Publications by authors named "Robbin Bouwmeester"

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Koina: Democratizing machine learning for proteomics research.
Ludwig Lautenbacher, Kevin L Yang, Tobias Kockmann, Christian Panse, Wassim Gabriel, Robbin Bouwmeester

Nat Commun· November 2025

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Potential of Proteomics in Forensic Phenotyping: A Focus on Biological Sex Estimation.
Shirin Alex, Ruben Almey, Rachel Sian Dennis, Olivier Tytgat, Robbin Bouwmeester

J Proteome Res· October 2025

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Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep.
Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Robbin Bouwmeester

Anal Chem· July 2025

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Open-Source and FAIR Research Software for Proteomics.
Yasset Perez-Riverol, Wout Bittremieux, William S Noble, Lennart Martens, Aivett Bilbao, Robbin Bouwmeester

J Proteome Res· May 2025

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Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring.
Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Robbin Bouwmeester

J Proteome Res· April 2025

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Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline.
Ian Engels, Alexandra Burnett, Prudence Robert, Camille Pironneau, Grégory Abrams, Robbin Bouwmeester

J Proteome Res· April 2025

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TIMSRescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MSRescore.
Arthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Robbin Bouwmeester

J Proteome Res· March 2025

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MSRescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0.
Louise M Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve

J Proteome Res· August 2024

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Predicting ion mobility collision cross sections and assessing prediction variation by combining conventional and data driven modeling.
Robbin Bouwmeester, Keith Richardson, Richard Denny, Ian D Wilson, Sven Degroeve

Talanta· July 2024

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Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows.
An Staes, Teresa Mendes Maia, Sara Dufour, Robbin Bouwmeester, Ralf Gabriels

J Proteome Res· June 2024

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Bioinformatics Pipeline for Processing Single-Cell Data.
Arthur Declercq, Nina Demeulemeester, Ralf Gabriels, Robbin Bouwmeester, Sven Degroeve

Methods Mol Biol· June 2024

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Intensity and retention time prediction improves the rescoring of protein-nucleic acid cross-links.
Arslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev

Proteomics· April 2024

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FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data.
Mikaela Koutrouli, Katerina Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen

Bioinformatics· February 2024

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The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions.
Myrsini Sakarika, Frederiek-Maarten Kerckhof, Lotte Van Peteghem, Alexandra Pereira, Tim Van Den Bossche, Robbin Bouwmeester

Microb Cell Fact· December 2023

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Updated MS²PIP web server supports cutting-edge proteomics applications.
Arthur Declercq, Robbin Bouwmeester, Cristina Chiva, Eduard Sabidó, Aurélie Hirschler

Nucleic Acids Res· July 2023

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Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins.
Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens

J Proteome Res· April 2023

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Toward an Integrated Machine Learning Model of a Proteomics Experiment.
Benjamin A Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester

J Proteome Res· March 2023

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psm_utils: A High-Level Python API for Parsing and Handling Peptide-Spectrum Matches and Proteomics Search Results.
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens

J Proteome Res· February 2023

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ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics.
Tobias G Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A Neely

J Proteome Res· February 2023

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Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit.
Morgane Boone, Pathmanaban Ramasamy, Jasper Zuallaert, Robbin Bouwmeester, Berre Van Moer

Nat Commun· February 2023

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MSRescore: Data-Driven Rescoring Dramatically Boosts Immunopeptide Identification Rates.
Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve

Mol Cell Proteomics· August 2022

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Sensitive and Specific Spectral Library Searching with CompOmics Spectral Library Searching Tool and Percolator.
Genet Abay Shiferaw, Ralf Gabriels, Robbin Bouwmeester, Tim Van Den Bossche, Elien Vandermarliere

J Proteome Res· May 2022

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How sticky are our proteins? Quantifying hydrophobicity of the human proteome.
Juami Hermine Mariama van Gils, Dea Gogishvili, Jan van Eck, Robbin Bouwmeester, Erik van Dijk

Bioinform Adv· January 2022

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Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit.
Morgane Boone, Pathmanaban Ramasamy, Jasper Zuallaert, Robbin Bouwmeester, Berre Van Moer

Nat Commun· November 2021

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Graph Convolutional Networks for Improved Prediction and Interpretability of Chromatographic Retention Data.
Alexander Kensert, Robbin Bouwmeester, Kyriakos Efthymiadis, Peter Van Broeck, Gert Desmet

Anal Chem· November 2021

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