Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance. - Mingxun Wang 001; Nuno Bandeira (RECOMB, 2013)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

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)

P-Massive: A Real-Time Search Engine for a Multi-Terabyte Mass Spectrometry Database. - Narangerelt Batsoyol; Benjamin S. Pullman; Mingxun Wang 001; Nuno Bandeira; Steven Swanson (SC, 2022)

TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats. - Gordon T. Luu; Michael A. Freitas; Itzel Lizama-Chamu; Catherine S. McCaughey; Laura M. Sanchez; Mingxun Wang 001 (Bioinform., 2022)

DeepSAT: Learning Molecular Structures from Nuclear Magnetic Resonance Data. - Hyun Woo Kim; Chen Zhang 022; Raphael Reher; Mingxun Wang 001; Kelsey L. Alexander; Louis-Félix Nothias; Yoo Kyong Han; Hyeji Shin; Ki Yong Lee; Kyu Hyeong Lee; Myeong Ji Kim; Pieter C. Dorrestein; et al. (J. Cheminformatics, 2023)

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)

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction. - Michael Strobel 002; Alberto Gil-de-la-Fuente; Mohammad Reza Shahneh; Yasin El Abiead; Roman Bushuiev; Anton Bushuiev; Tomás Pluskal; Mingxun Wang 001 (BMC Bioinform., 2025)