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Tim Van Den Bossche
Tim Van Den Bossche
VIB - UGent Center for Medical Biotechnology; Ghent University
Verified email at ugent.be
Title
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Cited by
Year
Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis
H Schiebenhoefer, T Van Den Bossche, S Fuchs, BY Renard, T Muth, ...
Expert Review of Proteomics 16 (5), 375-390, 2019
832019
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
T Van Den Bossche, BJ Kunath, K Schallert, SS Schäpe, PE Abraham, ...
Nature communications 12 (1), 7305, 2021
602021
A proteomics sample metadata representation for multiomics integration and big data analysis
C Dai, A Füllgrabe, J Pfeuffer, EM Solovyeva, J Deng, P Moreno, ...
Nature Communications 12 (1), 5854, 2021
572021
Universal Spectrum Identifier for mass spectra
EW Deutsch, Y Perez-Riverol, J Carver, S Kawano, L Mendoza, ...
Nature methods 18 (7), 768-770, 2021
562021
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes
T Van Den Bossche, MŘ Arntzen, D Becher, D Benndorf, VGH Eijsink, ...
Microbiome 9 (1), 243, 2021
46*2021
The age of data‐driven proteomics: how machine learning enables novel workflows
R Bouwmeester, R Gabriels, T Van Den Bossche, L Martens, S Degroeve
Proteomics 20 (21-22), 1900351, 2020
432020
Cov-MS: a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients
B Van Puyvelde, K Van Uytfanghe, O Tytgat, L Van Oudenhove, ...
Jacs Au 1 (6), 750-765, 2021
342021
Proteomics standards initiative extended FASTA format
PA Binz, J Shofstahl, JA Vizcaíno, H Barsnes, RJ Chalkley, G Menschaert, ...
Journal of proteome research 18 (6), 2686-2692, 2019
312019
Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool
P Verschaffelt, T Van Den Bossche, L Martens, P Dawyndt, B Mesuere
Journal of Proteome Research 20 (4), 2005-2009, 2021
272021
Proteomics standards initiative at twenty years: current activities and future work
EW Deutsch, JA Vizcaíno, AR Jones, PA Binz, H Lam, J Klein, ...
Journal of proteome research 22 (2), 287-301, 2023
202023
Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis
T Van Den Bossche, P Verschaffelt, K Schallert, H Barsnes, P Dawyndt, ...
Journal of proteome research 19 (8), 3562-3566, 2020
182020
Proteomics Standards Initiatives ProForma 2.0 Unifying the encoding of Proteoforms and Peptidoforms
RD LeDuc, EW Deutsch, PA Binz, RT Fellers, AJ Cesnik, JA Klein, ...
arXiv preprint arXiv:2109.11352, 2021
162021
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
M Munoz-Benavent, F Hartkopf, T Van Den Bossche, VC Piro, ...
NAR genomics and bioinformatics 2 (3), lqaa058, 2020
142020
Pout2Prot: An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files
K Schallert, P Verschaffelt, B Mesuere, D Benndorf, L Martens, ...
Journal of Proteome Research 21 (4), 1175-1180, 2022
13*2022
MegaGO: A Fast Yet Powerful Approach to Assess Functional Gene Ontology Similarity across Meta-Omics Data Sets
P Verschaffelt, T Van Den Bossche, W Gabriel, M Burdukiewicz, A Soggiu, ...
Journal of Proteome Research 20 (4), 2083-2088, 2021
132021
Research culture: science from bench to society
L Canti, A Chrzanowska, MG Doglio, L Martina, T Van Den Bossche
Biology open 10 (8), bio058919, 2021
112021
Unipept CLI 2.0: adding support for visualizations and functional annotations
P Verschaffelt, P Van Thienen, T Van Den Bossche, F Van der Jeugt, ...
Bioinformatics 36 (14), 4220-4221, 2020
112020
Proceedings of the EuBIC-MS 2020 Developers’ Meeting
C Ashwood, W Bittremieux, EW Deutsch, NT Doncheva, V Dorfer, ...
EuPA Open Proteomics 24, 1-6, 2020
62020
Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses
P Verschaffelt, A Tanca, M Abbondio, T Van Den Bossche, TV Moortele, ...
Journal of Proteome Research 22 (8), 2620-2628, 2023
52023
Sensitive and specific spectral library searching with CompOmics spectral library searching tool and percolator
GA Shiferaw, R Gabriels, R Bouwmeester, T Van Den Bossche, ...
Journal of Proteome Research 21 (5), 1365-1370, 2022
52022
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