PubMeth: a cancer methylation database combining text-mining and expert annotation. - Maté Ongenaert; Leander Van Neste; Tim De Meyer; Gerben Menschaert; Sofie Bekaert; Wim Van Criekinge (Nucleic Acids Res., 2008)

PIUS: peptide identification by unbiased search. - Eduardo P. Costa; Gerben Menschaert; Walter Luyten; Kurt De Grave; Jan Ramon (Bioinform., 2013)

An update on LNCipedia: a database for annotated human lncRNA sequences. - Pieter-Jan Volders; Kenneth Verheggen; Gerben Menschaert; Klaas Vandepoele; Lennart Martens; Jo Vandesompele; Pieter Mestdagh (Nucleic Acids Res., 2015)

sORFs.org: a repository of small ORFs identified by ribosome profiling. - Volodimir Olexiouk; Jeroen Crappé; Steven Verbruggen; Kenneth Verheggen; Lennart Martens; Gerben Menschaert (Nucleic Acids Res., 2016)

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. - Volodimir Olexiouk; Wim Van Criekinge; Gerben Menschaert (Nucleic Acids Res., 2018)

mQC: A post-mapping data exploration tool for ribosome profiling. - Steven Verbruggen; Gerben Menschaert (Comput. Methods Programs Biomed., 2019)

Explainability in transformer models for functional genomics. - Jim Clauwaert; Gerben Menschaert; Willem Waegeman (Briefings Bioinform., 2021)

CpG Transformer for imputation of single-cell methylomes. - Gaetan De Waele; Jim Clauwaert; Gerben Menschaert; Willem Waegeman (Bioinform., 2022)

Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction. - Gaetan De Waele; Gerben Menschaert; Peter Vandamme; Willem Waegeman (Comput. Biol. Medicine, 2025)