Academic Bibliography

Search 200 years of publications by Ghent University researchers.

Ralf Gabriels

Faculty of Medicine and Health Sciences > Department of Biomolecular Medicine

ORCID iD: 0000-0002-1679-1711

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- Journal Article
- A1
- open access
Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups

Robbin Bouwmeester (UGent) , Alireza Nameni (UGent) , Arthur Declercq (UGent) , Robbe Devreese (UGent) , Kevin Velghe (UGent) , Vladimir Gorshkov, Pelayo A. Penanes, Frank Kjeldsen, Magali Rompais, Christine Carapito, et al.

(2026) NATURE COMMUNICATIONS.
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The Escherichia coli PeptideAtlas build : characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

Caroline Jachmann (UGent) , Zhi Sun, Kevin Velghe (UGent) , Florence Arsène-Ploetze, Aurélie Hirschler, Jasper Zuallaert (UGent) , Christine Carapito, Robbin Bouwmeester (UGent) , Kay Nieselt, Eric W. Deutsch, et al.

(2026) JOURNAL OF PROTEOME RESEARCH. 25(2). p.1027-1041
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MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

Tim Van Den Bossche (UGent) , Theodore Alexandrov, Aivett Bilbao, Wout Bittremieux, Federico Ivan Brigante, Matthew Chase Chambers, Joshua Charkow, Eric Deutsch, Andrew W. Dowsey, Yasin El Abiead, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(11). p.5329-5335
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Koina : democratizing machine learning for proteomics research

Ludwig Lautenbacher, Kevin L. Yang, Tobias Kockmann, Christian Panse, Wassim Gabriel, Dulguun Bold, Elias Kahl, Matthew Chambers, Brendan X. MacLean, Kai Li, et al.

(2025) NATURE COMMUNICATIONS. 16(1).
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- Book Chapter
High-coverage immunopeptidomics using timsTOF mass spectrometers with thunder-DDA-PASEF boosted by MS2Rescore

David Gomez-Zepeda, Julian Beyrle, Annica Preikschat, Arthur Declercq (UGent) , Yannic Chen, Ralf Gabriels (UGent) , Lennart Martens (UGent) , Ute Distler and Stefan Tenzer

(2025) Immunoproteomics : methods and protocols. In Methods in molecular biology (MIMB) 2980. p.115-155
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- A1
- open access
MHCquant2 refines immunopeptidomics tumor antigen discovery

Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declercq (UGent) , Ralf Gabriels (UGent) , Jens Bauer, Marcel Wacker, Leon Bichmann, et al.

(2025) GENOME BIOLOGY. 26(1).
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Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Robbe Devreese (UGent) , Alireza Nameni (UGent) , Arthur Declercq (UGent) , Emmy Terryn, Ralf Gabriels (UGent) , Francis Impens (UGent) , Kris Gevaert (UGent) , Lennart Martens (UGent) and Robbin Bouwmeester (UGent)

(2025) ANALYTICAL CHEMISTRY. 97(28). p.15113-15121
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Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Patrick Willems (UGent) , Fabien Henri Thery (UGent) , Laura Van Moortel (UGent) , Margaux De Meyer (UGent) , An Staes (UGent) , Adillah Gul (UGent) , Lyudmila Kovalchuke (UGent) , Arthur Declercq (UGent) , Robbe Devreese (UGent) , Robbin Bouwmeester (UGent) , et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(4). p.2141-2151
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TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Arthur Declercq (UGent) , Robbe Devreese (UGent) , Jonas Scheid, Caroline Jachmann (UGent) , Tim Van Den Bossche (UGent) , Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurelie Hirschler, Jonathan R. Krieger, et al.

(2025) JOURNAL OF PROTEOME RESEARCH. 24(3). p.1067-1076
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- Book Chapter
Bioinformatics pipeline for processing single-cell data

Arthur Declercq (UGent) , Nina Demeulemeester, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) and Lennart Martens (UGent)

(2024) Mass spectrometry based single cell proteomics. In Methods in molecular biology (MIMB) 2817. p.221-239

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