Peter Dawyndt

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.

UMGAP is a metagenomics analysis pipeline that provides fast, memory-efficient, and accurate taxonomic profiling of shotgun metagenomes using protein code regions.

SMAP provides tools for read-backed haplotyping, generating haplotype calls from various sequencing data types and ploidy levels.

FragGeneScanRs improves gene prediction speed and performance for short reads using a Rust implementation of the FragGeneScan model.