Ghent University Academic Bibliography

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The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS) : an open community for bioinformatics training and research

Wout Bittremieux, David Bouyssié, Viktoria Dorfer, Marie Locard‐Paulet, Yasset Perez‐Riverol, Veit Schwämmle, Julian Uszkoreit and Tim Van Den Bossche (UGent)

(2023) RAPID COMMUNICATIONS IN MASS SPECTROMETRY.
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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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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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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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Universal Spectrum Identifier for mass spectra

Eric W. Deutsch, Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche (UGent) , Ralf Gabriels (UGent) , Pierre-Alain Binz, Benjamin Pullman, Zhi Sun, et al.

(2021) NATURE METHODS. 18(7). p.768-770
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Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

Alexander A. Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L. F. Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Melissa Nothias-Esposito, Katherine N. Maloney, et al.

(2021) NATURE BIOTECHNOLOGY. 39(2). p.169-173
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- Conference Paper
- C3
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The HUPO-PSI standardized spectral library format

Ralf Gabriels (UGent) , Nuno Bandeira, Wout Bittremieux, Jeremy J Carver, Matthew Chambers, Shin Kawano, Henry Lam, Tytus Mak, Yasset Perez-Riverol, Benjamin J Pullman, et al.

(2020) EuBIC 2020 developers' meeting.
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Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Christopher Ashwood, Wout Bittremieux, Eric W. Deutsch, Nadezhda T. Doncheva, Viktoria Dorfer, Ralf Gabriels (UGent) , Vladimir Gorshkov, Surya Gupta (UGent) , Andrew R. Jones, Lukas Käll, et al.

(2020) EUPA OPEN PROTEOMICS. 24. p.1-6
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- Miscellaneous
- open access
Algorithmic learning for auto-deconvolution of GC-MS data to enable molecular networking within GNPS

Alexander A. Aksenov, Ivan Laponogov, Zheng Zhang, Sophie LF Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Mélissa Nothias-Esposito, Katherine N. Maloney, et al.

(2020) bioRxiv.
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Mining the enriched subgraphs for specific vertices in a biological graph

Pieter Meysman, Yvan Saeys (UGent) , Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer (UGent) , Bart Goethals and Kris Laukens

(2019) IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 16(5). p.1496-1507

Academic Bibliography

The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS) : an open community for bioinformatics training and research

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

A comprehensive evaluation of consensus spectrum generation methods in proteomics

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

Universal Spectrum Identifier for mass spectra

Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data

The HUPO-PSI standardized spectral library format

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Algorithmic learning for auto-deconvolution of GC-MS data to enable molecular networking within GNPS

Mining the enriched subgraphs for specific vertices in a biological graph

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