Paul Wilmes

A biomolecular isolation framework for eco-systems biology.

Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant.

The complex exogenous RNA spectra in human plasma: an interface with human gut biota?

Condensing the omics fog of microbial communities.

Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample.

From meta-omics to causality: experimental models for human microbiome research.

A hundred years of activated sludge: time for a rethink.

Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

Lipid-based biofuel production from wastewater.

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.

The extracellular RNA complement of Escherichia coli.

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data.

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

A decade of metaproteomics: where we stand and what the future holds.

In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella.

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

The human gut microbiome in health: establishment and resilience of microbiota over a lifetime.

A microfluidics-based in vitro model of the gastrointestinal human-microbe interface.

Sources and Functions of Extracellular Small RNAs in Human Circulation.

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.

ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.

Measuring soil sustainability via soil resilience.

First draft genome sequence of a strain belonging to the genus and its gene expression in situ.

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum.

Human Gut Microbiome: Function Matters.

Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles.

Small RNA profiling of low biomass samples: identification and removal of contaminants.

Resolving host-microbe interactions in the gut: the promise of in vitro models to complement in vivo research.

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems.

Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms.

Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.

The RNA Complement of Outer Membrane Vesicles From Serovar Typhimurium Under Distinct Culture Conditions.

Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions.

Expanding the Use of Spectral Libraries in Proteomics.

The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials.

Dark matter in host-microbiome metabolomics: Tackling the unknowns-A review.

Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential.

Weak Iron Oxidation by Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching.

Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition.

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.

Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges.

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome.

The microbiome-gut-brain axis in acute and chronic brain diseases.

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.

Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms".

Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function.

Microbial Community Redundancy and Resilience Underpins High-Rate Anaerobic Treatment of Dairy-Processing Wastewater at Ambient Temperatures.

Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?

Genetic and metabolic links between the murine microbiome and memory.

Correction to: Genetic and metabolic links between the murine microbiome and memory.

Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.

Building an international consortium for tracking coronavirus health status.

Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites.

Publisher Correction: Building an international consortium for tracking coronavirus health status.

Systems biology of acidophile biofilms for efficient metal extraction.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.

Dichloromethane Degradation Pathway from Unsequenced sp. MC8b Rapidly Explored by Pan-Proteomics.

Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.

Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity FomA and TLR2.

IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches.

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.

Generalisation of COVID-19 incidences provides a biased view of the actual epidemiological situation.

SARS-CoV-2 transmission in educational settings during an early summer epidemic wave in Luxembourg, 2020.

Unification of functional annotation descriptions using text mining.

SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg.

Mantis: flexible and consensus-driven genome annotation.

Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies.

Emulating the gut-liver axis: Dissecting the microbiome's effect on drug metabolism using multiorgan-on-chip models.

Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome.

Reporting guidelines for human microbiome research: the STORMS checklist.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.

The benefits, costs and feasibility of a low incidence COVID-19 strategy.

Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics.

Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

The gut microbial metabolite formate exacerbates colorectal cancer progression.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.

Toward hypothesis-driven, personalized microbiome screening.

Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients.

Evolution of the murine gut resistome following broad-spectrum antibiotic treatment.

The microbiome of cryospheric ecosystems.

Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study.

Long COVID Symptomatology After 12 Months and Its Impact on Quality of Life According to Initial Coronavirus Disease 2019 Disease Severity.

The gut microbiome molecular complex in human health and disease.

SnapShot: The Expobiome Map.

Mobilome-driven segregation of the resistome in biological wastewater treatment.

Disease Progression, Resilience, and Inflammation Markers During the Coronavirus Disease 2019 Pandemic in Parkinson's Disease.

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

Long COVID Classification: Findings from a Clustering Analysis in the Predi-COVID Cohort Study.

Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.

Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.

Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life.

Altered infective competence of the human gut microbiome in COVID-19.

Reservoirs of antimicrobial resistance in the context of One Health.

Lower gastric sensitivity in quiescent inflammatory bowel disease than in irritable bowel syndrome.

Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.