Ralf Gabriels

Miscellaneous
open access

ProteomicsML : an online platform for community-curated datasets and tutorials for machine learning in proteomics

Tobias Rehfeldt, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Siegfried Gessulat, Benjamin Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno and Eric Deutsch

(2022) ChemRxiv.

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Miscellaneous
open access

Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

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

(2022) ChemRxiv.

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Journal Article
A1
open access

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes

Rupert Mayer (UGent) , Rein Verbeke (UGent) , Caroline Asselman (UGent) , Ilke Aernout (UGent) , Adillah Gul (UGent) , Denzel Eggermont (UGent) , Katie Boucher (UGent) , Fabien Henri Thery (UGent) , Teresa Maia (UGent) , Hans Demol (UGent) , et al.

(2022) NATURE COMMUNICATIONS. 13(1).

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Journal Article
A1
open access

Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche (UGent) , Ralf Gabriels (UGent) , Arshika Yalavarthi, Yasset Perez-Riverol, et al.

(2022) JOURNAL OF PROTEOME RESEARCH. 21(4). p.1189-1195

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Journal Article
A1
open access

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay Shiferaw, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Tim Van Den Bossche (UGent) , Elien Vandermarliere (UGent) , Lennart Martens (UGent) and Pieter-Jan Volders (UGent)

(2022) JOURNAL OF PROTEOME RESEARCH. 21(5). p.1365-1370

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Journal Article
A1
open access

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

Bart Van Puyvelde (UGent) , Simon Daled (UGent) , Sander Willems, Ralf Gabriels (UGent) , Anne Gonzalez de Peredo, Karima Chaoui, Emmanuelle Mouton-Barbosa, David Bouyssié, Kurt Boonen, Christopher J. Hughes, et al.

(2022) SCIENTIFIC DATA. 9(1).

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Journal Article
A1
open access

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur Declercq (UGent) , Robbin Bouwmeester (UGent) , Aurélie Hirschler, Christine Carapito, Sven Degroeve (UGent) , Lennart Martens (UGent) and Ralf Gabriels (UGent)

(2022) MOLECULAR & CELLULAR PROTEOMICS. 21(8).

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PhD Thesis
open access

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ralf Gabriels (UGent)

(2022)

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Miscellaneous
open access

Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

Sven Degroeve (UGent) , Ralf Gabriels (UGent) , Kevin Velghe (UGent) , Robbin Bouwmeester (UGent) , Natalia Tichshenko (UGent) and Lennart Martens (UGent)

(2022) BIORXIV.

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Journal Article
A1
open access

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin Bouwmeester (UGent) , Ralf Gabriels (UGent) , Niels Hulstaert (UGent) , Lennart Martens (UGent) and Sven Degroeve (UGent)

(2021) NATURE METHODS. 18(11). p.1363-+

Academic Bibliography

Ralf Gabriels

ProteomicsML : an online platform for community-curated datasets and tutorials for machine learning in proteomics

Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes

Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods

Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

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