Stephan Fuchs

ProteoDUDes improves taxonomic profiling in metaproteomics by reducing false positives, achieving higher accuracy in identifying active organisms in complex samples.

This paper presents a framework for peptide identification using commercial nanopore sequencing platforms, achieving single-amino-acid resolution and reliable performance across sequencing runs.

This paper develops a workflow for detecting carbapenemase-producing Klebsiella pneumoniae in wastewater using wet-lab methods and genomics, finding high prevalence and specific genetic markers.

The paper introduces seq2squiggle, a transformer-based model for simulating nanopore sequencing signals, which outperforms existing tools on real data.

CIEVaD provides lightweight workflows for generating synthetic test data and evaluating genomic variant detection accuracy.

MpoxRadar tracks Mpox virus mutations globally through an interactive dashboard, allowing users to analyze mutation profiles and filter data by various parameters.

The paper uses complementary Ribo-seq methods to map the translatome of Campylobacter jejuni, identifying novel small open reading frames and refining gene annotations.

smORFer detects small ORFs in prokaryotes using a modular algorithm that integrates structural features and Fourier transform for accurate identification.

CovRadar provides a platform for tracking and filtering SARS-CoV-2 mutations in the spike gene, enabling users to analyze and visualize mutational changes and spatio-temporal distributions.

This paper evaluates six metaproteomics tools for functional annotation using GO terms, finding differences in sensitivity and specificity, and integrates two into Galaxy for broader accessibility.

The paper presents a proteogenomics workflow to identify small proteins in Staphylococcus aureus, finding 185 SP100, 69 of which were previously unannotated.

seq-seq-pan constructs a dynamic whole genome alignment framework for pan-genomics, enabling efficient updates and integration of multiple reference genomes.