Search Results - "Samaras, Patroklos"

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning by Gessulat, Siegfried, Schmidt, Tobias, Zolg, Daniel Paul, Samaras, Patroklos, Schnatbaum, Karsten, Zerweck, Johannes, Knaute, Tobias, Rechenberger, Julia, Delanghe, Bernard, Huhmer, Andreas, Reimer, Ulf, Ehrlich, Hans-Christian, Aiche, Stephan, Kuster, Bernhard, Wilhelm, Mathias

“…In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral…”
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Mass-spectrometry-based draft of the Arabidopsis proteome by Mergner, Julia, Frejno, Martin, List, Markus, Papacek, Michael, Chen, Xia, Chaudhary, Ajeet, Samaras, Patroklos, Richter, Sandra, Shikata, Hiromasa, Messerer, Maxim, Lang, Daniel, Altmann, Stefan, Cyprys, Philipp, Zolg, Daniel P., Mathieson, Toby, Bantscheff, Marcus, Hazarika, Rashmi R., Schmidt, Tobias, Dawid, Corinna, Dunkel, Andreas, Hofmann, Thomas, Sprunck, Stefanie, Falter-Braun, Pascal, Johannes, Frank, Mayer, Klaus F. X., Jürgens, Gerd, Wilhelm, Mathias, Baumbach, Jan, Grill, Erwin, Schneitz, Kay, Schwechheimer, Claus, Kuster, Bernhard

“…Plants are essential for life and are extremely diverse organisms with unique molecular capabilities 1 . Here we present a quantitative atlas of the…”
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The emerging landscape of single-molecule protein sequencing technologies by Alfaro, Javier Antonio, Bohländer, Peggy, Dai, Mingjie, Filius, Mike, Howard, Cecil J., van Kooten, Xander F., Ohayon, Shilo, Pomorski, Adam, Schmid, Sonja, Aksimentiev, Aleksei, Anslyn, Eric V., Bedran, Georges, Cao, Chan, Chinappi, Mauro, Coyaud, Etienne, Dekker, Cees, Dittmar, Gunnar, Drachman, Nicholas, Eelkema, Rienk, Goodlett, David, Hentz, Sébastien, Kalathiya, Umesh, Kelleher, Neil L., Kelly, Ryan T., Kelman, Zvi, Kim, Sung Hyun, Kuster, Bernhard, Rodriguez-Larrea, David, Lindsay, Stuart, Maglia, Giovanni, Marcotte, Edward M., Marino, John P., Masselon, Christophe, Mayer, Michael, Samaras, Patroklos, Sarthak, Kumar, Sepiashvili, Lusia, Stein, Derek, Wanunu, Meni, Wilhelm, Mathias, Yin, Peng, Meller, Amit, Joo, Chirlmin

“…Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at…”
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Proteome activity landscapes of tumor cell lines determine drug responses by Frejno, Martin, Meng, Chen, Ruprecht, Benjamin, Oellerich, Thomas, Scheich, Sebastian, Kleigrewe, Karin, Drecoll, Enken, Samaras, Patroklos, Hogrebe, Alexander, Helm, Dominic, Mergner, Julia, Zecha, Jana, Heinzlmeir, Stephanie, Wilhelm, Mathias, Dorn, Julia, Kvasnicka, Hans-Michael, Serve, Hubert, Weichert, Wilko, Kuster, Bernhard

“…Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular…”
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Meltome atlas—thermal proteome stability across the tree of life by Jarzab, Anna, Kurzawa, Nils, Hopf, Thomas, Moerch, Matthias, Zecha, Jana, Leijten, Niels, Bian, Yangyang, Musiol, Eva, Maschberger, Melanie, Stoehr, Gabriele, Becher, Isabelle, Daly, Charlotte, Samaras, Patroklos, Mergner, Julia, Spanier, Britta, Angelov, Angel, Werner, Thilo, Bantscheff, Marcus, Wilhelm, Mathias, Klingenspor, Martin, Lemeer, Simone, Liebl, Wolfgang, Hahne, Hannes, Savitski, Mikhail M., Kuster, Bernhard

“…We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from…”
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Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics by Zecha, Jana, Meng, Chen, Zolg, Daniel Paul, Samaras, Patroklos, Wilhelm, Mathias, Kuster, Bernhard

