List of works - Paul Wilmes

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

scientific article

A biomolecular isolation framework for eco-systems biology.

scientific article

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

scientific article published on 28 August 2015

A hundred years of activated sludge: time for a rethink

scientific article

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

scientific article published on 11 May 2016

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

scientific article

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

scientific article published on 19 July 2018

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

scientific article

Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms

article

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

scientific article published in Nature Communications

Building an International Consortium for Tracking Coronavirus Health Status

scientific article published on 06 April 2020

Building an international consortium for tracking coronavirus health status

scientific article published on 02 June 2020

Characterization of extracellular polymeric substances from acidophilic microbial biofilms

scientific article

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

scientific article

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

scientific article

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

scientific article

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

scientific article

Condensing the omics fog of microbial communities.

scientific article

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

scientific article published on 01 September 2019

Correlative TEM/FISH Imaging of Microbial Communities

Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities

scientific article published on 22 August 2011

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

scientific article published on 15 December 2021

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

scholarly article by B.Y. Loulou Peisl et al published December 2017 in Analytica Chimica Acta

Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities

Dichloromethane Degradation Pathway from Unsequenced <i>Hyphomicrobium</i> sp. MC8b Rapidly Explored by Pan-Proteomics

scientific article published on 27 November 2020

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

scientific article

Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface

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

scientific article published in 2022

Expanding the use of spectral libraries in proteomics

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

scientific article published in Scientific Reports

Extensive transmission of microbes along the gastrointestinal tract

article

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

scientific article published in January 2018

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

scientific article published on 18 October 2017

Forecasting the dynamics of a complex microbial community using integrated meta-omics

scientific article published in January 2024

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

scientific article published on 03 May 2013

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

scientific article

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

scientific article

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

scientific article published on 20 April 2022

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

scientific article published in 2022

Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease

scientific article published on 6 April 2024

Human Gut Microbiome: Function Matters

scientific article

Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson′s disease

scientific article published on 30 December 2024

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

scientific article

IMP: a pipeline for reproducible metagenomic and metatranscriptomic analyses

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.

scientific article

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

scientific article published on 21 June 2016

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

scientific article published on 27 October 2015

Integrated in Vitro and in Silico Modelling Delineates the Molecular Effects of a Symbiotic Regimen on Colorectal Cancer-Derived Cells

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

scientific article

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

scientific article published on 10 October 2016

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

scientific article published on 12 February 2015

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

scientific article published on 19 October 2020

Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants

Lipid-based biofuel production from wastewater.

scientific article published on 23 April 2014

Measuring soil sustainability via soil resilience

scientific article published on 17 October 2017

Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

scientific article

Metabolome-proteome differentiation coupled to microbial divergence

scientific article

Metaproteomics provides functional insight into activated sludge wastewater treatment

scientific article

Metaproteomics: studying functional gene expression in microbial ecosystems

scientific article

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction

scientific article published on 01 April 2015

Microbial Community Proteomics

Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles

scientific article

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

scientific article published in 2021

Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T).

scientific article

Natural acidophilic biofilm communities reflect distinct organismal and functional organization

scientific article

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

scientific article published on 21 July 2017

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

scientific article published on 27 October 2020

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

scientific article published on 11 December 2024

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

scientific article published on 17 February 2021

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

scientific article published on 19 November 2020

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

scientific article published on 30 November 2015

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

scientific article

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

scientific article published on 26 June 2020

RNA in Circulation: Sources and Functions of Extracellular Exogenous RNA in the Blood

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

scientific article published on 21 January 2020

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

scientific article published on 02 November 2020

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

scientific article published on 19 September 2019

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

scientific article published on 01 January 2018

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

scientific article published in January 2013

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

scientific article

Sources and Functions of Extracellular Small RNAs in Human Circulation

scientific article

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

scientific article

Systems Biology of Acidophile Biofilms for Efficient Metal Extraction

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

scientific article published on 04 October 2018

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

article

The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms

scientific article published in September 2004

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

scientific article

The dynamic genetic repertoire of microbial communities

scientific article (publication date: 2009)

The extracellular RNA complement of Escherichia coli

scientific article

The gut microbial metabolite formate exacerbates colorectal cancer progression

scientific article published on 18 April 2022

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

scientific article published on 5 April 2016

The microbiome of cryospheric ecosystems

scientific article published on 01 January 2022

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

scientific article published on 26 August 2017

The sequential isolation of metabolites, RNA, DNA, and proteins from a single, undivided mixed microbial community sample

Three-Dimensional Analysis of Microbial Communities

Towards exposure of elusive metabolic mixed-culture processes: the application of metaproteomic analyses to activated sludge

Towards the Identification of Condition-Specific Microbial Populations from Human Metagenomic Data

Unification of functional annotation descriptions using text mining

scientific article published in 2021

Using metabolic networks to resolve ecological properties of microbiomes

scientific article published in April 2018

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

scientific article

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

scientific article published on 12 December 2018

List of works by Paul Wilmes

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

A biomolecular isolation framework for eco-systems biology.

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

A hundred years of activated sludge: time for a rethink

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

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

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

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

Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms

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

Building an International Consortium for Tracking Coronavirus Health Status

Building an international consortium for tracking coronavirus health status

Characterization of extracellular polymeric substances from acidophilic microbial biofilms

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal

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

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

Condensing the omics fog of microbial communities.

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

Correlative TEM/FISH Imaging of Microbial Communities

Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities

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

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

Deuterium-exchange metabolomics identifies N-methyl lyso phosphatidylethanolamines as abundant lipids in acidophilic mixed microbial communities

Dichloromethane Degradation Pathway from Unsequenced <i>Hyphomicrobium</i> sp. MC8b Rapidly Explored by Pan-Proteomics

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface

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

Expanding the use of spectral libraries in proteomics

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

Extensive transmission of microbes along the gastrointestinal tract

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

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

Forecasting the dynamics of a complex microbial community using integrated meta-omics

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

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

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

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

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

Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease

Human Gut Microbiome: Function Matters

Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson′s disease

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

IMP: a pipeline for reproducible metagenomic and metatranscriptomic analyses

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses.

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

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

Integrated in Vitro and in Silico Modelling Delineates the Molecular Effects of a Symbiotic Regimen on Colorectal Cancer-Derived Cells

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

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

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

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

Isolation of nucleic acids from low biomass samples: detection and removal of sRNA contaminants

Lipid-based biofuel production from wastewater.

Measuring soil sustainability via soil resilience

Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid.

Metabolome-proteome differentiation coupled to microbial divergence

Metaproteomics provides functional insight into activated sludge wastewater treatment

Metaproteomics: studying functional gene expression in microbial ecosystems

Method Optimization for Fecal Sample Collection and Fecal DNA Extraction

Microbial Community Proteomics

Microbial community proteomics: elucidating the catalysts and metabolic mechanisms that drive the Earth's biogeochemical cycles

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

Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilum(T).

Natural acidophilic biofilm communities reflect distinct organismal and functional organization

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

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

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

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

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

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

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

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

RNA in Circulation: Sources and Functions of Extracellular Exogenous RNA in the Blood

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

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

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

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

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