Paul Wilmes

Luxembourg Centre for Systems Biomedicine, University of Luxembourg

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 10	2023

Other Publications

Article	Year
A biomolecular isolation framework for eco-systems biology. The ISME journal\| PubMed ID: 22763648	2013
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\| PubMed ID: 23144412	2012
The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PloS one\| PubMed ID: 23251414	2012
Condensing the omics fog of microbial communities. Trends in microbiology\| PubMed ID: 23764387	2013
Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample. Methods in enzymology\| PubMed ID: 24060123	2013
From meta-omics to causality: experimental models for human microbiome research. Microbiome\| PubMed ID: 24450613	2013
A hundred years of activated sludge: time for a rethink. Frontiers in microbiology\| PubMed ID: 24624120	2014
Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Scientific reports\| PubMed ID: 24682077	2014
Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PloS one\| PubMed ID: 24755918	2014
Lipid-based biofuel production from wastewater. Current opinion in biotechnology\| PubMed ID: 24768793	2014
Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature communications\| PubMed ID: 25424998	2014
The extracellular RNA complement of Escherichia coli. MicrobiologyOpen\| PubMed ID: 25611733	2015
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome\| PubMed ID: 25621171	2015
Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities. Microbial biotechnology\| PubMed ID: 25678254	2015
A decade of metaproteomics: where we stand and what the future holds. Proteomics\| PubMed ID: 26315987	2015
In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella. The ISME journal\| PubMed ID: 26505828	2016
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome\| PubMed ID: 26617277	2015
The human gut microbiome in health: establishment and resilience of microbiota over a lifetime. Environmental microbiology\| PubMed ID: 27059297	2016
A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nature communications\| PubMed ID: 27168102	2016
Sources and Functions of Extracellular Small RNAs in Human Circulation. Annual review of nutrition\| PubMed ID: 27215587	2016
Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome\| PubMed ID: 27377779	2016
Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract. Frontiers in microbiology\| PubMed ID: 27445992	2016
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature biotechnology\| PubMed ID: 27893703	2017
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. BMC bioinformatics\| PubMed ID: 28464793	2017
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\| PubMed ID: 28686852	2017
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. NPJ biofilms and microbiomes\| PubMed ID: 28721231	2015
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation. The ISME journal\| PubMed ID: 28731473	2017
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\| PubMed ID: 28843021	2018
Measuring soil sustainability via soil resilience. The Science of the total environment\| PubMed ID: 29054651	2018
First draft genome sequence of a strain belonging to the genus and its gene expression in situ. Standards in genomic sciences\| PubMed ID: 29075368	2017
Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum. Applied and environmental microbiology\| PubMed ID: 29150517	2018
Human Gut Microbiome: Function Matters. Trends in microbiology\| PubMed ID: 29173869	2018
Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29484596	2018
Small RNA profiling of low biomass samples: identification and removal of contaminants. BMC biology\| PubMed ID: 29759067	2018
Resolving host-microbe interactions in the gut: the promise of in vitro models to complement in vivo research. Current opinion in microbiology\| PubMed ID: 30031243	2018
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\| PubMed ID: 30038663	2018
Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms. Applied and environmental microbiology\| PubMed ID: 30076195	2018
Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics. Scientific reports\| PubMed ID: 30087358	2018
The RNA Complement of Outer Membrane Vesicles From Serovar Typhimurium Under Distinct Culture Conditions. Frontiers in microbiology\| PubMed ID: 30214435	2018
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.)\| PubMed ID: 30259493	2018
Expanding the Use of Spectral Libraries in Proteomics. Journal of proteome research\| PubMed ID: 30270626	2018
The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials. Journal of innate immunity\| PubMed ID: 30286447	2019
Dark matter in host-microbiome metabolomics: Tackling the unknowns-A review. Analytica chimica acta\| PubMed ID: 30292286	2018
Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. Nature communications\| PubMed ID: 30504906	2018
Weak Iron Oxidation by Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching. Frontiers in microbiology\| PubMed ID: 30631311	2018
Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. Biotechnology reports (Amsterdam, Netherlands)\| PubMed ID: 30949441	2019
Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell reports\| PubMed ID: 31042485	2019
Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges. Environmental science. Processes & impacts\| PubMed ID: 31305828	2019
Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. Microorganisms\| PubMed ID: 31546776	2019
The microbiome-gut-brain axis in acute and chronic brain diseases. Current opinion in neurobiology\| PubMed ID: 31812830	2020
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signa... BMC bioinformatics\| PubMed ID: 31964336	2020
Correction for Bellenberg et al., "Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms". Applied and environmental microbiology\| PubMed ID: 31964679	2020
Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function. Cell metabolism\| PubMed ID: 32213345	2020
