MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

Reproducible MS/MS library cleaning pipeline in matchms. - Niek F. de Jonge; Helge Hecht; Michael Strobel 002; Mingxun Wang 001; Justin J. J. van der Hooft; Florian Huber (J. Cheminformatics, 2024)

To Bin or not to Bin: Alternative Representations of Mass Spectra. - Niek F. de Jonge; Justin J. J. van der Hooft; Daniel Probst (CoRR, 2025)