Prof. Dr. Paul Wilmes
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| Faculté ou Centre | Luxembourg Centre for Systems Biomedicine | ||||
| Department | Systems Ecology | ||||
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Campus Belval, Université du Luxembourg 7, Avenue des Hauts Fourneaux L-4362 Esch-sur-Alzette |
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| Bureau sur le campus | BioTech I, 4.11 | ||||
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| Téléphone | (+352) 46 66 44 6188 | ||||
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Prof. Dr. Paul Wilmes (LCSB)
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Paul Wilmes is Professor of Systems Ecology at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg, where he is Head of the Systems Ecology research group (Wilmes Lab). Paul obtained his PhD in 2006 from the School of Environmental Sciences at the University of East Anglia in Norwich (UK), a part of his doctoral research having been conducted at the Max Planck Institute for Marine Microbiology in Bremen (Germany). After three years of postdoctoral research at the University of California, Berkeley (USA), he returned to his native Luxembourg in early 2010 through an ATTRACT Fellowship of the Luxembourg National Research Fund (FNR). He initially established his research group at the Centre de Recherche Public – Gabriel Lippmann but later joined the LCSB.
Paul’s main primary research focus is on using Systems Biology approaches to identify key functionalities of microbial communities including human-associated microbiota. His group has pioneered appropriate methodologies for carrying out systematic molecular measurements of microbial consortia over space and time. This allows, for example, to define lifestyle strategies of distinct populations and link these to genetic and functional traits. The same approaches allow the study of microbiome-host molecular interactions. In this context, his group has pioneered the development of a microfluidics-based in vitro model of the human-microbial gastrointestinal interface called HuMiX.
Paul has authored more than 80 peer-review publications. He is a frequently invited speaker at international scientific symposia and academic institutions. Paul is a member of several national and international scientific organizations, and he has won several prizes for his scientific work.
Personal website: http://www.paulwilmes.eu
FNR ATTRACT Fellows in Biomedicine (Video)
Last updated on: mercredi 27 janvier 2021
| 2018 – present |
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Head of the Integrative Molecular Biomedicine Department, LCSB, University of Luxembourg, Luxembourg |
| May 2017 – present |
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Deputy Head of the Systems Biomedicine Department, University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg |
| December 2017 – May 2018 |
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Career break, parental leave |
| February 2015 – present |
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Associate Professor; Head of the Eco-Systems Biology research group, University of Luxembourg, Luxembourg |
| October 2011 – January 2015 |
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Principal investigator, ATTRACT Research Fellow; Head of the Eco-Systems Biology research group, |
| February 2010 – September 2011 |
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Project leader (Luxembourg National Research Fund ATTRACT fellow), Centre de Recherche Public – Gabriel Lippmann, Belvaux, Luxembourg |
| May 2006 – December 2009 |
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Postdoctoral research scholar; Host: Prof. Dr. Jillian F. Banfield, University of California, Berkeley, USA |
Last updated on: 07 fév 2019
2023
Altered infective competence of the human gut microbiome in COVID-19; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Microbiome (2023), 11(1), 46
Reservoirs of antimicrobial resistance in the context of One Health; ; ;
in Current Opinion in Microbiology (2023), 73
2022
Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell Reports Medicine (2022), 3(4), 100600
Mobilome-driven segregation of the resistome in biological wastewater treatment; ; ; ;
in eLife (2022), 11
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment.; ; ; ; ;
in Nature communications (2022), 13(1), 2296
Forecasting of a complex microbial community using meta-omics; ; ; ; ; ; ; ; ;
E-print/Working paper (2022)
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets; ; ; ;
in Briefings in Bioinformatics (2022)
Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Microbiome (2022)
Parkinson's Disease progression, resilience and inflammation markers during the COVID-19 pandemic; ; ; ; ; ; ; ;
