Publications by authors named "Thilo Muth"

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From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.
Thilo Muth, Roger Karlsson, Yi-Kuo Yu, Gelio Alves

J Proteome Res· November 2025

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Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing.
Tim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck, Tomi Suomi, Tanja Holstein, Thilo Muth

Proteomics· September 2025

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MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.
Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth

J Proteome Res· June 2025

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FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events.
Yannek Nowatzky, Francesco Friedrich Russo, Jan Lisec, Alexander Kister, Knut Reinert, Thilo Muth

Nat Commun· March 2025

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Machine learning methods for compound annotation in non-targeted mass spectrometry-A brief overview of fingerprinting, in silico fragmentation and de novo methods.
Francesco F Russo, Yannek Nowatzky, Carsten Jaeger, Maria K Parr, Phillipp Benner, Thilo Muth

Rapid Commun Mass Spectrom· October 2024

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Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.
Franziska Singer, Mathias Kuhring, Bernhard Y Renard, Thilo Muth

Methods Mol Biol· October 2024

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Bioinformatic Workflows for Metaproteomics.
Tanja Holstein, Thilo Muth

Methods Mol Biol· June 2024

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gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes.
Muzaffer Arikan, Thilo Muth

Gigascience· January 2024

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Metaproteogenomic analysis of saliva samples from Parkinson's disease patients with cognitive impairment.
Muzaffer Arıkan, Tuğçe Kahraman Demir, Zeynep Yıldız, Özkan Ufuk Nalbantoğlu, Nur Damla Korkmaz, Thilo Muth

NPJ Biofilms Microbiomes· November 2023

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Integrated multi-omics analyses of microbial communities: a review of the current state and future directions.
Muzaffer Arıkan, Thilo Muth

Mol Omics· September 2023

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The importance of graph databases and graph learning for clinical applications.
Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth, David Broneske

Database (Oxford)· July 2023

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Mistle: bringing spectral library predictions to metaproteomics with an efficient search index.
Yannek Nowatzky, Philipp Benner, Knut Reinert, Thilo Muth

Bioinformatics· June 2023

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PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.
Tanja Holstein, Franziska Kistner, Lennart Martens, Thilo Muth

Bioinformatics· May 2023

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Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly.
Denis Beslic, Georg Tscheuschner, Bernhard Y Renard, Michael G Weller, Thilo Muth

Brief Bioinform· January 2023

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MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour.
Georg Tscheuschner, Melanie N Kaiser, Jan Lisec, Denis Beslic, Thilo Muth

Antibodies (Basel)· April 2022

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Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.
Tim Van Den Bossche, Benoit J Kunath, Kay Schallert, Stephanie S Schäpe, Paul E Abraham, Thilo Muth

Nat Commun· December 2021

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The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes.
Tim Van Den Bossche, Magnus Ø Arntzen, Dörte Becher, Dirk Benndorf, Vincent G H Eijsink, Thilo Muth

Microbiome· December 2021

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An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action.
Hartwig Anzt, Felix Bach, Stephan Druskat, Frank Löffler, Axel Loewe, Thilo Muth

F1000Res· March 2021

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Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins.
Sabine Pech, Markus Rehberg, Robert Janke, Dirk Benndorf, Yvonne Genzel, Thilo Muth

Appl Microbiol Biotechnol· March 2021

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Survey of metaproteomics software tools for functional microbiome analysis.
Ray Sajulga, Caleb Easterly, Michael Riffle, Bart Mesuere, Thilo Muth

PLoS One· December 2020

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Erratum: gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.
Maria Muñoz-Benavent, Felix Hartkopf, Tim Van Den Bossche, Vitor C Piro, Carlos García-Ferris, Thilo Muth

NAR Genom Bioinform· December 2020

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Perspective on Proteomics for Virus Detection in Clinical Samples.
Marica Grossegesse, Felix Hartkopf, Andreas Nitsche, Lars Schaade, Joerg Doellinger, Thilo Muth

J Proteome Res· November 2020

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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.
Henning Schiebenhoefer, Kay Schallert, Bernhard Y Renard, Kathrin Trappe, Emanuel Schmid, Thilo Muth

Nat Protoc· October 2020

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gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.
Maria Muñoz-Benavent, Felix Hartkopf, Tim Van Den Bossche, Vitor C Piro, Carlos García-Ferris, Thilo Muth

NAR Genom Bioinform· September 2020

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Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis.
Tim Van Den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Thilo Muth

J Proteome Res· August 2020

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