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Thilo Muth - Publications

Affiliations: 
Max Planck Institute Magdeburg 
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Russo FF, Nowatzky Y, Jaeger C, Parr MK, Benner P, Muth T, Lisec J. Machine learning methods for compound annotation in non-targeted mass spectrometry-A brief overview of fingerprinting, in silico fragmentation and de novo methods. Rapid Communications in Mass Spectrometry : Rcm. 38: e9876. PMID 39180507 DOI: 10.1002/rcm.9876  0.301
2024 Arikan M, Muth T. gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes. Gigascience. 13. PMID 38995144 DOI: 10.1093/gigascience/giae038  0.351
2024 Holstein T, Muth T. Bioinformatic Workflows for Metaproteomics. Methods in Molecular Biology (Clifton, N.J.). 2820: 187-213. PMID 38941024 DOI: 10.1007/978-1-0716-3910-8_16  0.333
2023 Holstein T, Kistner F, Martens L, Muth T. PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores. Bioinformatics (Oxford, England). 39. PMID 37129543 DOI: 10.1093/bioinformatics/btad289  0.517
2021 Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, et al. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome. 9: 243. PMID 34930457 DOI: 10.1186/s40168-021-01176-w  0.7
2021 Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, ... ... Muth T, et al. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nature Communications. 12: 7305. PMID 34911965 DOI: 10.1038/s41467-021-27542-8  0.751
2020 Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T. Erratum: gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Nar Genomics and Bioinformatics. 2: lqaa083. PMID 33577626 DOI: 10.1093/nargab/lqaa083  0.676
2020 Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T. gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. Nar Genomics and Bioinformatics. 2: lqaa058. PMID 33575609 DOI: 10.1093/nargab/lqaa058  0.731
2020 Anzt H, Bach F, Druskat S, Löffler F, Loewe A, Renard BY, Seemann G, Struck A, Achhammer E, Aggarwal P, Appel F, Bader M, Brusch L, Busse C, Chourdakis G, ... ... Muth T, et al. An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action. F1000research. 9: 295. PMID 33552475 DOI: 10.12688/F1000Research.23224.1  0.304
2020 Sajulga R, Easterly C, Riffle M, Mesuere B, Muth T, Mehta S, Kumar P, Johnson J, Gruening BA, Schiebenhoefer H, Kolmeder CA, Fuchs S, Nunn BL, Rudney J, Griffin TJ, et al. Survey of metaproteomics software tools for functional microbiome analysis. Plos One. 15: e0241503. PMID 33170893 DOI: 10.1371/journal.pone.0241503  0.373
2020 Schiebenhoefer H, Schallert K, Renard BY, Trappe K, Schmid E, Benndorf D, Riedel K, Muth T, Fuchs S. A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. Nature Protocols. PMID 32859984 DOI: 10.1038/S41596-020-0368-7  0.533
2020 Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, Muth T. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis. Journal of Proteome Research. PMID 32431147 DOI: 10.1021/Acs.Jproteome.0C00136  0.756
2020 Kuhring M, Doellinger J, Nitsche A, Muth T, Renard BY. TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples. Journal of Proteome Research. PMID 32362126 DOI: 10.1021/Acs.Jproteome.9B00714  0.459
2019 Heyer R, Schallert K, Büdel A, Zoun R, Dorl S, Behne A, Kohrs F, Püttker S, Siewert C, Muth T, Saake G, Reichl U, Benndorf D. A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer. Frontiers in Microbiology. 10: 1883. PMID 31474963 DOI: 10.3389/Fmicb.2019.01883  0.428
2019 Lechner J, Hartkopf F, Hiort P, Nitsche A, Grossegesse M, Doellinger J, Renard BY, Muth T. Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics. Viruses. 11. PMID 31181768 DOI: 10.3390/V11060536  0.38
2019 Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Review of Proteomics. PMID 31002542 DOI: 10.1080/14789450.2019.1609944  0.783
2019 Fischer M, Muth T, Renard BY. Peptide-to-Protein Summarization: An Important Step for Accurate Quantification in Label-Based Proteomics. Methods in Molecular Biology (Clifton, N.J.). 1977: 159-180. PMID 30980328 DOI: 10.1007/978-1-4939-9232-4_11  0.404
2019 Seifert J, Muth T. Editorial for Special Issue: Metaproteomics. Proteomes. 7. PMID 30841491 DOI: 10.3390/Proteomes7010009  0.358
2018 Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come - Current Tools, Recent Use Cases, and Future Avenues for de novo Sequencing in Proteomics. Proteomics. e1700150. PMID 29968278 DOI: 10.1002/Pmic.201700150  0.681
2018 Blank C, Easterly C, Gruening B, Johnson J, Kolmeder CA, Kumar P, May D, Mehta S, Mesuere B, Brown Z, Elias JE, Hervey WJ, McGowan T, Muth T, Nunn B, et al. Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework. Proteomes. 6. PMID 29385081 DOI: 10.3390/Proteomes6010007  0.424