in Movement Disorders (2022), in press (doi: 10.1002/mds.29212)(in press),
Individual factors and beliefs determining COVID-19 vaccination willingness; ; ; ; ; ; ; ; ;
Poster (2022, April)
Gastrische Interozeption und gastrische myoelektrische Aktivität bei chronisch-entzündlichen Darmerkrankungen und Reizdarmsyndrom; ; ; ; ; ; ; ; ; ; ; ;
in Heinrichs, Markus; Schönauer, Monika (Eds.) 47. Jahrestagung Psychologie und Gehirn (2022)
Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study; ; ; ; ; ; ; ; ;
in Analytical and Bioanalytical Chemistry (2022)
The gut microbial metabolite formate exacerbates colorectal cancer progression; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Metabolism (2022)
An archaeal compound as a driver of Parkinson’s disease pathogenesis; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
E-print/Working paper (2022)
The ecology of the unseenin Archives des Sciences Naturelles, Physiques et Mathématiques (2022), XLVIII
The gut microbiome molecular complex in human health and disease; ; ; ; ; ;
in Cell Host and Microbe (2022), 30(9), 1201-1206
2021
Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams 2021.10.07.463499; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
E-print/Working paper (2021)
Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life; ; ; ; ; ; ; ; ;
in ISME Communications (2021)
Glacier-fed stream biofilms harbour diverse resistomes and biosynthetic gene clusters 2021.11.18.469141; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
E-print/Working paper (2021)
The benefits, costs and feasibility of a low incidence COVID-19 strategy; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in The Lancet Regional Health - Europe (2021), 12(100193),
Mobilome-driven segregation of the resistome in biological wastewater treatment 2021.11.15.468621; ; ; ;
E-print/Working paper (2021)
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data; ; ; ; ; ; ;
in Microbiome (2021)
Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in ISME Communications (2021)
Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome; ; ; ; ; ; ; ; ; ; ; ; ;
in ISME Journal (2021)
Functional meta-omics provide critical insights into long- and short-read assemblies; ; ; ; ; ; ; ;
in Briefings in Bioinformatics (2021)
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater; ; ; ; ; ; ; ; ; ;
in Water (2021), 13(21 3018),
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets 2021.12.22.473795; ; ; ;
E-print/Working paper (2021)
Emulating the gut–liver axis: Dissecting the microbiome's effect on drug metabolism using multiorgan-on-chip models; ; ; ;
in Current Opinion in Endocrine and Metabolic Research (2021)
Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies; ; ; ; ; ; ; ;
in Frontiers in Genetics (2021)
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2021), 6(1), 123--135
Unification of functional annotation descriptions using text mining; ; ;
in Biological Chemistry (2021)
The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Microbiome (2021), 9(1), 243
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Communications (2021), 12(1), 7305
SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in The Lancet Regional Health. Europe (2021), 4
2020
Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams; ; ; ; ; ; ;
in PeerJ (2020)
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.; ; ; ; ; ; ; ; ; ; ; ; ;
in Communications Biology (2020)
Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics; ; ; ; ; ; ; ; ; ; ;
in Microorganisms (2020)
Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Communications (2020)
Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams; ; ; ; ; ; ; ; ; ; ;
in Frontiers in Microbiology (2020), 11
Glutathione Restricts Serine Metabolism to Preserve Regulatory T Cell Function; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell Metabolism (2020), 31(5), 920--9367
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2020)
Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites.; ; ; ; ; ; ; ; ;
in Microbiome (2020)
SARS-CoV-2 Transmission in Educational Settings During an Early Summer Epidemic Wave in Luxembourg; ; ; ; ; ; ; ;
E-print/Working paper (2020)
Understanding the role of Fusobacterium nucleatum metabolism in colon cancer initiation and progression; ; ; ; ; ; ; ; ; ; ;
Poster (2020, February 22)
Microbiome in Colorectal Cancer: How to Getfrom Meta-omics to Mechanism?; ; ; ; ;
in Trends in Microbiology (2020)
2019
Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition; ; ; ; ; ; ; ; ; ; ;
in Biotechnology Reports (2019)
Influence of Macro-Substrate Composition in Wastewater on Micropollutant Removal; ; ; ; ;
in the mobile app "MICROPOL 2019" (2019)
Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell Reports (2019), 27
