Publications
2026
- Organizing the interface—Plasma membrane architecture and receptor dynamics in virus-cell interactionsJan Schlegel, Christian SiebenFEBS Lettersdoi: https://doi.org/10.1002/1873-3468.70347
- The Escherichia coli PeptideAtlas Build: Characterizing the Observed Escherichia coli Pan-Proteome and Its Post-Translational ModificationsCaroline Jachmann; Zhi Sun; Kevin Velghe; Florence Arsène-Ploetze; Aurélie Hirschler; Jasper Zuallaert; Christine Carapito; Robbin Bouwmeester; Kay Nieselt; Eric W. Deutsch; Lennart Martens; Ralf Gabriels; Tim Van Den BosscheJournal of proteome researchdoi: https://doi.org/10.1021/acs.jproteome.5c00902
- Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setupsRobbin Bouwmeester, Alireza Nameni, Arthur Declercq, Robbe Devreese, Kevin Velghe, Vladimir Gorshkov, Pelayo A. Penanes, Frank Kjeldsen, Magali Rompais, Christine Carapito, Ralf Gabriels & Lennart MartensNature Communicationsdoi: https://doi.org/10.1038/s41467-026-68981-5
- omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomicsAlexandre Segers, Cristian Castiglione, Christophe Vanderaa, Lennart Martens, Davide Risso & Lieven ClementNature Communicationsdoi: https://doi.org/10.1038/s41467-026-73402-8
- iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen ModificationsAlireza Nameni; Arthur Declercq; Ralf Gabriels; Robbe Devreese; Sven Degroeve; Amélie De Maesschalck; Maarten Dhaenens; Cristina Chiva; Eduard Sabidó; Lennart Martens; Robbin BouwmeesterAnalytical Chemistrydoi: https://doi.org/10.1021/acs.analchem.5c08017
- MLMarker: a machine learning framework for tissue inference and biomarker discoveryTine Claeys, Sam van Puyenbroeck, Kris Gevaert & Lennart MartensGenome Biologydoi: https://doi.org/10.1186/s13059-026-04125-8
- Instrument–Software Synergy in Proteomics: Systematic Evaluation across Mass Spectrometry Platforms, Search Engines, and Rescoring MethodsSander Heyndrickx; Robbin Bouwmeester; Arthur Declercq; Robbe Devreese; Magnus Palmblad; Wout Bittremieux; Tess AV Afanasyeva; Joel Lapin; Arzu Tugce Guler; Pierre-Olivier Schmit; Christine Carapito; Lennart Martens; Ralf GabrielsJournal of proteome researchdoi: https://doi.org/10.1021/acs.jproteome.6c00295
2025
- Single influenza A viruses induce nanoscale cellular reprogramming at the virus-cell interfaceLukas Broich, Hannah Wullenkord, Maria Kaukab Osman, Yang Fu, Mathias Müsken, Peter Reuther, Mark Brönstrup & Christian SiebenNature Communicationsdoi: https://doi.org/10.1038/s41467-025-58935-8
- TIMS²Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS²RescoreArthur Declercq; Robbe Devreese; Jonas Scheid; Caroline Jachmann; Tim Van Den Bossche; Annica Preikschat; David Gomez-Zepeda; Jeewan Babu Rijal; Aurélie Hirschler; Jonathan R Krieger; Tharan Srikumar; George Rosenberger; Claudia Martelli; Dennis Trede; Christine Carapito; Stefan Tenzer; Juliane S Walz; Sven Degroeve; Robbin Bouwmeester; Lennart Martens; Ralf GabrielsJournal of proteome researchdoi: https://doi.org/10.1021/acs.jproteome.4c00609
- MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using ProteogenomicsJulian Pipart; Tanja Holstein; Lennart Martens; Thilo MuthJournal of proteome researchdoi: https://doi.org/10.1021/acs.jproteome.4c00901
- msqrob₂TMT: Robust Linear Mixed Models for Inferring Differential Abundant Proteins in Labeled Experiments With Arbitrarily Complex DesignStijn Vandenbulcke; Christophe Vanderaa; Oliver Crook; Lennart Martens; Lieven ClementMolecular & Cellular Proteomicsdoi: https://doi.org/10.1016/j.mcpro.2025.101002
- Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2DeepRobbe Devreese; Alireza Nameni; Arthur Declercq; Emmy Terryn; Ralf Gabriels; Francis Impens; Kris Gevaert; Lennart Martens; Robbin BouwmeesterAnalytical Chemistrydoi: https://doi.org/10.1021/acs.analchem.5c01142