2018 Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY. MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go. Analytical Chemistry. 90: 685-689. PMID 29215871 DOI: 10.1021/Acs.Analchem.7B03544  0.642
2017 Muth T, Renard BY. Evaluating de novo sequencing in proteomics: already an accurate alternative to database-driven peptide identification? Briefings in Bioinformatics. PMID 28369237 DOI: 10.1093/Bib/Bbx033  0.459
2016 Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics. Advances in Experimental Medicine and Biology. 919: 217-226. PMID 27975219 DOI: 10.1007/978-3-319-41448-5_10  0.769
2016 Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S. The impact of sequence database choice on metaproteomic results in gut microbiota studies. Microbiome. 4: 51. PMID 27671352 DOI: 10.1186/S40168-016-0196-8  0.603
2016 Muth T, Renard BY, Martens L. Metaproteomic data analysis at a glance: advances in computational microbial community proteomics. Expert Review of Proteomics. PMID 27376173 DOI: 10.1080/14789450.2016.1209418  0.562
2015 Kolmeder CA, Ritari J, Verdam FJ, Muth T, Keskitalo S, Varjosalo M, Fuentes S, Greve JW, Buurman WA, Reichl U, Rapp E, Martens L, Palva A, Salonen A, Rensen SS, et al. Colonic metaproteomic signatures of active bacteria and the host in obesity. Proteomics. PMID 26255997 DOI: 10.1002/Pmic.201500049  0.56
2015 Muth T, Kolmeder CA, Salojärvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, Martens L. Navigating through metaproteomics data: A logbook of database searching. Proteomics. PMID 25778831 DOI: 10.1002/Pmic.201400560  0.624
2015 Muth T, Behne A, Heyer R, Kohrs F, Benndorf D, Hoffmann M, Lehtevä M, Reichl U, Martens L, Rapp E. The MetaProteomeAnalyzer: a powerful open-source software suite for metaproteomics data analysis and interpretation. Journal of Proteome Research. 14: 1557-65. PMID 25660940 DOI: 10.1021/Pr501246W  0.664
2015 Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H. Viewing the proteome: how to visualize proteomics data? Proteomics. 15: 1341-55. PMID 25504833 DOI: 10.1002/Pmic.201400412  0.72
2014 Huffman JE, Pučić-Baković M, Klarić L, Hennig R, Selman MH, Vučković F, Novokmet M, KriÅ¡tić J, Borowiak M, Muth T, PolaÅ¡ek O, Razdorov G, Gornik O, Plomp R, Theodoratou E, et al. Comparative performance of four methods for high-throughput glycosylation analysis of immunoglobulin G in genetic and epidemiological research. Molecular & Cellular Proteomics : McP. 13: 1598-610. PMID 24719452 DOI: 10.1074/Mcp.M113.037465  0.367
2014 Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U. Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants Anaerobe. 29: 59-67. PMID 24309213 DOI: 10.1016/J.Anaerobe.2013.11.009  0.459
2014 Muth T, Weilnböck L, Rapp E, Huber CG, Martens L, Vaudel M, Barsnes H. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra. Journal of Proteome Research. 13: 1143-6. PMID 24295440 DOI: 10.1021/Pr4008078  0.77
2013 Behne A, Muth T, Borowiak M, Reichl U, Rapp E. glyXalign: high-throughput migration time alignment preprocessing of electrophoretic data retrieved via multiplexed capillary gel electrophoresis with laser-induced fluorescence detection-based glycoprofiling. Electrophoresis. 34: 2311-5. PMID 23637070 DOI: 10.1002/Elps.201200696  0.424
2013 Muth T, Peters J, Blackburn J, Rapp E, Martens L. Proteocloud: A full-featured open source proteomics cloud computing pipeline Journal of Proteomics. 88: 104-108. PMID 23305951 DOI: 10.1016/J.Jprot.2012.12.026  0.587
2013 Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: Challenges in metaproteomics data analysis Molecular Biosystems. 9: 578-585. PMID 23238088 DOI: 10.1039/C2Mb25415H  0.643
2012 Muth T, García-Martín JA, Rausell A, Juan D, Valencia A, Pazos F. JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics (Oxford, England). 28: 584-6. PMID 22171333 DOI: 10.1093/Bioinformatics/Btr688  0.369
2010 Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A. XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results. Proteomics. 10: 1522-4. PMID 20140905 DOI: 10.1002/Pmic.200900759  0.774
2010 Muth T, Keller D, Puetz SM, Martens L, Sickmann A, Boehm AM. jTraqX: a free, platform independent tool for isobaric tag quantitation at the protein level. Proteomics. 10: 1223-5. PMID 20058250 DOI: 10.1002/Pmic.200900374  0.615
2010 Helsens K, Colaert N, Barsnes H, Muth T, Flikka K, Staes A, Timmerman E, Wortelkamp S, Sickmann A, Vandekerckhove J, Gevaert K, Martens L. ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics. 10: 1261-4. PMID 20058248 DOI: 10.1002/Pmic.200900409  0.704
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