Simon Van de Vyver

This paper develops a method to identify species in mixed palaeoproteomic samples by analyzing both physical and genetic mixtures, revealing new faunal information from ancient bone fragments.

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 Peptonizer2000, a tool that improves taxonomic identification in metaproteomics by combining peptide scores and taxon links with statistical models, showing higher specificity and confidence.

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.

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

The paper introduces b-move, a bidirectional extension of the move structure for run-length compressed indices, achieving faster character extensions than existing methods while maintaining memory efficiency.