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Researcher
Tim Van Den Bossche
Profile
Projects
Publications
Activities
Awards & Distinctions
33
Results
2023
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.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
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
Tim Van Den Bossche
A1
Journal Article
in
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
2023
Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses
Pieter Verschaffelt
Alessandro Tanca
Marcello Abbondio
Tim Van Den Bossche
Tibo Vande Moortele
Peter Dawyndt
Lennart Martens
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation
Tine Claeys
Tim Van Den Bossche
Yasset Perez-Riverol
Kris Gevaert
Juan Antonio Vizcaíno
Lennart Martens
A1
Journal Article
in
NATURE COMMUNICATIONS
2023
2022
Benchmark and improving methods in metaproteomics informatics
Tim Van Den Bossche
Lennart Martens
Bart Mesuere
Thilo Muth
Dissertation
2022
Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files
Kay Schallert
Pieter Verschaffelt
Bart Mesuere
Dirk Benndorf
Lennart Martens
Tim Van Den Bossche
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
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
Ralf Gabriels
Arshika Yalavarthi
Yasset Perez-Riverol
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
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
Lennart Martens
Pieter-Jan Volders
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
2021
A proteomics sample metadata representation for multiomics integration and big data analysis
Chengxin Dai
Anja Füllgrabe
Julianus Pfeuffer
Elizaveta M. Solovyeva
Jingwen Deng
Pablo Moreno
Selvakumar Kamatchinathan
Deepti Jaiswal Kundu
Nancy George
Silvie Fexova
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2021
Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients
Bart Van Puyvelde
Katleen Van Uytfanghe
Olivier Tytgat
Laurence Van Oudenhove
Ralf Gabriels
Robbin Bouwmeester
Simon Daled
Tim Van Den Bossche
Pathmanaban Ramasamy
Sigrid Verhelst
et al.
A2
Journal Article
in
JACS AU
2021
Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows
Tim Van Den Bossche
Benoit J. Kunath
Kay Schallert
Stephanie S. Schäpe
Paul E. Abraham
Jean Armengaud
Magnus Ø. Arntzen
Ariane Bassignani
Dirk Benndorf
Stephan Fuchs
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2021
Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows
Tim Van Den Bossche
Benoit J. Kunath
Kay Schallert
Stephanie S. Schäpe
Paul E. Abraham
Jean Armengaud
Magnus Ø. Arntzen
Ariane Bassignani
Dirk Benndorf
Stephan Fuchs
et al.
Preprint
2021
MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets
Pieter Verschaffelt
Tim Van Den Bossche
Wassim Gabriel
Michał Burdukiewicz
Alessio Soggiu
Lennart Martens
Bernhard Y. Renard
Henning Schiebenhoefer
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files
Tim Van Den Bossche
Kay Schallert
Pieter Verschaffelt
Bart Mesuere
Dirk Benndorf
Lennart Martens
Preprint
2021
Research culture : science from bench to society
Lorenzo Canti
Anna Chrzanowska
Maria Giulia Doglio
Lia Martina
Tim Van Den Bossche
A1
Journal Article
in
BIOLOGY OPEN
2021
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes
Tim Van Den Bossche
Magnus Ø. Arntzen
Dörte Becher
Dirk Benndorf
Vincent G. H. Eijsink
Céline Henry
Pratik D. Jagtap
Nico Jehmlich
Catherine Juste
Benoit J. Kunath
et al.
A1
Journal Article
in
MICROBIOME
2021
Unipept Desktop : a faster, more powerful metaproteomics results analysis tool
Pieter Verschaffelt
Tim Van Den Bossche
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
Universal Spectrum Identifier for mass spectra
Eric W. Deutsch
Yasset Perez-Riverol
Jeremy Carver
Shin Kawano
Luis Mendoza
Tim Van Den Bossche
Ralf Gabriels
Pierre-Alain Binz
Benjamin Pullman
Zhi Sun
et al.
A1
Journal Article
in
NATURE METHODS
2021
2020
An unforgettable PhD conference : VIBes2020
Tim Van Den Bossche
Maria Giulia Doglio
Anna Chrzanowska
Blog post
2020
Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis
Tim Van Den Bossche
Pieter Verschaffelt
Kay Schallert
Harald Barsnes
Peter Dawyndt
Dirk Benndorf
Bernhard Y. Renard
Bart Mesuere
Lennart Martens
Thilo Muth
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement : an explorative study
Mette Elise Tunset
Hanne Haslene-Hox
Tim Van Den Bossche
Arne Einar Vaaler
Einar Sulheim
Daniel Kondziella
A1
Journal Article
in
PEERJ
2020
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
Christopher Ashwood
Wout Bittremieux
Eric W. Deutsch
Nadezhda T. Doncheva
Viktoria Dorfer
Ralf Gabriels
Vladimir Gorshkov
Surya Gupta
Andrew R. Jones
Lukas Käll
et al.
A2
Journal Article
in
EUPA OPEN PROTEOMICS
2020
The HUPO-PSI standardized spectral library format
Ralf Gabriels
Nuno Bandeira
Wout Bittremieux
Jeremy J Carver
Matthew Chambers
Shin Kawano
Henry Lam
Tytus Mak
Yasset Perez-Riverol
Benjamin J Pullman
et al.
C3
Conference
2020
The age of data-driven proteomics : how machine learning enables novel workflows
Robbin Bouwmeester
Ralf Gabriels
Tim Van Den Bossche
Lennart Martens
Sven Degroeve
A1
Journal Article
in
PROTEOMICS
2020
Unipept CLI 2.0 : adding support for visualizations and functional annotations
Pieter Verschaffelt
Philippe Van Thienen
Tim Van Den Bossche
Felix Van der Jeugt
Caroline De Tender
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
BIOINFORMATICS
2020
gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
Maria Muñoz-Benavent
Felix Hartkopf
Tim Van Den Bossche
Vitor C Piro
Carlos García-Ferris
Amparo Latorre
Bernhard Y Renard
Thilo Muth
A2
Journal Article
in
NAR GENOMICS AND BIOINFORMATICS
2020
gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms (vol 2, 10.1093/nargab/lqaa058, 2020)
Maria Munoz-Benavent
Felix Hartkopf
Tim Van Den Bossche
Vitor C. Piro
Carlos Garcia-Ferris
Amparo Latorre
Bernhard Y. Renard
Thilo Muth
Correction
2020
2019
Challenges and promise at the interface of metaproteomics and genomics : an overview of recent progress in metaproteogenomic data analysis
Henning Schiebenhoefer
Tim Van Den Bossche
Stephan Fuchs
Bernhard Y Renard
Thilo Muth
Lennart Martens
A1
Journal Article
in
EXPERT REVIEW OF PROTEOMICS
2019
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2019
Proteomics Standards Initiative extended FASTA format
Pierre-Alain Binz
Jim Shofstahl
Juan Antonio Vizcaíno
Harald Barsnes
Robert J Chalkley
Gerben Menschaert
Emanuele Alpi
Karl Clauser
Jimmy K Eng
Lydie Lane
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2019
Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics
Tim Van Den Bossche
Ana Sílvia Ferreira Diamantino Coelho e Silva
Bernhard Y Renard
Thilo Muth
Lennart Martens
C3
Conference
2019
2018
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2018
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2018