Search Results - "Muth, Thilo"

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

“…One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However,…”
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A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane by Schiebenhoefer, Henning, Schallert, Kay, Renard, Bernhard Y., Trappe, Kathrin, Schmid, Emanuel, Benndorf, Dirk, Riedel, Katharina, Muth, Thilo, Fuchs, Stephan

“…Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial…”
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Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows by Van Den Bossche, Tim, Kunath, Benoit J., Schallert, Kay, Schäpe, Stephanie S., Abraham, Paul E., Armengaud, Jean, Arntzen, Magnus Ø., Bassignani, Ariane, Benndorf, Dirk, Fuchs, Stephan, Giannone, Richard J., Griffin, Timothy J., Hagen, Live H., Halder, Rashi, Henry, Céline, Hettich, Robert L., Heyer, Robert, Jagtap, Pratik, Jehmlich, Nico, Jensen, Marlene, Juste, Catherine, Kleiner, Manuel, Langella, Olivier, Lehmann, Theresa, Leith, Emma, May, Patrick, Mesuere, Bart, Miotello, Guylaine, Peters, Samantha L., Pible, Olivier, Queiros, Pedro T., Reichl, Udo, Renard, Bernhard Y., Schiebenhoefer, Henning, Sczyrba, Alexander, Tanca, Alessandro, Trappe, Kathrin, Trezzi, Jean-Pierre, Uzzau, Sergio, Verschaffelt, Pieter, von Bergen, Martin, Wilmes, Paul, Wolf, Maximilian, Martens, Lennart, Muth, Thilo

“…Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available,…”
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Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins by Pech, Sabine, Rehberg, Markus, Janke, Robert, Benndorf, Dirk, Genzel, Yvonne, Muth, Thilo, Sickmann, Albert, Rapp, Erdmann, Reichl, Udo

“…Adaptations of animal cells to growth in suspension culture concern in particular viral vaccine production, where very specific aspects of virus-host cell…”
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A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer by Heyer, Robert, Schallert, Kay, Büdel, Anja, Zoun, Roman, Dorl, Sebastian, Behne, Alexander, Kohrs, Fabian, Püttker, Sebastian, Siewert, Corina, Muth, Thilo, Saake, Gunter, Reichl, Udo, Benndorf, Dirk

“…The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and…”
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Survey of metaproteomics software tools for functional microbiome analysis by Sajulga, Ray, Easterly, Caleb, Riffle, Michael, Mesuere, Bart, Muth, Thilo, Mehta, Subina, Kumar, Praveen, Johnson, James, Gruening, Bjoern Andreas, Schiebenhoefer, Henning, Kolmeder, Carolin A, Fuchs, Stephan, Nunn, Brook L, Rudney, Joel, Griffin, Timothy J, Jagtap, Pratik D

“…To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be…”
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Comparative Performance of Four Methods for High-throughput Glycosylation Analysis of Immunoglobulin G in Genetic and Epidemiological Research by Huffman, Jennifer E., Pučić-Baković, Maja, Klarić, Lucija, Hennig, René, Selman, Maurice H.J., Vučković, Frano, Novokmet, Mislav, Krištić, Jasminka, Borowiak, Matthias, Muth, Thilo, Polašek, Ozren, Razdorov, Genadij, Gornik, Olga, Plomp, Rosina, Theodoratou, Evropi, Wright, Alan F., Rudan, Igor, Hayward, Caroline, Campbell, Harry, Deelder, André M., Reichl, Udo, Aulchenko, Yurii S., Rapp, Erdmann, Wuhrer, Manfred, Lauc, Gordan

“…The biological and clinical relevance of glycosylation is becoming increasingly recognized, leading to a growing interest in large-scale clinical and…”
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DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra by Muth, Thilo, Weilnböck, Lisa, Rapp, Erdmann, Huber, Christian G, Martens, Lennart, Vaudel, Marc, Barsnes, Harald

“…De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence…”
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The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes by Van Den Bossche, Tim, Arntzen, Magnus Ø, Becher, Dörte, Benndorf, Dirk, Eijsink, Vincent G H, Henry, Céline, Jagtap, Pratik D, Jehmlich, Nico, Juste, Catherine, Kunath, Benoit J, Mesuere, Bart, Muth, Thilo, Pope, Phillip B, Seifert, Jana, Tanca, Alessandro, Uzzau, Sergio, Wilmes, Paul, Hettich, Robert L, Armengaud, Jean

“…Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The…”
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Colonic metaproteomic signatures of active bacteria and the host in obesity by Kolmeder, Carolin A., Ritari, Jarmo, Verdam, Froukje J., Muth, Thilo, Keskitalo, Salla, Varjosalo, Markku, Fuentes, Susana, Greve, Jan Willem, Buurman, Wim A., Reichl, Udo, Rapp, Erdmann, Martens, Lennart, Palva, Airi, Salonen, Anne, Rensen, Sander S., de Vos, Willem M.