“…The coordination of protein synthesis and degradation regulating protein abundance is a fundamental process in cellular homeostasis. Today, mass…”
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ProteomicsDB: toward a FAIR open-source resource for life-science research by Lautenbacher, Ludwig, Samaras, Patroklos, Muller, Julian, Grafberger, Andreas, Shraideh, Marwin, Rank, Johannes, Fuchs, Simon T, Schmidt, Tobias K, The, Matthew, Dallago, Christian, Wittges, Holger, Rost, Burkhard, Krcmar, Helmut, Kuster, Bernhard, Wilhelm, Mathias

“…Abstract ProteomicsDB (https://www.ProteomicsDB.org) is a multi-omics and multi-organism resource for life science research. In this update, we present our…”
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A proteomics sample metadata representation for multiomics integration and big data analysis by Dai, Chengxin, Füllgrabe, Anja, Pfeuffer, Julianus, Solovyeva, Elizaveta M., Deng, Jingwen, Moreno, Pablo, Kamatchinathan, Selvakumar, Kundu, Deepti Jaiswal, George, Nancy, Fexova, Silvie, Grüning, Björn, Föll, Melanie Christine, Griss, Johannes, Vaudel, Marc, Audain, Enrique, Locard-Paulet, Marie, Turewicz, Michael, Eisenacher, Martin, Uszkoreit, Julian, Van Den Bossche, Tim, Schwämmle, Veit, Webel, Henry, Schulze, Stefan, Bouyssié, David, Jayaram, Savita, Duggineni, Vinay Kumar, Samaras, Patroklos, Wilhelm, Mathias, Choi, Meena, Wang, Mingxun, Kohlbacher, Oliver, Brazma, Alvis, Papatheodorou, Irene, Bandeira, Nuno, Deutsch, Eric W., Vizcaíno, Juan Antonio, Bai, Mingze, Sachsenberg, Timo, Levitsky, Lev I., Perez-Riverol, Yasset

“…The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the…”
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High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development by Krumm, Johannes, Sekine, Keisuke, Samaras, Patroklos, Brazovskaja, Agnieska, Breunig, Markus, Yasui, Ryota, Kleger, Alexander, Taniguchi, Hideki, Wilhelm, Mathias, Treutlein, Barbara, Camp, J. Gray, Kuster, Bernhard

“…Primary human hepatocytes are widely used to evaluate liver toxicity of drugs, but they are scarce and demanding to culture. Stem cell-derived hepatocytes are…”
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Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics by Wilhelm, Mathias, Zolg, Daniel P., Graber, Michael, Gessulat, Siegfried, Schmidt, Tobias, Schnatbaum, Karsten, Schwencke-Westphal, Celina, Seifert, Philipp, de Andrade Krätzig, Niklas, Zerweck, Johannes, Knaute, Tobias, Bräunlein, Eva, Samaras, Patroklos, Lautenbacher, Ludwig, Klaeger, Susan, Wenschuh, Holger, Rad, Roland, Delanghe, Bernard, Huhmer, Andreas, Carr, Steven A., Clauser, Karl R., Krackhardt, Angela M., Reimer, Ulf, Kuster, Bernhard

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Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae by Rechenberger, Julia, Samaras, Patroklos, Jarzab, Anna, Behr, Juergen, Frejno, Martin, Djukovic, Ana, Sanz, Jaime, González-Barberá, Eva M, Salavert, Miguel, López-Hontangas, Jose Luis, Xavier, Karina B, Debrauwer, Laurent, Rolain, Jean-Marc, Sanz, Miguel, Garcia-Garcera, Marc, Wilhelm, Mathias, Ubeda, Carles, Kuster, Bernhard

“…The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting…”
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Proceedings of the EuBIC-MS 2020 Developers’ Meeting by Ashwood, Christopher, Bittremieux, Wout, Deutsch, Eric W., Doncheva, Nadezhda T., Dorfer, Viktoria, Gabriels, Ralf, Gorshkov, Vladimir, Gupta, Surya, Jones, Andrew R., Käll, Lukas, Kopczynski, Dominik, Lane, Lydie, Lautenbacher, Ludwig, Legeay, Marc, Locard-Paulet, Marie, Mesuere, Bart, Perez-Riverol, Yasset, Netz, Eugen, Pfeuffer, Julianus, Sachsenberg, Timo, Salz, Renee, Samaras, Patroklos, Schiebenhoefer, Henning, Schmidt, Tobias, Schwämmle, Veit, Soggiu, Alessio, Uszkoreit, Julian, Van Den Bossche, Tim, Van Puyvelde, Bart, Van Strien, Joeri, Verschaffelt, Pieter, Webel, Henry, Willems, Sander

