Paul Wilmes

Publications

• Spatio-functional Organization in Virocells of Small Uncultivated Archaea from the Deep Biosphere
  The ISME Journal. Jul, 2023  |   Pubmed ID: 37468677
• Lower Gastric Sensitivity in Quiescent Inflammatory Bowel Disease Than in Irritable Bowel Syndrome
  Physiology & Behavior. Jul, 2023  |   Pubmed ID: 37468056
• Reservoirs of Antimicrobial Resistance in the Context of One Health
  Current Opinion in Microbiology. Jun, 2023  |   Pubmed ID: 36913905
• Altered Infective Competence of the Human Gut Microbiome in COVID-19
  Microbiome. Mar, 2023  |   Pubmed ID: 36894986
• Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters
  Microbiology Spectrum. Feb, 2023  |   Pubmed ID: 36688698
• Alterations of Oral Microbiota and Impact on the Gut Microbiome in Type 1 Diabetes Mellitus Revealed by Integrated multi-omic Analyses
  Microbiome. Dec, 2022  |   Pubmed ID: 36578059
• Long COVID Classification: Findings from a Clustering Analysis in the Predi-COVID Cohort Study
  International Journal of Environmental Research and Public Health. Nov, 2022  |   Pubmed ID: 36498091
• Binny: an Automated Binning Algorithm to Recover High-quality Genomes from Complex Metagenomic Datasets
  Briefings in Bioinformatics. Nov, 2022  |   Pubmed ID: 36239393
• Disease Progression, Resilience, and Inflammation Markers During the Coronavirus Disease 2019 Pandemic in Parkinson's Disease
  Movement Disorders : Official Journal of the Movement Disorder Society. Nov, 2022  |   Pubmed ID: 36148927
• Mobilome-driven Segregation of the Resistome in Biological Wastewater Treatment
  ELife. Sep, 2022  |   Pubmed ID: 36111782
• SnapShot: The Expobiome Map
  Cell Host & Microbe. Sep, 2022  |   Pubmed ID: 36108614
• The Gut Microbiome Molecular Complex in Human Health and Disease
  Cell Host & Microbe. Sep, 2022  |   Pubmed ID: 36108612
• Long COVID Symptomatology After 12 Months and Its Impact on Quality of Life According to Initial Coronavirus Disease 2019 Disease Severity
  Open Forum Infectious Diseases. Aug, 2022  |   Pubmed ID: 35983269
• Studying the Parkinson's Disease Metabolome and Exposome in Biological Samples Through Different Analytical and Cheminformatics Approaches: a Pilot Study
  Analytical and Bioanalytical Chemistry. Oct, 2022  |   Pubmed ID: 35829770
• The Microbiome of Cryospheric Ecosystems
  Nature Communications. Jun, 2022  |   Pubmed ID: 35655063
• Evolution of the Murine Gut Resistome Following Broad-spectrum Antibiotic Treatment
  Nature Communications. Apr, 2022  |   Pubmed ID: 35484157
• Combinatorial Analysis Reveals Highly Coordinated Early-stage Immune Reactions That Predict Later Antiviral Immunity in Mild COVID-19 Patients
  Cell Reports. Medicine. Apr, 2022  |   Pubmed ID: 35480624
• Toward Hypothesis-driven, Personalized Microbiome Screening
  Cell Reports Methods. Jan, 2022  |   Pubmed ID: 35474872
• Genomic and Metabolic Adaptations of Biofilms to Ecological Windows of Opportunity in Glacier-fed Streams
  Nature Communications. Apr, 2022  |   Pubmed ID: 35444202
• The Gut Microbial Metabolite Formate Exacerbates Colorectal Cancer Progression
  Nature Metabolism. Apr, 2022  |   Pubmed ID: 35437333
• Glacier Shrinkage Will Accelerate Downstream Decomposition of Organic Matter and Alters Microbiome Structure and Function
  Global Change Biology. Jun, 2022  |   Pubmed ID: 35320603
• The Benefits, Costs and Feasibility of a Low Incidence COVID-19 Strategy
  The Lancet Regional Health. Europe. Feb, 2022  |   Pubmed ID: 35005678
• Microdiversity Characterizes Prevalent Phylogenetic Clades in the Glacier-fed Stream Microbiome
  The ISME Journal. Mar, 2022  |   Pubmed ID: 34522009
• Persistence of Birth Mode-dependent Effects on Gut Microbiome Composition, Immune System Stimulation and Antimicrobial Resistance During the First Year of Life
  ISME Communications. Mar, 2021  |   Pubmed ID: 36717704
• Systematic Characterization of Human Gut Microbiome-secreted Molecules by Integrated Multi-omics
