arXiv subjects
Publications and source records attributed to Pieter Verschaffelt.
NORI performs probabilistic inference to resolve ambiguous mappings between experimental observations and biological entities orders of magnitude faster than state-of-the-art methods. This makes large-scale analysis and extensive hyperparameter optimization possible, and supports a broader range of bioinformatics applications, including protein inference, taxonomic and functional analysis in omics-fields.
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as an invaluable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.