Extensive transmission of microbes along the gastrointestinal tract; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in eLife (2019)
Connecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges; ; ; ; ; ; ; ; ; ;
in Environmental Science. Processes and Impacts (2019)
2018
Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms.; ; ; ; ; ; ; ; ; ; ;
in Applied and environmental microbiology (2018), 84(20),
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.; ; ; ; ;
in Biotechnology for biofuels (2018), 11
Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics.; ; ; ; ; ; ; ;
in Scientific reports (2018), 8(1), 11795
Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching; ; ; ; ; ; ; ; ;
in Frontiers in Microbiology (2018), 9(December), 1-12
Expanding the use of spectral libraries in proteomics.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Journal of proteome research (2018)
Cominatorial effect of dietary fibre and Lactobacillus rhamnosus in the context of colorectal cancer therapy; ; ; ; ; ; ; ; ; ;
Poster (2018, February 16)
Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles; ; ; ; ; ; ;
in Arluison, Véronique; Valverde, Claudio Valverde (Eds.) Bacterial Regulatory RNA (2018)
Small RNA profiling of low biomass samples: identification and removal of contaminants; ; ; ; ; ; ; ; ; ;
in BMC Biology (2018), 16(52),
Integrated time-resolved multi-omics for understanding microbial niche ecology; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2018, August)
Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Environmental Science and Technology (2018), 52(9), 5386-5397
Measuring soil sustainability via soil resilience.; ;
in The Science of the total environment (2018), 626
The RNA Complement of Outer Membrane Vesicles From Salmonella enterica Serovar Typhimurium Under Distinct Culture Conditions; ; ; ; ; ; ; ; ;
in Frontiers in Microbiology (2018), 9
A multi-omic view of invasive genetic elements and their linked prokaryotic population dynamics within a mixed microbial community; ; ; ; ; ; ; ; ; ; ; ;
Poster (2018, September 11)
Critical transitions in microbial communities: mobile genetic elements as drivers of the microbial community dynamics within activated sludge of wastewater treatment; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2018, October 19)
Using metabolic networks to resolve ecological properties of microbiomes; ; ; ; ;
in Current Opinion in Systems Biology (2018)
The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials.; ; ;
in Journal of innate immunity (2018)
Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease; ; ; ; ; ; ; ; ;
Poster (2018, August)
Microbiome-derived Multi-omicBiomarkers for Early-stage Detection and Stratification of Parkinson's Disease; ; ; ; ; ; ; ; ;
Poster (2018, October)
Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Communications (2018)
L’écologie systémique du microbiote humain : Identification des fonctions essentielles au maintient de la physiologie humaineScientific Conference (2018, November)
Understanding the role of the microbiome in Parkinson’s diseaseScientific Conference (2018, October)
Microbial Systems Ecology for identifying key functions driving host-microbiome-diet interactionsScientific Conference (2018, September)
Unraveling the combinatorial mechanisms linking the gut microbiome to Parkinson’s diseaseScientific Conference (2018, September)
The integration of quantitative big data from microbial consortia: what is there to gain?Scientific Conference (2018, August)
Systems ecology reveals key functions underpinning host-microbiome interactions in health and diseaseScientific Conference (2018, June)
Systems ecology of microbiome-human interactions: identifying which functions are keyScientific Conference (2018, April)
Resolving host–microbe interactions in the gut: the promise of in vitro models to complement in vivo research; ;
in Current Opinion in Microbiology (2018)
2017
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.; ; ; ; ; ; ; ;
in BMC bioinformatics (2017), 18(1), 233
Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T).; ; ; ; ; ; ; ; ;
in Applied and environmental microbiology (2017)
The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder.; ; ; ; ; ; ; ; ;
in Movement Disorders (2017)
Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants; ; ; ; ; ; ; ; ; ;
E-print/Working paper (2017)
Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic hematopoietic stem cell transplantation.; ; ; ; ; ; ; ; ; ; ;
in Translational Research: the Journal of Laboratory and Clinical Medicine (2017)
Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface; ; ; ; ;
in Engineering (2017)
Comparative integrated-omic analyses of phage-host interactions within natural and engineered microbial communities; ; ; ;
Poster (2017, July 21)
