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Buur LM, Declercq A, Strobl M, et al. (2024) MSRescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0. Journal of Proteome Research |
Koutrouli M, Nastou K, Líndez PP, et al. (2024) FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics (Oxford, England) |
Sakarika M, Kerckhof FM, Van Peteghem L, et al. (2023) The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions. Microbial Cell Factories. 22: 254 |
Claeys T, Van Den Bossche T, Perez-Riverol Y, et al. (2023) lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation. Nature Communications. 14: 6743 |
Verschaffelt P, Tanca A, Abbondio M, et al. (2023) Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses. Journal of Proteome Research |
Declercq A, Bouwmeester R, Chiva C, et al. (2023) Updated MS²PIP web server supports cutting-edge proteomics applications. Nucleic Acids Research |
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 |
Claeys T, Menu M, Bouwmeester R, et al. (2023) Machine Learning on Large-Scale Proteomics Data Identifies Tissue and Cell-Type Specific Proteins. Journal of Proteome Research |
Boone M, Ramasamy P, Zuallaert J, et al. (2023) Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit. Nature Communications. 14: 1072 |
Neely BA, Dorfer V, Martens L, et al. (2023) Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research |