  ISME Communications. Dec, 2021  |   Pubmed ID: 35106519
• The Metaproteomics Initiative: a Coordinated Approach for Propelling the Functional Characterization of Microbiomes
  Microbiome. Dec, 2021  |   Pubmed ID: 34930457
• Critical Assessment of MetaProteome Investigation (CAMPI): a Multi-laboratory Comparison of Established Workflows
  Nature Communications. Dec, 2021  |   Pubmed ID: 34911965
• Reporting Guidelines for Human Microbiome Research: the STORMS Checklist
  Nature Medicine. Nov, 2021  |   Pubmed ID: 34789871
• Emulating the Gut-liver Axis: Dissecting the Microbiome's Effect on Drug Metabolism Using Multiorgan-on-chip Models
  Current Opinion in Endocrine and Metabolic Research. Jun, 2021  |   Pubmed ID: 34239997
• Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies
  Frontiers in Genetics. 2021  |   Pubmed ID: 34194470
• Mantis: Flexible and Consensus-driven Genome Annotation
  GigaScience. Jun, 2021  |   Pubmed ID: 34076241
• SARS-CoV-2 Transmission Risk from Asymptomatic Carriers: Results from a Mass Screening Programme in Luxembourg
  The Lancet Regional Health. Europe. May, 2021  |   Pubmed ID: 33997830
• Unification of Functional Annotation Descriptions Using Text Mining
  Biological Chemistry. Jul, 2021  |   Pubmed ID: 33984880
• SARS-CoV-2 Transmission in Educational Settings During an Early Summer Epidemic Wave in Luxembourg, 2020
  BMC Infectious Diseases. May, 2021  |   Pubmed ID: 33947340
• Generalisation of COVID-19 Incidences Provides a Biased View of the Actual Epidemiological Situation
  The Lancet Regional Health. Europe. Jun, 2021  |   Pubmed ID: 33937902
• PathoFact: a Pipeline for the Prediction of Virulence Factors and Antimicrobial Resistance Genes in Metagenomic Data
  Microbiome. Feb, 2021  |   Pubmed ID: 33597026
• Roles of Bacteriophages, Plasmids and CRISPR Immunity in Microbial Community Dynamics Revealed Using Time-series Integrated Meta-omics
  Nature Microbiology. Jan, 2021  |   Pubmed ID: 33139880
• IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches
  Frontiers in Immunology. 2020  |   Pubmed ID: 33584660
• Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity FomA and TLR2
  Frontiers in Immunology. 2020  |   Pubmed ID: 33408714
• Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams
  Frontiers in Microbiology. 2020  |   Pubmed ID: 33329472
• Dichloromethane Degradation Pathway from Unsequenced Sp. MC8b Rapidly Explored by Pan-Proteomics
  Microorganisms. Nov, 2020  |   Pubmed ID: 33260855
• Optimised Biomolecular Extraction for Metagenomic Analysis of Microbial Biofilms from High-mountain Streams
  PeerJ. 2020  |   Pubmed ID: 33194372
• Integration of Time-series Meta-omics Data Reveals How Microbial Ecosystems Respond to Disturbance
  Nature Communications. Oct, 2020  |   Pubmed ID: 33077707
• Systems Biology of Acidophile Biofilms for Efficient Metal Extraction
  Scientific Data. Jul, 2020  |   Pubmed ID: 32636389
• Publisher Correction: Building an International Consortium for Tracking Coronavirus Health Status
  Nature Medicine. Aug, 2020  |   Pubmed ID: 32591764
• Compositional and Functional Characterisation of Biomass-degrading Microbial Communities in Guts of Plant Fibre- and Soil-feeding Higher Termites
  Microbiome. Jun, 2020  |   Pubmed ID: 32576253
• Building an International Consortium for Tracking Coronavirus Health Status
  Nature Medicine. Aug, 2020  |   Pubmed ID: 32488218
• Integrative Omics Analysis of the Termite Gut System Adaptation to Miscanthus Diet Identifies Lignocellulose Degradation Enzymes
  Communications Biology. Jun, 2020  |   Pubmed ID: 32483294
• Correction To: Genetic and Metabolic Links Between the Murine Microbiome and Memory
  Microbiome. May, 2020  |   Pubmed ID: 32466793
• Genetic and Metabolic Links Between the Murine Microbiome and Memory
  Microbiome. Apr, 2020  |   Pubmed ID: 32299497
• Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?
