| Year |
Citation |
Score |
| 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 |
0.519 |
|
| 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 |
0.712 |
|
| 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 |
0.758 |
|
| 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 |
0.689 |
|
| 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 |
0.741 |
|
| 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 |
0.374 |
|
| 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 |
0.755 |
|
| 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 |
0.458 |
|
| 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 |
0.429 |
|
| 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 |
0.788 |
|
| 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 |
0.403 |
|
| 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 |
0.684 |
|
| 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 |
0.425 |
|
| 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 |
0.643 |
|
| 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 |
0.77 |
|
| 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 |
0.605 |
|
| 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 |
0.565 |
|
| 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 |
0.561 |
|
| 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 |
0.665 |
|
| 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 |
0.721 |
|
| 2014 |
Huffman JE, PuÄić-Baković M, Klarić L, Hennig R, Selman MH, VuÄković 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 |
0.366 |
|
| 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 |
0.457 |
|
| 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 |
0.772 |
|
| 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 |
0.588 |
|
| 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 |
0.645 |
|
| 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 |
0.776 |
|
| 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 |
0.616 |
|
| 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 |
0.706 |
|
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