“…The 2020 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers’ meeting was held from January 13th to January 17th 2020 in Nyborg,…”
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Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups by The, Matthew, Samaras, Patroklos, Kuster, Bernhard, Wilhelm, Mathias

“…Estimating false discovery rates (FDRs) of protein identification continues to be an important topic in mass spectrometry–based proteomics, particularly when…”
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ProteomicsDB by Schmidt, Tobias, Samaras, Patroklos, Frejno, Martin, Gessulat, Siegfried, Barnert, Maximilian, Kienegger, Harald, Krcmar, Helmut, Schlegl, Judith, Ehrlich, Hans-Christian, Aiche, Stephan, Kuster, Bernhard, Wilhelm, Mathias

“…Abstract ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass…”
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ProteomicsDB: a multi-omics and multi-organism resource for life science research by Samaras, Patroklos, Schmidt, Tobias, Frejno, Martin, Gessulat, Siegfried, Reinecke, Maria, Jarzab, Anna, Zecha, Jana, Mergner, Julia, Giansanti, Piero, Ehrlich, Hans-Christian, Aiche, Stephan, Rank, Johannes, Kienegger, Harald, Krcmar, Helmut, Kuster, Bernhard, Wilhelm, Mathias

“…Abstract ProteomicsDB (https://www.ProteomicsDB.org) started as a protein-centric in-memory database for the exploration of large collections of quantitative…”
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Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison by Schmidt, Tobias, Samaras, Patroklos, Dorfer, Viktoria, Panse, Christian, Kockmann, Tobias, Bichmann, Leon, van Puyvelde, Bart, Perez-Riverol, Yasset, Deutsch, Eric W, Kuster, Bernhard, Wilhelm, Mathias

“…Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison…”
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Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics by Wilhelm, Mathias, Zolg, Daniel P., Graber, Michael, Gessulat, Siegfried, Schmidt, Tobias, Schnatbaum, Karsten, Schwencke-Westphal, Celina, Seifert, Philipp, de Andrade Krätzig, Niklas, Zerweck, Johannes, Knaute, Tobias, Bräunlein, Eva, Samaras, Patroklos, Lautenbacher, Ludwig, Klaeger, Susan, Wenschuh, Holger, Rad, Roland, Delanghe, Bernard, Huhmer, Andreas, Carr, Steven A., Clauser, Karl R., Krackhardt, Angela M., Reimer, Ulf, Kuster, Bernhard

“…Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for…”
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FIFS: A data mining method for informative marker selection in high dimensional population genomic data by Kavakiotis, Ioannis, Samaras, Patroklos, Triantafyllidis, Alexandros, Vlahavas, Ioannis

“…Single Nucleotide Polymorphism (SNPs) are, nowadays, becoming the marker of choice for biological analyses involving a wide range of applications with great…”
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Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors by Reinecke, Maria, Brear, Paul, Vornholz, Larsen, Berger, Benedict-Tilmann, Seefried, Florian, Wilhelm, Stephanie, Samaras, Patroklos, Gyenis, Laszlo, Litchfield, David William, Médard, Guillaume, Müller, Susanne, Ruland, Jürgen, Hyvönen, Marko, Wilhelm, Mathias, Kuster, Bernhard

“…Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to…”
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Decrypting drug actions and protein modifications by dose- and time-resolved proteomics by Zecha, Jana, Bayer, Florian P, Wiechmann, Svenja, Woortman, Julia, Berner, Nicola, Müller, Julian, Schneider, Annika, Kramer, Karl, Abril-Gil, Mar, Hopf, Thomas, Reichart, Leonie, Chen, Lin, Hansen, Fynn M, Lechner, Severin, Samaras, Patroklos, Eckert, Stephan, Lautenbacher, Ludwig, Reinecke, Maria, Hamood, Firas, Prokofeva, Polina, Vornholz, Larsen, Falcomatà, Chiara, Dorsch, Madeleine, Schröder, Ayla, Venhuizen, Anton, Wilhelm, Stephanie, Médard, Guillaume, Stoehr, Gabriele, Ruland, Jürgen, Grüner, Barbara M, Saur, Dieter, Buchner, Maike, Ruprecht, Benjamin, Hahne, Hannes, The, Matthew, Wilhelm, Mathias, Kuster, Bernhard

“…Although most cancer drugs modulate the activities of cellular pathways by changing posttranslational modifications (PTMs), little is known regarding the…”
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