  Trends in Microbiology. May, 2020  |   Pubmed ID: 32298617
• Microbial Community Redundancy and Resilience Underpins High-Rate Anaerobic Treatment of Dairy-Processing Wastewater at Ambient Temperatures
  Frontiers in Bioengineering and Biotechnology. 2020  |   Pubmed ID: 32232038
• Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function
  Cell Metabolism. May, 2020  |   Pubmed ID: 32213345
• Correction for Bellenberg Et Al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms"
  Applied and Environmental Microbiology. Jan, 2020  |   Pubmed ID: 31964679
• Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities with Approximate Bayesian Computation and Steady-state Signalling Simulations
  BMC Bioinformatics. Jan, 2020  |   Pubmed ID: 31964336
• The Microbiome-gut-brain Axis in Acute and Chronic Brain Diseases
  Current Opinion in Neurobiology. Apr, 2020  |   Pubmed ID: 31812830
• Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome
  Microorganisms. Sep, 2019  |   Pubmed ID: 31546776
• Connecting Environmental Exposure and Neurodegeneration Using Cheminformatics and High Resolution Mass Spectrometry: Potential and Challenges
  Environmental Science. Processes & Impacts. Sep, 2019  |   Pubmed ID: 31305828
• Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells
  Cell Reports. Apr, 2019  |   Pubmed ID: 31042485
• Deep Neural Networks Outperform Human Expert's Capacity in Characterizing Bioleaching Bacterial Biofilm Composition
  Biotechnology Reports (Amsterdam, Netherlands). Jun, 2019  |   Pubmed ID: 30949441
• The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials
  Journal of Innate Immunity. 2019  |   Pubmed ID: 30286447
• Weak Iron Oxidation by Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching
  Frontiers in Microbiology. 2018  |   Pubmed ID: 30631311
• Birth Mode is Associated with Earliest Strain-conferred Gut Microbiome Functions and Immunostimulatory Potential
  Nature Communications. Nov, 2018  |   Pubmed ID: 30504906
• Dark Matter in Host-microbiome Metabolomics: Tackling the Unknowns-A Review
  Analytica Chimica Acta. Dec, 2018  |   Pubmed ID: 30292286
• Expanding the Use of Spectral Libraries in Proteomics
  Journal of Proteome Research. Dec, 2018  |   Pubmed ID: 30270626
• Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host-Microbiota Interactions
  Methods in Molecular Biology (Clifton, N.J.). 2018  |   Pubmed ID: 30259493
• The RNA Complement of Outer Membrane Vesicles From Serovar Typhimurium Under Distinct Culture Conditions
  Frontiers in Microbiology. 2018  |   Pubmed ID: 30214435
• Expressed Protein Profile of a Tectomicrobium and Other Microbial Symbionts in the Marine Sponge Aplysina Aerophoba As Evidenced by Metaproteomics
  Scientific Reports. Aug, 2018  |   Pubmed ID: 30087358
• Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms
  Applied and Environmental Microbiology. 10, 2018  |   Pubmed ID: 30076195
• 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
  Biotechnology for Biofuels. 2018  |   Pubmed ID: 30038663
• Resolving Host-microbe Interactions in the Gut: the Promise of in Vitro Models to Complement in Vivo Research
  Current Opinion in Microbiology. Aug, 2018  |   Pubmed ID: 30031243
• Small RNA Profiling of Low Biomass Samples: Identification and Removal of Contaminants
  BMC Biology. May, 2018  |   Pubmed ID: 29759067
• Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles
  Methods in Molecular Biology (Clifton, N.J.). 2018  |   Pubmed ID: 29484596
• Human Gut Microbiome: Function Matters
  Trends in Microbiology. Jul, 2018  |   Pubmed ID: 29173869
• Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum Ferriphilum
  Applied and Environmental Microbiology. 02, 2018  |   Pubmed ID: 29150517
• Measuring Soil Sustainability Via Soil Resilience
  The Science of the Total Environment. Jun, 2018  |   Pubmed ID: 29054651
• The Nasal and Gut Microbiome in Parkinson's Disease and Idiopathic Rapid Eye Movement Sleep Behavior Disorder
  Movement Disorders : Official Journal of the Movement Disorder Society. Jan, 2018  |   Pubmed ID: 28843021
• First Draft Genome Sequence of a Strain Belonging to the Genus and Its Gene Expression in Situ
