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| Van Den Bossche T, Beslic D, van Puyenbroeck S, et al. (2025) Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing. Proteomics. e202400321 |
| Singer F, Kuhring M, Renard BY, et al. (2024) Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics. Methods in Molecular Biology (Clifton, N.J.). 2859: 297-318 |
| Russo FF, Nowatzky Y, Jaeger C, et al. (2024) Machine learning methods for compound annotation in non-targeted mass spectrometry-A brief overview of fingerprinting, in silico fragmentation and de novo methods. Rapid Communications in Mass Spectrometry : Rcm. 38: e9876 |
| Arikan M, Muth T. (2024) gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Gigascience. 13 |
| Holstein T, Muth T. (2024) Bioinformatic Workflows for Metaproteomics. Methods in Molecular Biology (Clifton, N.J.). 2820: 187-213 |
| Holstein T, Kistner F, Martens L, et al. (2023) PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores. Bioinformatics (Oxford, England). 39 |
| Beslic D, Tscheuschner G, Renard BY, et al. (2022) Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly. Briefings in Bioinformatics |
| Van Den Bossche T, Arntzen MØ, Becher D, et al. (2021) The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome. 9: 243 |
| Van Den Bossche T, Kunath BJ, Schallert K, et al. (2021) Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12: 7305 |
| Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, et al. (2020) Erratum: gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Nar Genomics and Bioinformatics. 2: lqaa083 |