Ghent University Academic Bibliography

Journal Article
A1
open access

Toward an integrated machine learning model of a proteomics experiment

Benjamin A. Neely, Viktoria Dorfer, Lennart Martens (UGent) , Isabell Bludau, Robbin Bouwmeester (UGent) , Sven Degroeve (UGent) , Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, et al.

(2023) JOURNAL OF PROTEOME RESEARCH.

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Journal Article
A1
open access

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Tine Claeys (UGent) , Maxime Menu, Robbin Bouwmeester (UGent) , Kris Gevaert (UGent) and Lennart Martens (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(4). p.1181-1192

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Journal Article
A1
open access

Proteomics standards initiative at twenty years : current activities and future work

Eric W. Deutsch, Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, et al.

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.287-301

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Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

Pieter Verschaffelt (UGent) , Alessandro Tanca, Marcello Abbondio, Tim Van Den Bossche (UGent) , Tibo Vande Moortele (UGent) , Peter Dawyndt (UGent) , Lennart Martens (UGent) and Bart Mesuere (UGent)

(2023) JOURNAL OF PROTEOME RESEARCH. 22(8). p.2620-2628

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Journal Article
A1
open access

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

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

(2023) JOURNAL OF PROTEOME RESEARCH. 22(2). p.632-636

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Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files

Kay Schallert, Pieter Verschaffelt (UGent) , Bart Mesuere (UGent) , Dirk Benndorf, Lennart Martens (UGent) and Tim Van Den Bossche (UGent)

(2022) JOURNAL OF PROTEOME RESEARCH. 21(4). p.1175-1180

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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

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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A comprehensive evaluation of consensus spectrum generation methods in proteomics

Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, Julia A. Bubis, Ralf Gabriels (UGent) , Henry Webel, et al.

(2022) JOURNAL OF PROTEOME RESEARCH. 21(6). p.1566-1574

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Journal Article
A1
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) JOURNAL OF PROTEOME RESEARCH. 22(2). p.557-560

Academic Bibliography

Toward an integrated machine learning model of a proteomics experiment

Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins

Proteomics standards initiative at twenty years : current activities and future work

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

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

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files

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

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

A comprehensive evaluation of consensus spectrum generation methods in proteomics

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

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