First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ; ; ; ; ; ; ; ; ; ;
in Standards in Genomic Sciences (2017), 12(64),
Dark Matter in host-microbiome metabolomics: Tackling the unknowns-A review; ;
in Analytica Chimica Acta (2017)
Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.; ; ; ; ; ; ; ; ; ; ; ;
in The ISME journal (2017), 11(11), 2538-2551
From meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer; ; ;
Poster (2017, February 05)
Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life; ; ; ; ; ; ; ; ; ; ;
in Frontiers in Microbiology (2017)
Form follows function: integrated multi-omics of the human gut microbiomeScientific Conference (2017, September)
Systems ecology of microbiomes: a new frontier of discovery in microbiologyScientific Conference (2017, September)
From integrated multi-omics to microbial systems ecology: quo vadis?Scientific Conference (2017, August)
Systems ecology of microbiomes: a new frontier of discovery in microbiologyPresentation (2017, August)
Systems ecology of microbiomes: a new frontier of discovery in microbiologyPresentation (2017, August)
Integrated multi-omics for identifying discriminant features in the human microbiomeScientific Conference (2017, June)
Untangling the microbial ecology of anaerobic digestion through integrated multi-omicsScientific Conference (2017, May)
Systems Ecology of Microbiomes: A New Frontier of Discovery in MicrobiologyScientific Conference (2017, May)
From integrated multi-omics to causality: how to distil data, how to design experiments and how to conduct themScientific Conference (2017, April)
Metaproteomics and integrated multi-omics: What do they tell us about microbial community function?Scientific Conference (2017, April)
Systems Ecology of Microbiomes: A New Frontier of Discovery in MicrobiologyScientific Conference (2017, March)
From gut to sludge: how to sustainably manage microbial communities in futureScientific Conference (2017, February)
2016
A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell (2016), 167(5), 1339-135321
Sources and Functions of Extracellular Small RNAs in Human Circulation.; ; ; ; ; ;
in Annual review of nutrition (2016)
A study of the molecular mechanisms underlying the response of human colorectal adenomacarcinoma enterocytes to prebiotics and probiotics; ; ; ; ; ; ; ; ; ;
Poster (2016, June)
The human gut microbiome in health: establishment and resilience of microbiota over a lifetime; ; ;
in Environmental Microbiology (2016), 18(7), 21032116
Erratum: Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2016), 2
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2016), 2
Identification, recovery, and refinement of hitherto undescribed population-level genomes from the human gastrointestinal tract; ; ; ; ; ; ; ;
in Frontiers in Microbiology (2016), 7(884),
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota; ; ; ; ; ; ; ; ; ; ;
in Nature Biotechnology (2016)
IMP: a pipeline for reproducible referenceindependent integrated metagenomic and metatranscriptomic analyses; ; ; ; ; ; ; ; ;
in Genome Biology (2016), 17
A microfluidics-based in vitro model of the gastrointestinal human-microbe interface.; ; ; ; ; ; ; ; ; ; ;
in Nature communications (2016), 7
HuMiX, an in vitro model to study the human gut microbiome and immune systemScientific Conference (2016, November)
Beyond the shadow of Koch’s postulates: doesn’t expressed function ultimately count in microbiomes?Scientific Conference (2016, September)
Integrated multi-omics of oleaginous microbial consortia in biological wastewater treatment plantsScientific Conference (2016, June)
From meta-omics to microbial systems ecology: What to measure and what is there to learn?Scientific Conference (2016, March)
Piecing together the puzzle: integrated omics of microbial consortiaScientific Conference (2016, February)
2015
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires; ; ; ;
in Microbiome (2015), 3(55), 1-13
Integrated omics analyses of the human gut microbiome in a multiplex family study of type 1 diabetes mellitus.; ; ; ; ; ; ; ;
Poster (2015, March)
Systems Biology of Acidophile Biofilms for Efficient Metal Extraction; ; ; ; ; ; ; ; ; ;
in Advanced Materials Research (2015), 1130
Changes in the human gastrointestinal microbiome during cancer treatments; ; ; ; ; ; ; ;
Poster (2015, March)
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data; ; ; ; ; ; ; ; ;
in Microbiome (2015)
Method optimization for fecal sample collection and fecal DNA extraction.; ; ; ; ; ; ; ; ; ;
in Biopreservation and biobanking (2015), 13(2), 79-93
Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities; ; ;
in Microbial Biotechnology (2015)
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Biofilms and Microbiomes (2015), 1(15007),
