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| Buur LM, Declercq A, Strobl M, et al. (2024) MSRescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0. Journal of Proteome Research |
| Declercq A, Bouwmeester R, Chiva C, et al. (2023) Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Research |
| Boone M, Ramasamy P, Zuallaert J, et al. (2023) Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 14: 1072 |
| Neely BA, Dorfer V, Martens L, et al. (2023) Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research |
| Gabriels R, Declercq A, Bouwmeester R, et al. (2022) psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results. Journal of Proteome Research |
| Declercq A, Bouwmeester R, Hirschler A, et al. (2022) MSRescore: Data-driven rescoring dramatically boosts immunopeptide identification rates. Molecular & Cellular Proteomics : McP. 100266 |
| Delhaye L, De Bruycker E, Volders PJ, et al. (2022) Orthogonal proteomics methods to unravel the HOTAIR interactome. Scientific Reports. 12: 1513 |
| Boone M, Ramasamy P, Zuallaert J, et al. (2021) Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 12: 6414 |
| Bouwmeester R, Gabriels R, Hulstaert N, et al. (2021) DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Nature Methods. 18: 1363-1369 |
| Van Puyvelde B, Van Uytfanghe K, Tytgat O, et al. (2021) Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. Jacs Au. 1: 750-765 |