Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry. - Joe Wandy; Yunfeng Zhu; Justin J. J. van der Hooft; Rónán Daly; Michael P. Barrett; Simon Rogers (Bioinform., 2018)

Propagating annotations of molecular networks using in silico fragmentation. - Ricardo Roberto da Silva; Mingxun Wang 001; Louis-Félix Nothias; Justin J. J. van der Hooft; Andrés Mauricio Caraballo-Rodríguez; Evan Fox; Marcy J. Balunas; Jonathan L. Klassen; Norberto Peporine Lopes; Pieter C. Dorrestein (PLoS Comput. Biol., 2018)

matchms - processing and similarity evaluation of mass spectrometry data. - Florian Huber; Stefan Verhoeven; Christiaan Meijer; Hanno Spreeuw; Efraín Castilla; Cunliang Geng; Justin J. J. van der Hooft; Simon Rogers; Adam Belloum; Faruk Diblen; Jurriaan H. Spaaks (J. Open Source Softw., 2020)

MIBiG 2.0: a repository for biosynthetic gene clusters of known function. - Satria A. Kautsar; Kai Blin; Simon Shaw; Jorge C. Navarro-Muñoz; Barbara R. Terlouw; Justin J. J. van der Hooft; Jeffrey A. van Santen; Vittorio Tracanna; Hernando G. Suarez Duran; Victòria Pascal Andreu; Nelly Sélem-Mojica; Mohammad Alanjary; et al. (Nucleic Acids Res., 2020)

MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. - Florian Huber; Sven van der Burg; Justin J. J. van der Hooft; Lars Ridder (J. Cheminformatics, 2021)

Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. - Fidele Ntie-Kang; Kiran K. Telukunta; Serge A. T. Fobofou; Victor Chukwudi Osamor; Samuel A. Egieyeh; Marilia Valli; Yannick Djoumbou Feunang; Maria Sorokina; Conrad Stork; Neann Mathai; Paul F. Zierep; Ana L. Chávez-Hernández; et al. (J. Cheminformatics, 2021)

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. - Grímur Hjörleifsson Eldjárn; Andrew Ramsay; Justin J. J. van der Hooft; Katherine R. Duncan; Sylvia Soldatou; Juho Rousu; Rónán Daly; Joe Wandy; Simon Rogers (PLoS Comput. Biol., 2021)

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. - Florian Huber; Lars Ridder; Stefan Verhoeven; Jurriaan H. Spaaks; Faruk Diblen; Simon Rogers; Justin J. J. van der Hooft (PLoS Comput. Biol., 2021)

Homologue series detection and management in LC-MS data with homologueDiscoverer. - Kevin Mildau; Justin J. J. van der Hooft; Mira Flasch; Benedikt Warth; Yasin El Abiead; Gunda Koellensperger; Jürgen Zanghellini; Christoph Bueschl (Bioinform., 2022)

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. - Barbara R. Terlouw; Kai Blin; Jorge C. Navarro-Muñoz; Nicole E. Avalon; Marc G. Chevrette; Susan Egbert; Sanghoon Lee; David Meijer; Michael J. Recchia; Zachary L. Reitz; Jeffrey A. van Santen; Nelly Sélem-Mojica; et al. (Nucleic Acids Res., 2023)

iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. - Joris J. R. Louwen; Satria A. Kautsar; Sven van der Burg; Marnix H. Medema; Justin J. J. van der Hooft (PLoS Comput. Biol., 2023)

Deep Learning Models for LC-MS Untargeted Metabolomics Data Analysis. - Francesco Russo 004; Filip Ottosson; Justin J. J. van der Hooft; Madeleine Ernst (From Computational Logic to Computational Biology, 2024)

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)

Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181). - Timothy M. D. Ebbels; Soha Hassoun; Ewy A. Mathé; Justin J. J. van der Hooft; Haley Chatelaine (Dagstuhl Reports, 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)

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer. - David Meijer; Marnix H. Medema; Justin J. J. van der Hooft (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)

Chemical characteristics vectors map the chemical space of natural biomes from untargeted mass spectrometry data. - Pilleriin Peets; Aristeidis Litos; Kai Dührkop; Daniel R. Garza; Justin J. J. van der Hooft; Sebastian Böcker; Bas E. Dutilh (J. Cheminformatics, 2025)

Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids. - Sarah Szwarc; Adriano Rutz; Kyungha Lee; Yassine Mejri; Olivier Bonnet; Hazrina Hazni; Adrien Jagora; Rany B. Mbeng Obame; Jin Kyoung Noh; Elvis Otogo N'Nang; Stephenie C. Alaribe; Khalijah Awang; et al. (J. Cheminformatics, 2025)