Microbial Community Redundancy and Resilience Underpins High-Rate Anaerobic Treatment of Dairy-Processing Wastewater at Ambient Temperatures. Frontiers in bioengineering and biotechnology\| PubMed ID: 32232038	2020
Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism? Trends in microbiology\| PubMed ID: 32298617	2020
Genetic and metabolic links between the murine microbiome and memory. Microbiome\| PubMed ID: 32299497	2020
Correction to: Genetic and metabolic links between the murine microbiome and memory. Microbiome\| PubMed ID: 32466793	2020
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. Communications biology\| PubMed ID: 32483294	2020
Building an international consortium for tracking coronavirus health status. Nature medicine\| PubMed ID: 32488218	2020
Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites. Microbiome\| PubMed ID: 32576253	2020
Publisher Correction: Building an international consortium for tracking coronavirus health status. Nature medicine\| PubMed ID: 32591764	2020
Systems biology of acidophile biofilms for efficient metal extraction. Scientific data\| PubMed ID: 32636389	2020
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nature communications\| PubMed ID: 33077707	2020
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature microbiology\| PubMed ID: 33139880	2021
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams. PeerJ\| PubMed ID: 33194372	2020
Dichloromethane Degradation Pathway from Unsequenced sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms\| PubMed ID: 33260855	2020
Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams. Frontiers in microbiology\| PubMed ID: 33329472	2020
Extracellular Vesicles Modulate Gut Epithelial Cell Innate Immunity FomA and TLR2. Frontiers in immunology\| PubMed ID: 33408714	2020
IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches. Frontiers in immunology\| PubMed ID: 33584660	2020
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. Microbiome\| PubMed ID: 33597026	2021
Generalisation of COVID-19 incidences provides a biased view of the actual epidemiological situation. The Lancet regional health. Europe\| PubMed ID: 33937902	2021
SARS-CoV-2 transmission in educational settings during an early summer epidemic wave in Luxembourg, 2020. BMC infectious diseases\| PubMed ID: 33947340	2021
Unification of functional annotation descriptions using text mining. Biological chemistry\| PubMed ID: 33984880	2021
SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg. The Lancet regional health. Europe\| PubMed ID: 33997830	2021
Mantis: flexible and consensus-driven genome annotation. GigaScience\| PubMed ID: 34076241	2021
Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Frontiers in genetics\| PubMed ID: 34194470	2021
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\| PubMed ID: 34239997	2021
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome. The ISME journal\| PubMed ID: 34522009	2022
Reporting guidelines for human microbiome research: the STORMS checklist. Nature medicine\| PubMed ID: 34789871	2021
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature communications\| PubMed ID: 34911965	2021
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome\| PubMed ID: 34930457	2021
The benefits, costs and feasibility of a low incidence COVID-19 strategy. The Lancet regional health. Europe\| PubMed ID: 35005678	2022
Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics. ISME communications\| PubMed ID: 35106519	2021
Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function. Global change biology\| PubMed ID: 35320603	2022
The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature metabolism\| PubMed ID: 35437333	2022
Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams. Nature communications\| PubMed ID: 35444202	2022
Toward hypothesis-driven, personalized microbiome screening. Cell reports methods\| PubMed ID: 35474872	2022
Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients. Cell reports. Medicine\| PubMed ID: 35480624	2022
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment. Nature communications\| PubMed ID: 35484157	2022
The microbiome of cryospheric ecosystems. Nature communications\| PubMed ID: 35655063	2022
Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study. Analytical and bioanalytical chemistry\| PubMed ID: 35829770	2022
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\| PubMed ID: 35983269	2022
The gut microbiome molecular complex in human health and disease. Cell host & microbe\| PubMed ID: 36108612	2022
SnapShot: The Expobiome Map. Cell host & microbe\| PubMed ID: 36108614	2022
Mobilome-driven segregation of the resistome in biological wastewater treatment. eLife\| PubMed ID: 36111782	2022
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\| PubMed ID: 36148927	2022
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets. Briefings in bioinformatics\| PubMed ID: 36239393	2022
Long COVID Classification: Findings from a Clustering Analysis in the Predi-COVID Cohort Study. International journal of environmental research and public health\| PubMed ID: 36498091	2022
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses. Microbiome\| PubMed ID: 36578059	2022
Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters. Microbiology spectrum\| PubMed ID: 36688698	2023
Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. ISME communications\| PubMed ID: 36717704	2021
Altered infective competence of the human gut microbiome in COVID-19. Microbiome\| PubMed ID: 36894986	2023
Reservoirs of antimicrobial resistance in the context of One Health. Current opinion in microbiology\| PubMed ID: 36913905	2023
Lower gastric sensitivity in quiescent inflammatory bowel disease than in irritable bowel syndrome. Physiology & behavior\| PubMed ID: 37468056	2023
Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere. The ISME journal\| PubMed ID: 37468677	2023