Tibo Vande Moortele

The paper examines how changes to UniProtKB and taxonomic restrictions affect metaproteomics analysis, finding reduced peptide mapping coverage but stable dominant taxonomic profiles.

The paper introduces a method to directly construct sparse suffix arrays with reduced memory and time usage, using a text encoding and Libsais library for bioinformatics applications.

PathwayPilot is a web tool for visualizing and comparing metabolic pathways using metaproteomic data, demonstrating its effectiveness in analyzing enzyme expression shifts in gut microbiota under caloric restriction.

The paper updates the Unipept software to support analysis of non-tryptic and semi-tryptic peptides, improving performance while maintaining accuracy.

Unipept Desktop 2.0 enables the construction of targeted protein reference databases for proteogenomics analyses, improving taxonomic and functional resolution while enhancing privacy and analysis speed.