| DeepLC can predict retention times for peptides that carry as-yet unseen modifications R Bouwmeester, R Gabriels, N Hulstaert, L Martens, S Degroeve Nature Methods 18, 1363-1369, 2021 | 140 | 2021 |
| Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction R Bouwmeester, L Martens, S Degroeve Analytical chemistry 91 (5), 3694-3703, 2019 | 77 | 2019 |
| Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions AS C. Silva, R Bouwmeester, L Martens, S Degroeve Bioinformatics 35 (24), 5243-5248, 2019 | 59 | 2019 |
| MS2Rescore: data-driven rescoring dramatically boosts immunopeptide identification rates A Declercq, R Bouwmeester, A Hirschler, C Carapito, S Degroeve, ... Molecular & Cellular Proteomics 21 (8), 2022 | 44 | 2022 |
| The age of data‐driven proteomics: how machine learning enables novel workflows R Bouwmeester, R Gabriels, T Van Den Bossche, L Martens, S Degroeve Proteomics 20 (21-22), 1900351, 2020 | 43 | 2020 |
| A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass … LC Nye, JP Williams, NC Munjoma, MPM Letertre, M Coen, ... Journal of chromatography A 1602, 386-396, 2019 | 43 | 2019 |
| Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times R Bouwmeester, L Martens, S Degroeve Analytical chemistry 92 (9), 6571-6578, 2020 | 32 | 2020 |
| Cov-MS: a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients B Van Puyvelde, K Van Uytfanghe, O Tytgat, L Van Oudenhove, ... Jacs Au 1 (6), 750-765, 2021 | 30 | 2021 |
| ionbot: a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification S Degroeve, R Gabriels, K Velghe, R Bouwmeester, N Tichshenko, ... BioRxiv, 2021.07. 02.450686, 2021 | 24 | 2021 |
| Toward an integrated machine learning model of a proteomics experiment BA Neely, V Dorfer, L Martens, I Bludau, R Bouwmeester, S Degroeve, ... Journal of proteome research 22 (3), 681-696, 2023 | 19 | 2023 |
| Graph convolutional networks for improved prediction and interpretability of chromatographic retention data A Kensert, R Bouwmeester, K Efthymiadis, P Van Broeck, G Desmet, ... Analytical Chemistry 93 (47), 15633-15641, 2021 | 18 | 2021 |
| Personalized proteome: Comparing proteogenomics and open variant search approaches for single amino acid variant detection R Salz, R Bouwmeester, R Gabriels, S Degroeve, L Martens, PJ Volders, ... Journal of Proteome Research 20 (6), 3353-3364, 2021 | 15 | 2021 |
| ProteomicsML: an online platform for community-curated data sets and tutorials for machine learning in proteomics TG Rehfeldt, R Gabriels, R Bouwmeester, S Gessulat, BA Neely, ... Journal of proteome research 22 (2), 632-636, 2023 | 9 | 2023 |
| How sticky are our proteins? Quantifying hydrophobicity of the human proteome JHM van Gils, D Gogishvili, J van Eck, R Bouwmeester, E van Dijk, ... Bioinformatics advances 2 (1), vbac002, 2022 | 9 | 2022 |
| Updated MS²PIP web server supports cutting-edge proteomics applications A Declercq, R Bouwmeester, C Chiva, E Sabidó, A Hirschler, C Carapito, ... Nucleic Acids Research 51 (W1), W338-W342, 2023 | 8 | 2023 |
| Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins T Claeys, M Menu, R Bouwmeester, K Gevaert, L Martens Journal of Proteome Research 22 (4), 1181-1192, 2023 | 8 | 2023 |
| Predicting ion mobility collision cross sections by combining conventional and data driven modelling R Bouwmeester, L Martens, S Degroeve, K Richardson, JPC Vissers ASMS Proc, 366, 2019 | 6 | 2019 |
| FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data M Koutrouli, K Nastou, P Piera Líndez, R Bouwmeester, S Rasmussen, ... Bioinformatics 40 (2), btae010, 2024 | 5 | 2024 |
| Sensitive and specific spectral library searching with CompOmics spectral library searching tool and percolator GA Shiferaw, R Gabriels, R Bouwmeester, T Van Den Bossche, ... Journal of Proteome Research 21 (5), 1365-1370, 2022 | 5 | 2022 |
| psm_utils: A high-level python API for parsing and handling peptide-spectrum matches and proteomics search results R Gabriels, A Declercq, R Bouwmeester, S Degroeve, L Martens Journal of Proteome Research 22 (2), 557-560, 2022 | 4 | 2022 |
Lennart MartensSenior Full Professor of Systems Biology, Ghent University and VIB, Ghent, BelgiumVerified email at UGent.be
