Search Results - "Claassen, Manfred"

Sensitive detection of rare disease-associated cell subsets via representation learning by Arvaniti, Eirini, Claassen, Manfred

“…Rare cell populations play a pivotal role in the initiation and progression of diseases such as cancer. However, the identification of such subpopulations…”
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Automated Gleason grading of prostate cancer tissue microarrays via deep learning by Arvaniti, Eirini, Fricker, Kim S., Moret, Michael, Rupp, Niels, Hermanns, Thomas, Fankhauser, Christian, Wey, Norbert, Wild, Peter J., Rüschoff, Jan H., Claassen, Manfred

“…The Gleason grading system remains the most powerful prognostic predictor for patients with prostate cancer since the 1960s. Its application requires…”
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Exhausted CD8+ T cells exhibit low and strongly inhibited TCR signaling during chronic LCMV infection by Sandu, Ioana, Cerletti, Dario, Claassen, Manfred, Oxenius, Annette

“…Chronic viral infections are often associated with impaired CD8 + T cell function, referred to as exhaustion. Although the molecular and cellular circuits…”
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Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations by Zampieri, Mattia, Zimmermann, Michael, Claassen, Manfred, Sauer, Uwe

“…Microbes have shown a remarkable ability in evading the killing actions of antimicrobial agents, such that treatment of bacterial infections represents once…”
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Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability by Leuenberger, Pascal, Ganscha, Stefan, Kahraman, Abdullah, Cappelletti, Valentina, Boersema, Paul J., von Mering, Christian, Claassen, Manfred, Picotti, Paola

“…Temperature-induced cell death is thought to be due to protein denaturation, but the determinants of thermal sensitivity of proteomes remain largely…”
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Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry by Ludwig, Christina, Claassen, Manfred, Schmidt, Alexander, Aebersold, Ruedi

“…For many research questions in modern molecular and systems biology, information about absolute protein quantities is imperative. This information includes,…”
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The quantitative proteome of a human cell line by Beck, Martin, Schmidt, Alexander, Malmstroem, Johan, Claassen, Manfred, Ori, Alessandro, Szymborska, Anna, Herzog, Franz, Rinner, Oliver, Ellenberg, Jan, Aebersold, Ruedi

“…The generation of mathematical models of biological processes, the simulation of these processes under different conditions, and the comparison and integration…”
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Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data by Kopf, Andreas, Fortuin, Vincent, Somnath, Vignesh Ram, Claassen, Manfred

“…Clustering high-dimensional data, such as images or biological measurements, is a long-standing problem and has been studied extensively. Recently, Deep…”
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Latent representation learning in biology and translational medicine by Kopf, Andreas, Claassen, Manfred

“…Current data generation capabilities in the life sciences render scientists in an apparently contradicting situation. While it is possible to simultaneously…”
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Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series by Klimovskaia, Anna, Ganscha, Stefan, Claassen, Manfred

“…Stochastic chemical reaction networks constitute a model class to quantitatively describe dynamics and cell-to-cell variability in biological systems. The…”
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Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition by Bues, Johannes, Biočanin, Marjan, Pezoldt, Joern, Dainese, Riccardo, Chrisnandy, Antonius, Rezakhani, Saba, Saelens, Wouter, Gardeux, Vincent, Gupta, Revant, Sarkis, Rita, Russeil, Julie, Saeys, Yvan, Amstad, Esther, Claassen, Manfred, Lutolf, Matthias P., Deplancke, Bart

“…Single-cell RNA sequencing (scRNA-seq) approaches have transformed our ability to resolve cellular properties across systems, but are currently tailored toward…”
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TGF-β induces oncofetal fibronectin that, in turn, modulates TGF-β superfamily signaling in endothelial cells by Ventura, Elisa, Weller, Michael, Macnair, Will, Eschbach, Katja, Beisel, Christian, Cordazzo, Cinzia, Claassen, Manfred, Zardi, Luciano, Burghardt, Isabel

“…Gene splicing profiles are frequently altered in cancer, and the splice variants of fibronectin (FN) that contain the extra-domains A (EDA) or B (EDB),…”
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Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics by de Vargas Roditi, Laura, Claassen, Manfred

“…Graphical abstract…”
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Author Correction: Automated Gleason grading of prostate cancer tissue microarrays via deep learning by Arvaniti, Eirini, Fricker, Kim S., Moret, Michael, Rupp, Niels, Hermanns, Thomas, Fankhauser, Christian, Wey, Norbert, Wild, Peter J., Rüschoff, Jan H., Claassen, Manfred

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Directed mass spectrometry: towards hypothesis-driven proteomics by Schmidt, Alexander, Claassen, Manfred, Aebersold, Ruedi

“…To date, the vast majority of the proteomic data sets collected by mass spectrometry (MS) have been generated by nondirected methods, whereby the identified…”
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Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry by Reiter, Lukas, Claassen, Manfred, Schrimpf, Sabine P., Jovanovic, Marko, Schmidt, Alexander, Buhmann, Joachim M., Hengartner, Michael O., Aebersold, Ruedi

“…Comprehensive characterization of a proteome is a fundamental goal in proteomics. To achieve saturation coverage of a proteome or specific subproteome via…”
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Landscape of Exhausted Virus-Specific CD8 T Cells in Chronic LCMV Infection by Sandu, Ioana, Cerletti, Dario, Oetiker, Nathalie, Borsa, Mariana, Wagen, Franziska, Spadafora, Ilaria, Welten, Suzanne P.M., Stolz, Ugne, Oxenius, Annette, Claassen, Manfred

“…A hallmark of chronic infections is the presence of exhausted CD8 T cells, characterized by a distinct transcriptional program compared with functional…”
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Positive feedback induces switch between distributive and processive phosphorylation of Hog1 by Mosbacher, Maximilian, Lee, Sung Sik, Yaakov, Gilad, Nadal-Ribelles, Mariona, de Nadal, Eulàlia, van Drogen, Frank, Posas, Francesc, Peter, Matthias, Claassen, Manfred

“…Cellular decision making often builds on ultrasensitive MAPK pathways. The phosphorylation mechanism of MAP kinase has so far been described as either…”
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The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis by Schubert, Olga T., Mouritsen, Jeppe, Ludwig, Christina, Röst, Hannes L., Rosenberger, George, Arthur, Patrick K., Claassen, Manfred, Campbell, David S., Sun, Zhi, Farrah, Terry, Gengenbacher, Martin, Maiolica, Alessio, Kaufmann, Stefan H.E., Moritz, Robert L., Aebersold, Ruedi

“…Research advancing our understanding of Mycobacterium tuberculosis (Mtb) biology and complex host-Mtb interactions requires consistent and precise quantitative…”
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Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming by Taylor-King, Jake P, Riseth, Asbjørn N, Macnair, Will, Claassen, Manfred

“…Recent high-dimensional single-cell technologies such as mass cytometry are enabling time series experiments to monitor the temporal evolution of cell state…”
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