In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella; ; ; ; ; ;
in ISME Journal (2015)
Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood.; ; ; ; ; ; ;
Poster (2015, June)
Early dynamics of the gastrointestinal microbiome in infants at risk of metabolic disease in adulthood; ; ; ; ; ; ;
Poster (2015, March)
From integrated omic analyses of the human gastrointestinal microbiome to treatment strategies for improved patient careScientific Conference (2015, November)
Microbial Systems Ecology: from defining niches to reconstructing matter flows through microbial consortiaScientific Conference (2015, April)
2014
RNA in circulation: sources and functions of extracellular exogenous RNA in blood; ;
in Nelson, Karen (Ed.) Encyclopedia of Metagenomics (2014)
Integrated Omic Analyses of the Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus; ; ; ; ; ; ; ;
Poster (2014, April 30)
Characterization of the gastrointestinal microbiome in patients with REM-sleep behaviour disorder and newly diagnosed Parkinson’s disease; ; ; ; ;
Scientific Conference (2014, October)
Systematic Design of 18S rRNA Gene Primers for Determining Eukaryotic Diversity in Microbial Consortia; ; ; ; ; ; ;
in PLoS ONE (2014)
Identification of condition-specific microbial populations from human metagenomic data; ; ;
Poster (2014, March)
Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction; ; ;
in Scientific Reports (2014)
Towards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data;
in Keller, Andreas; Meese, Eckart (Eds.) Nucleic Acids as Molecular Diagnostics (2014)
The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample; ; ; ;
in Methods in Enzymology (2014)
Community integrated omics links the dominance of a microbial generalist to fine-tuned resource usage; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2014)
Community integrated omics links the dominance of a microbial generalist to fine-tuned resource usage; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Scientific Conference (2014)
Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Communications (2014)
In situ single-cell investigations of substrate utilisation by Candidatus Microthrix parvicella; ; ; ; ;
Poster (2014, October 16)
Bet-hedging strategy for substrate usage among single cells of Candidatus Microthrix parvicella?; ; ; ; ;
Scientific Conference (2014, September 29)
A hundred years of activated sludge: time for a rethink; ;
in Frontiers in Microbiology (2014), 5(47), 1-7
Eco-Systems Biology: from integrated omics to control strategies for mixed microbial communitiesScientific Conference (2014, October)
Eco-Systems Biology of human-microbe molecular interactions along the gastrointestinal tractScientific Conference (2014, June)
Integrated omics to eluciate structure-function relationships in microbial biofilmsScientific Conference (2014, May)
HuMiX: A MICROFLUIDICS-BASED IN VITRO CO-CULTURE DEVICE FOR INVESTIGATING HOST-MICROBE INTERACTIONS; ; ; ;
Scientific Conference (2014, October 30)
2013
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature (2013), 500
The exogenous RNA spectrum in human plasma and the gastrointestinal tract; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2013, October)
From meta-omics to causality: experimental models for human microbiome research; ; ; ;
in Microbiome (2013), 1(14),
Meta-omic Analyses of the Microbiome in a Family Study of Diabetes Mellitus; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2013, October)
Reproducibility: In praise of open research measures; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature (2013), 498
Condensing the omics fog of microbial communities; ; ; ;
in Trends in Microbiology (2013), 21(7), 325333
Systematic molecular measurements reveal key microbial populations driving community-wide phenotype; ; ; ; ; ; ; ; ; ; ; ;
Poster (2013)
Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample; ; ;
in Methods in Enzymology (2013), 531
A biomolecular isolation framework for eco-systems biology; ; ; ; ;
in ISME Journal (2013), 7(1), 110-121
Integrated omics highlights keystone genes in community-wide metabolic networks; ; ; ; ;
Poster (2013)
Integrated omics highlights keystone genes in community-wide metabolic networks; ; ; ; ;
Poster (2013)
From integrated omics to Eco-Systems Biology of mixed microbial communitiesPresentation (2013, July)
From sludge to gut: towards eco-systems biology of the human microbiomeScientific Conference (2013, June)
From integrated omics to Eco-Systems Biology of microbial community-driven processesScientific Conference (2013, May)
2012
Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities; ; ; ;
in Metabolomics : Official journal of the Metabolomic Society (2012), 8(4), 566-578
Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant; ; ; ; ; ; ; ; ; ; ; ;
