Paul Wilmes

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Integrated multi-omics for enhanced metaproteomics

Paul Wilmes, 2017 .

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

Emma L. Schymanski, Nancy C Baker, Antony J Williams, 2019, Environmental science. Processes & impacts.

Mantis: flexible and consensus-driven genome annotation

Paul Wilmes, Patrick May, Pedro Queirós, 2020, bioRxiv.

Multi-omics approach for microbial communities

Paul Wilmes, 2018 .

From meta-omics to microbial systems ecology: What to measure and what is there to learn?

Paul Wilmes, 2016 .

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

Piotr Gawron, Valentin Plugaru, Nikos Vlassis, 2015, Microbiome.

Expanding the Use of Spectral Libraries in Proteomics.

Johannes Griss, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2018, Journal of proteome research.

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

Paul Wilmes, Ran Friedman, Ansgar Poetsch, 2020, BMC Bioinformatics.

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

Paul Wilmes, Vanni Galli, Igor V. Pivkin, 2019, Biotechnology reports.

The promise and pitfalls of proteomic analyses in the environment

Paul Wilmes, Philip L. Bond, 2006 .

Short and long term road map for the development of a robust mechanistic and dynamic model of the MELiSSA C1 compartment based on microbial community characterization

Laurent Poughon, Christophe Lasseur, Kristel Bernaerts, 2016 .

From integrated multi-omics to causality: how to distil data, how to design experiments and how to conduct them

Paul Wilmes, 2017 .

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

Adam Zemla, Brian C. Thomas, Jillian F. Banfield, 2011, PLoS Comput. Biol..

From integrated omics to causality: how to close the loop

Paul Wilmes, 2015 .

Metaproteomics and integrated multi-omics: highlighting unknowns

Paul Wilmes, 2017 .

From integrated multi-omics to microbial systems ecology: quo vadis?

Paul Wilmes, 2017 .

From meta-omics to microbial systems ecology: What can we learn?

Paul Wilmes, 2016 .

Integration of meta-omics data: approaches and applications

Paul Wilmes, 2016 .

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

Francesco Bongiovanni, Fintan McGee, Bertjan Broeksema, 2017, BMC Bioinformatics.

The integration of quantitative big data from microbial consortia: what is there to gain?

Paul Wilmes, 2018 .

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

Paul Wilmes, Frederic Zenhausern, Marc Mac Giolla Eain, 2017 .

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

Paul Wilmes, Anna Heintz-Buschart, A. Heintz‐Buschart, 2013, Methods in enzymology.

Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms

Paul Wilmes, Vanni Galli, Igor V. Pivkin, 2018, Applied and Environmental Microbiology.

Metaproteomics: studying functional gene expression in microbial ecosystems.

Paul Wilmes, Philip L Bond, P. Wilmes, 2006, Trends in microbiology.

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

Paul Wilmes, Philip L. Bond, A. Heintz‐Buschart, 2015, Proteomics.

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

Eugen Bauer, Ines Thiele, Paul Wilmes, 2015, Microbiome.

Extensive transmission of microbes along the gastrointestinal tract

Peer Bork, Shinichi Sunagawa, Paul Wilmes, 2019, eLife.

Alignment-free Visualization of Metagenomic Data by Nonlinear Dimension Reduction

Paul Wilmes, Nikos Vlassis, Nicolás Pinel, 2014, Scientific Reports.

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

Paul Wilmes, Thomas Sauter, Patrick May, 2015, npj Biofilms and Microbiomes.

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

Ronan M. T. Fleming, Eugen Bauer, Ines Thiele, 2016, Nature Biotechnology.

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

Paul Wilmes, Shaman Narayanasamy, P. Wilmes, 2015, Microbial biotechnology.

RNA in circulation: sources and functions of extracellular exogenous RNA in blood

David J. Galas, Paul Wilmes, P. Wilmes, 2014 .

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

Matej Oresic, Hedi Peterson, Casey S. Greene, 2020, Nature Medicine.

Human Gut Microbiome: Function Matters.

Paul Wilmes, Anna Heintz-Buschart, A. Heintz‐Buschart, 2017, Trends in microbiology.

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

Nitin S. Baliga, Paul Wilmes, Patrick May, 2014, Nature Communications.

Metaproteomics Provides Functional Insight into Activated Sludge Wastewater Treatment

Paul Wilmes, Philip L. Bond, P. Wilmes, 2008, PloS one.

Microbiome in Colorectal Cancer: How to Get from Meta-omics to Mechanism?: (Trends in Microbiology 28, 401-423; 2020).

Paul Wilmes, Serge Haan, Dominik Ternes, 2020, Trends in microbiology.

A biomolecular isolation framework for eco-systems biology

Paul Wilmes, Jenny Renaut, Karsten Hiller, 2012, The ISME Journal.

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

Paul Wilmes, Enrico Glaab, Frederic Zenhausern, 2016, Nature Communications.

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

Paul Wilmes, Pranjul Shah, J. Schneider, 2013, Microbiome.

The dynamic genetic repertoire of microbial communities

Paul Wilmes, Jillian F Banfield, J. Banfield, 2009, FEMS microbiology reviews.

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

Paul Wilmes, Serge Haan, P. Wilmes, 2020, Trends in microbiology.

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

Vincent J. Denef, Paul Wilmes, Ryan S. Mueller, 2010, Proceedings of the National Academy of Sciences.