Saulo Aflitos; Hannes L. Röst; Julian Uszkoreit; Harald Barsnes; Marc Vaudel; Pablo A. Moreno; Laurent Gatto; Jonas Weber; Mingze Bai; Rafael C. Jiménez; et al. (Bioinform., 2017)

PDV: an integrative proteomics data viewer. - Kai Li; Marc Vaudel; Bing Zhang; Yan Ren; Bo Wen (Bioinform., 2019)

Extending protein interaction networks using proteoforms and small molecules. - Luis Francisco Hernández Sánchez; Bram Burger; Rodrigo Alexander Castro Campos; Stefan Johansson; Pål R. Njølstad; Harald Barsnes; Marc Vaudel (Bioinform., 2023)

The MoBa Pregnancy and Child Development Dashboard: A Design Study. - Roxanne Ziman; Beatrice Budich; Marc Vaudel; Laura A. Garrison (VCBM, 2024)

Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline. - Haydee Artaza; Ksenia Lavrichenko; Anette S. B. Wolff; Ellen C. Røyrvik; Marc Vaudel; Stefan Johansson (BMC Bioinform., 2024)

ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets. - Jakub Vasícek; Dafni Skiadopoulou; Ksenia Kuznetsova; Lukas Käll; Marc Vaudel; Stefan Bruckner (CoRR, 2025)