in Journal of Bacteriology (2012), 194(23), 6670-6671
From gut to sludge: Molecular Eco-Systems Biology of Microbial Consortia;
Scientific Conference (2012)
humix: a microfluidics-based in vitro co-culture device for investigating human-microbial molecular interactions;
Scientific Conference (2012, August 25)
The complex exogenous RNA spectra in human plasma: an interface with human gut biota?; ; ; ; ; ; ;
in PLoS ONE (2012), 7(12),
Eco-Systems Biology: from wastewater plant to the human gastrointestinal tractScientific Conference (2012, June)
Inferring basic ecological and evolutionary processes in microbial communities from molecular network analysisScientific Conference (2012, June)
Inferring synergism and antagonism in microbial communities from network dynamicsPresentation (2012, May)
Genome-based and functional differentiation: hallmarks of microbial adaptation, divergence and speciation?in Ogilvie, L.A.; Hirsch, P.R (Eds.) Microbial Ecological Theory: Current Perspectives (2012)
2011
Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities; ; ; ; ; ;
in Environmental Microbiology Reports (2011)
Eco-Systems Biology of Natural Lipid-Accumulating Microbial Communities; ; ;
Poster (2011, September 27)
Architecture reflects function: high-resolution microscopic and molecular insights into acid mine drainage biofilmsScientific Conference (2011, August)
Microbial community proteomicsin de Bruijn, Frans (Ed.) Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (2011)
Capturing the Structure and Dynamics of Complex Microbial CommunitiesScientific Conference (2011, January)
A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes; ; ; ; ; ; ;
in PLoS Computational Biology (2011), 7(10), 1002230
2010
Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities; ; ; ; ; ; ; ;
in Proceedings of the National Academy of Sciences of the United States of America (2010), 107(6), 2383-2390
Characterization of Extracellular Polymeric Substances from Acidophilic Microbial Biofilms; ; ; ; ; ; ;
in Applied and Environmental Microbiology (2010), 76(9), 2916-2922
Ecological distribution and population physiology defined by proteomics in a natural microbial community; ; ; ; ; ; ; ; ; ; ; ;
in Molecular Systems Biology (2010), 6
From molecules to ecosystems and back: bioinformatic approaches for Eco-Systems BiologyScientific Conference (2010, November)
Tandem proteomics and metabolomics for elucidating cryptic metabolic transformations within mixed microbial communitiesScientific Conference (2010, October)
Metabolome-proteome differentiation reflects bacterial divergenceScientific Conference (2010, March)
Metabolome-Proteome Differentiation Coupled to Microbial Divergence; ; ; ; ; ; ; ;
in mBio (2010), 1(5), 00246-10
2009
Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles;
in Current Opinion in Microbiology (2009), 12(3), 310-317
Natural acidophilic biofilm communities reflect distinct organismal and functional organization; ; ; ; ;
in ISME Journal (2009), 3(2), 266-270
The dynamic genetic repertoire of microbial communities; ; ;
in FEMS Microbiology Reviews (2009), 33(1), 109-132
2008
Organismal and functional partitioning within natural microbial communitiesScientific Conference (2008, August)
Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal; ; ; ; ; ; ; ; ;
in ISME Journal (2008), 2(8), 853-864
Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment; ;
in PLoS ONE (2008), 3(3), 1-2
2007
Natural microbial assemblages reflect distinct organismal and functional partitioningScientific Conference (2007, December)
2006
Environmental proteomics, a new window on microbial community functionScientific Conference (2006, July)
Metaproteomic investigations of enhanced biological phosphorus removal in activated sludgeScientific Conference (2006, June)
Metaproteomics: studying functional gene expression in microbial ecosystemsScientific Conference (2006)
Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge;
in Water Science & Technology (2006), 54(1), 217-226
Metaproteomics: studying functional gene expression in microbial ecosystems;
in Trends in Microbiology (2006), 14(2), 92-97
2005
Metaproteomics: studying functional gene expression in microbial ecosystemsScientific Conference (2005, September)
Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludgeScientific Conference (2005, July)
Finding the proteomic keys to unlock the metabolic mysteries of enhanced biological phosphorus removalScientific Conference (2005, July)
The metaproteome: dynamic function of a complex microbial systemScientific Conference (2005, January)
2004
Metaproteomic investigations of enhanced biological phosphorus removal in activated sludgeScientific Conference (2004, July)
The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms;
in Environmental Microbiology (2004), 6(9), 911-920
