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Robbin Bouwmeester - Publications

Affiliations: 
Ghent University, Ghent, Vlaanderen, Belgium 
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20 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Buur LM, Declercq A, Strobl M, Bouwmeester R, Degroeve S, Martens L, Dorfer V, Gabriels R. 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. PMID 38491990 DOI: 10.1021/acs.jproteome.3c00785  0.566
2024 Koutrouli M, Nastou K, Líndez PP, Bouwmeester R, Rasmussen S, Martens L, Jensen LJ. FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics (Oxford, England). PMID 38192003 DOI: 10.1093/bioinformatics/btae010  0.506
2023 Sakarika M, Kerckhof FM, Van Peteghem L, Pereira A, Van Den Bossche T, Bouwmeester R, Gabriels R, Van Haver D, Ulčar B, Martens L, Impens F, Boon N, Ganigué R, Rabaey K. The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microbial Cell Factories. 22: 254. PMID 38072930 DOI: 10.1186/s12934-023-02265-1  0.719
2023 Declercq A, Bouwmeester R, Chiva C, Sabidó E, Hirschler A, Carapito C, Martens L, Degroeve S, Gabriels R. Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Research. PMID 37140039 DOI: 10.1093/nar/gkad335  0.769
2023 Claeys T, Menu M, Bouwmeester R, Gevaert K, Martens L. Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins. Journal of Proteome Research. PMID 36963412 DOI: 10.1021/acs.jproteome.2c00644  0.532
2023 Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 14: 1072. PMID 36828852 DOI: 10.1038/s41467-023-36844-y  0.674
2023 Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, et al. Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research. PMID 36744821 DOI: 10.1021/acs.jproteome.2c00711  0.737
2023 Rehfeldt TG, Gabriels R, Bouwmeester R, Gessulat S, Neely BA, Palmblad M, Perez-Riverol Y, Schmidt T, Vizcaíno JA, Deutsch EW. ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of Proteome Research. PMID 36693629 DOI: 10.1021/acs.jproteome.2c00629  0.347
2022 Gabriels R, Declercq A, Bouwmeester R, Degroeve S, Martens L. psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results. Journal of Proteome Research. PMID 36508242 DOI: 10.1021/acs.jproteome.2c00609  0.737
2022 Declercq A, Bouwmeester R, Hirschler A, Carapito C, Degroeve S, Martens L, Gabriels R. MSRescore: Data-driven rescoring dramatically boosts immunopeptide identification rates. Molecular & Cellular Proteomics : McP. 100266. PMID 35803561 DOI: 10.1016/j.mcpro.2022.100266  0.73
2022 Shiferaw GA, Gabriels R, Bouwmeester R, Van Den Bossche T, Vandermarliere E, Martens L, Volders PJ. Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator. Journal of Proteome Research. 21: 1365-1370. PMID 35446579 DOI: 10.1021/acs.jproteome.2c00075  0.69
2021 Boone M, Ramasamy P, Zuallaert J, Bouwmeester R, Van Moer B, Maddelein D, Turan D, Hulstaert N, Eeckhaut H, Vandermarliere E, Martens L, Degroeve S, De Neve W, Vranken W, Callewaert N. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 12: 6414. PMID 34741024 DOI: 10.1038/s41467-021-26720-y  0.7
2021 Bouwmeester R, Gabriels R, Hulstaert N, Martens L, Degroeve S. DeepLC can predict retention times for peptides that carry as-yet unseen modifications. Nature Methods. 18: 1363-1369. PMID 34711972 DOI: 10.1038/s41592-021-01301-5  0.727
2021 Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, et al. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. Jacs Au. 1: 750-765. PMID 34254058 DOI: 10.1021/jacsau.1c00048  0.709
2021 Salz R, Bouwmeester R, Gabriels R, Degroeve S, Martens L, Volders PJ, 't Hoen PAC. Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection. Journal of Proteome Research. 20: 3353-3364. PMID 33998808 DOI: 10.1021/acs.jproteome.1c00264  0.784
2020 Bouwmeester R, Martens L, Degroeve S. Generalized Calibration Across Liquid Chromatography Setups for Generic Prediction of Small-Molecule Retention Times. Analytical Chemistry. PMID 32281370 DOI: 10.1021/Acs.Analchem.0C00233  0.716
2020 Bouwmeester R, Gabriels R, Bossche TVD, Martens L, Degroeve S. The Age of Data-Driven Proteomics: How Machine Learning Enables Novel Workflows. Proteomics. e1900351. PMID 32267083 DOI: 10.1002/Pmic.201900351  0.759
2019 Nye LC, Williams JP, Munjoma NC, Letertre MPM, Coen M, Bouwmeester R, Martens L, Swann JR, Nicholson JK, Plumb RS, McCullagh M, Gethings LA, Lai S, Langridge JI, Vissers JPC, et al. A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry: Application to the characterisation of metabolites in rat urine. Journal of Chromatography. A. PMID 31285057 DOI: 10.1016/J.Chroma.2019.06.056  0.546
2019 Silva ASC, Bouwmeester R, Martens L, Degroeve S. Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions. Bioinformatics (Oxford, England). PMID 31077310 DOI: 10.1093/Bioinformatics/Btz383  0.757
2019 Bouwmeester R, Martens L, Degroeve S. Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction. Analytical Chemistry. PMID 30702864 DOI: 10.1021/Acs.Analchem.8B05820  0.733
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