Paul Wilmes

This study identifies a bacterial protease that influences phage susceptibility and links it to host epithelial responses in ulcerative colitis.

MAP annotates mobilome elements and their functional cargo in prokaryotic (meta)genomic assemblies, enabling identification of composite elements like ARG-carrying integrons.

The paper evaluates statistical methods for differential metaproteomics, finding that several approaches effectively identify differentially abundant proteins despite data challenges.

This study integrates microbiome and host transcriptome data from mice to show diet, age, and genetics influence gut microbiota, with machine learning models predicting body weight and age with high accuracy.

The paper identifies Acinetobacter sp. as a dominant bacterium in tomato plant microbiota and shows its functional role in nutrient mobilization and stress adaptation, while decoupling its presence from antimicrobial resistance genes.

This study shows that the maternal microbiome influences offspring behavior, body weight, and hippocampal DNA methylation and gene expression.

CAMPI-2 evaluates five fecal sample stabilization methods for metaproteomics, finding one commercial device offers the best reproducibility and stability during room-temperature storage.

This study identifies an alternative methylmalonyl-CoA pathway in Cloacimonadota, linking propionate degradation to poly-γ-glutamate biosynthesis and syntrophic interactions with methanogens.

This study identifies sRNA 84 as a conserved regulator in Enterococcaceae that enhances mucin adhesion and gut colonization by upregulating cell surface proteins.

The paper uses integrated multi-omics to identify functional gut microbiome alterations in Parkinson's disease and prodromal stages, finding changes in metabolites and microbial gene transcripts.

This study uses multi-omics data to reveal reduced taxonomic and functional diversity in the gut microbiome of Parkinson's disease patients.

PathoFact 2.0 improves prediction of antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters in metagenomes through updated models and tools.

binny is an automated binning tool that produces high-quality MAGs from metagenomic data, outperforming existing methods in recovering complete and pure genomes.

This study shows that dietary fibre deprivation and bacterial curli exposure worsen PD-like symptoms in mice overexpressing human alpha-synuclein.

UniFuncNet integrates data from multiple biological databases to create a flexible and comprehensive network for omics data analysis.

Mantis is a protein function annotation tool that integrates multiple data sources to produce high-quality, consensus-driven annotations with improved precision and flexibility.

The paper benchmarks nucleic acid extraction protocols for microbial biofilms in glacier-fed streams, finding an adapted phenol-chloroform method yields better DNA quality and taxonomic profiles than commercial methods.

This study investigates how a higher termite adapts to a Miscanthus diet using integrative omics, revealing shifts in microbial gene expression and potential industrial enzyme sources.

The paper identifies and removes small RNA contaminants from microRNA extraction kits, showing their presence in human plasma samples and published datasets.

IMP is a pipeline that integrates metagenomic and metatranscriptomic data for microbial community analysis, improving assembly quality and enabling abundance and activity estimation.