“…Obesity is associated with the intestinal microbiota in humans but the underlying mechanisms are yet to be fully understood. Our previous phylogenetic study…”
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The Intersection Between Semantic Web and Materials Science by Valdestilhas, Andre, Bayerlein, Bernd, Moreno Torres, Benjamin, Zia, Ghezal Ahmad Jan, Muth, Thilo

“…The application and benefits of Semantic Web Technologies (SWT) for managing, sharing, and (re‐)using of research data are demonstrated in implementations in…”
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Editorial for Special Issue: Metaproteomics by Seifert, Jana, Muth, Thilo

“…As the proteome-level counterpart of metagenomics, metaproteomics extends conventional single-organism proteomics and allows researchers to characterize the…”
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Ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides by Altenburg, Tom, Giese, Sven H., Wang, Shengbo, Muth, Thilo, Renard, Bernhard Y.

“…Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of living cells on a molecular level. Currently, only a few deep…”
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Purple: A Computational Workflow for Strategic Selection of Peptides for Viral Diagnostics Using MS-Based Targeted Proteomics by Lechner, Johanna, Hartkopf, Felix, Hiort, Pauline, Nitsche, Andreas, Grossegesse, Marica, Doellinger, Joerg, Renard, Bernhard Y, Muth, Thilo

“…Emerging virus diseases present a global threat to public health. To detect viral pathogens in time-critical scenarios, accurate and fast diagnostic assays are…”
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Metaproteogenomic analysis of saliva samples from Parkinson’s disease patients with cognitive impairment by Arıkan, Muzaffer, Demir, Tuğçe Kahraman, Yıldız, Zeynep, Nalbantoğlu, Özkan Ufuk, Korkmaz, Nur Damla, Yılmaz, Nesrin H., Şen, Aysu, Özcan, Mutlu, Muth, Thilo, Hanoğlu, Lütfü, Yıldırım, Süleyman

“…Cognitive impairment (CI) is very common in patients with Parkinson’s Disease (PD) and progressively develops on a spectrum from mild cognitive impairment…”
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An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved] by Anzt, Hartwig, Bach, Felix, Druskat, Stephan, Löffler, Frank, Loewe, Axel, Renard, Bernhard Y, Seemann, Gunnar, Struck, Alexander, Achhammer, Elke, Aggarwal, Piush, Appel, Franziska, Bader, Michael, Brusch, Lutz, Busse, Christian, Chourdakis, Gerasimos, Dabrowski, Piotr Wojciech, Ebert, Peter, Flemisch, Bernd, Friedl, Sven, Fritzsch, Bernadette, Funk, Maximilian D, Gast, Volker, Goth, Florian, Grad, Jean-Noël, Hegewald, Jan, Hermann, Sibylle, Hohmann, Florian, Janosch, Stephan, Kutra, Dominik, Linxweiler, Jan, Muth, Thilo, Peters-Kottig, Wolfgang, Rack, Fabian, Raters, Fabian H.C, Rave, Stephan, Reina, Guido, Reißig, Malte, Ropinski, Timo, Schaarschmidt, Joerg, Seibold, Heidi, Thiele, Jan P, Uekermann, Benjamin, Unger, Stefan, Weeber, Rudolf

“…Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research…”
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MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour by Tscheuschner, Georg, Kaiser, Melanie N, Lisec, Jan, Beslic, Denis, Muth, Thilo, Krüger, Maren, Mages, Hans Werner, Dorner, Brigitte G, Knospe, Julia, Schenk, Jörg A, Sellrie, Frank, Weller, Michael G

“…During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the…”
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Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework by Blank, Clemens, Easterly, Caleb, Gruening, Bjoern, Johnson, James, Kolmeder, Carolin A, Kumar, Praveen, May, Damon, Mehta, Subina, Mesuere, Bart, Brown, Zachary, Elias, Joshua E, Hervey, W Judson, McGowan, Thomas, Muth, Thilo, Nunn, Brook, Rudney, Joel, Tanca, Alessandro, Griffin, Timothy J, Jagtap, Pratik D

“…The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated…”
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gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes by Arikan, Muzaffer, Muth, Thilo

“…Abstract Background In recent years, omics technologies have offered an exceptional chance to gain a deeper insight into the structural and functional…”
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Bioinformatic Workflows for Metaproteomics by Holstein, Tanja, Muth, Thilo

“…The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques…”
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