| Unipept 4.0: functional analysis of metaproteome data R Gurdeep Singh, A Tanca, A Palomba, F Van der Jeugt, P Verschaffelt, ... Journal of proteome research 18 (2), 606-615, 2018 | 165 | 2018 |
| 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 | 89 | 2021 |
| 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 | 33 | 2021 |
| 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 | 20 | 2020 |
| 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 | 18 | 2022 |
| 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 | 17 | 2023 |
| 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 | 17 | 2021 |
| 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 | 15 | 2020 |
| UMGAP: the Unipept MetaGenomics analysis pipeline F Van der Jeugt, R Maertens, A Steyaert, P Verschaffelt, C De Tender, ... BMC genomics 23 (1), 433, 2022 | 10 | 2022 |
| Unipept Visualizations: an interactive visualization library for biological data P Verschaffelt, J Collier, A Botzki, L Martens, P Dawyndt, B Mesuere Bioinformatics 38 (2), 562-563, 2022 | 7 | 2022 |
| 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 | 6 | 2020 |
| Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial T Van Den Bossche, P Verschaffelt, T Vande Moortele, P Dawyndt, ... Protein Bioinformatics, 183-215, 2024 | 4 | 2024 |
| Unipept in 2024: Expanding Metaproteomics Analysis with Support for Missed Cleavages and Semitryptic and Nontryptic Peptides TV Moortele, B Devlaminck, S Van de Vyver, T Van Den Bossche, ... Journal of Proteome Research, 2024 | 4 | 2024 |
| Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun. 2021; 12: 7305 T Van Den Bossche, BJ Kunath, K Schallert, SS Schäpe, PE Abraham, ... | 3 | |
| The Peptonizer2000: graphical model based taxonomic identifications of metaproteomic samples T Holstein, P Verschaffelt, T Van den Bossche, L Martens, T Muth Cold Spring Harbor Laboratory, 2024 | 1 | 2024 |
| Building the Unipept Ecosystem: empowering high-throughput metaproteomics data analysis for characterizing complex microbial communities P Verschaffelt Ghent University, 2023 | 1 | 2023 |
| PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways TV Moortele, P Verschaffelt, Q Huang, NT Doncheva, T Holstein, ... Molecular & Cellular Proteomics, 100918, 2025 | | 2025 |
| The Microbiologist’s Guide to Metaproteomics T Van Den Bossche, J Armengaud, D Benndorf, JA Blakeley-Ruiz, ... | | 2025 |
| The Peptonizer2000: bringing confidence to metaproteomics T Holstein, P Verschaffelt, T Van den Bossche, S Van de Vyver, L Martens, ... bioRxiv, 2024.05. 20.594958, 2024 | | 2024 |
| Biodiversity analysis of metaproteomics samples with Unipept: a comprehensive tutorial TVD Bossche, P Verschaffelt, TV Moortele, P Dawyndt, L Martens, ... arXiv preprint arXiv:2311.07494, 2023 | | 2023 |