  Standards in Genomic Sciences. 2017  |   Pubmed ID: 29075368
• Ninety-nine De Novo Assembled Genomes from the Moose (Alces Alces) Rumen Microbiome Provide New Insights into Microbial Plant Biomass Degradation
  The ISME Journal. Nov, 2017  |   Pubmed ID: 28731473
• Integrated Meta-omic Analyses of the Gastrointestinal Tract Microbiome in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
  Translational Research : the Journal of Laboratory and Clinical Medicine. Aug, 2017  |   Pubmed ID: 28686852
• ICoVeR - an Interactive Visualization Tool for Verification and Refinement of Metagenomic Bins
  BMC Bioinformatics. May, 2017  |   Pubmed ID: 28464793
• Generation of Genome-scale Metabolic Reconstructions for 773 Members of the Human Gut Microbiota
  Nature Biotechnology. Jan, 2017  |   Pubmed ID: 27893703
• Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract
  Frontiers in Microbiology. 2016  |   Pubmed ID: 27445992
• Erratum To: Phenotypic Differentiation of Gastrointestinal Microbes is Reflected in Their Encoded Metabolic Repertoires
  Microbiome. Jul, 2016  |   Pubmed ID: 27377779
• Sources and Functions of Extracellular Small RNAs in Human Circulation
  Annual Review of Nutrition. Jul, 2016  |   Pubmed ID: 27215587
• A Microfluidics-based in Vitro Model of the Gastrointestinal Human-microbe Interface
  Nature Communications. May, 2016  |   Pubmed ID: 27168102
• The Human Gut Microbiome in Health: Establishment and Resilience of Microbiota over a Lifetime
  Environmental Microbiology. Jul, 2016  |   Pubmed ID: 27059297
• In Situ Phenotypic Heterogeneity Among Single Cells of the Filamentous Bacterium Candidatus Microthrix Parvicella
  The ISME Journal. May, 2016  |   Pubmed ID: 26505828
• Comparative Integrated Omics: Identification of Key Functionalities in Microbial Community-wide Metabolic Networks
  NPJ Biofilms and Microbiomes. 2015  |   Pubmed ID: 28721231
• Phenotypic Differentiation of Gastrointestinal Microbes is Reflected in Their Encoded Metabolic Repertoires
  Microbiome. Nov, 2015  |   Pubmed ID: 26617277
• A Decade of Metaproteomics: Where We Stand and What the Future Holds
  Proteomics. Oct, 2015  |   Pubmed ID: 26315987
• Integrated Omics for the Identification of Key Functionalities in Biological Wastewater Treatment Microbial Communities
  Microbial Biotechnology. May, 2015  |   Pubmed ID: 25678254
• VizBin - an Application for Reference-independent Visualization and Human-augmented Binning of Metagenomic Data
  Microbiome. 2015  |   Pubmed ID: 25621171
• The Extracellular RNA Complement of Escherichia Coli
  MicrobiologyOpen. Apr, 2015  |   Pubmed ID: 25611733
• Community-integrated Omics Links Dominance of a Microbial Generalist to Fine-tuned Resource Usage
  Nature Communications. Nov, 2014  |   Pubmed ID: 25424998
• Lipid-based Biofuel Production from Wastewater
  Current Opinion in Biotechnology. Dec, 2014  |   Pubmed ID: 24768793
• Systematic Design of 18S RRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia
  PloS One. 2014  |   Pubmed ID: 24755918
• Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction
  Scientific Reports. Mar, 2014  |   Pubmed ID: 24682077
• A Hundred Years of Activated Sludge: Time for a Rethink
  Frontiers in Microbiology. 2014  |   Pubmed ID: 24624120
• From Meta-omics to Causality: Experimental Models for Human Microbiome Research
  Microbiome. May, 2013  |   Pubmed ID: 24450613
• Sequential Isolation of Metabolites, RNA, DNA, and Proteins from the Same Unique Sample
  Methods in Enzymology. 2013  |   Pubmed ID: 24060123
• Condensing the Omics Fog of Microbial Communities
  Trends in Microbiology. Jul, 2013  |   Pubmed ID: 23764387
• A Biomolecular Isolation Framework for Eco-systems Biology
  The ISME Journal. Jan, 2013  |   Pubmed ID: 22763648
• The Complex Exogenous RNA Spectra in Human Plasma: an Interface with Human Gut Biota?
  PloS One. 2012  |   Pubmed ID: 23251414
• Genome Sequence of "Candidatus Microthrix Parvicella" Bio17-1, a Long-chain-fatty-acid-accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant
  Journal of Bacteriology. Dec, 2012  |   Pubmed ID: 23144412