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Nucleic Acids Research|February 13, 2019
DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patternsJim Clauwaert, Gerben Menschaert, Willem WaegemanBriefings in Bioinformatics|April 9, 2021
Explainability in transformer models for functional genomicsJim Clauwaert, Gerben Menschaert, Willem WaegemanAnnual Review of Cell and Developmental Biology|August 1, 2017
In Search of Lost Small PeptidesSerge Plaza, Gerben Menschaert, François PayreExperimental Cell Research|March 6, 2020
The hunt for sORFs: A multidisciplinary strategyMarlies K R Peeters, Gerben MenschaertElife|November 14, 2024
An antimicrobial drug recommender system using MALDI-TOF MS and dual-branch neural networksGaetan De Waele, Gerben Menschaert, Willem WaegemanNAR Genomics and Bioinformatics|March 7, 2023
TIS Transformer: remapping the human proteome using deep learningJim Clauwaert, Zahra McVey, Ramneek Gupta, et al.Bioinformatics (Oxford, England)|October 31, 2021
CpG Transformer for imputation of single-cell methylomesGaetan De Waele, Jim Clauwaert, Gerben Menschaert, et al.Computers in Biology and Medicine|January 23, 2025
Pre-trained Maldi Transformers improve MALDI-TOF MS-based predictionGaetan De Waele, Gerben Menschaert, Peter Vandamme, et al.Molecular & Cellular Proteomics : MCP|March 14, 2014
N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and menPetra Van Damme, Daria Gawron, Wim Van Criekinge, et al.Journal of Proteome Research|March 14, 2012
Spectral clustering in peptidomics studies allows homology searching and modification profiling: HomClus, a versatile toolGerben Menschaert, Eisuke Hayakawa, Liliane Schoofs, et al.Pageof 7