Publications @article{reiter2009protein, title={Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry}, author={Reiter, Lukas and Claassen, Manfred and Schrimpf, Sabine P and Jovanovic, Marko and Schmidt, Alexander and Buhmann, Joachim M and Hengartner, Michael O and Aebersold, Ruedi}, journal={Molecular \& Cellular Proteomics}, volume={8}, number={11}, pages={2405--2417}, year={2009}, publisher={Elsevier} } @article{schmidt2009directed, title={Directed mass spectrometry: towards hypothesis-driven proteomics}, author={Schmidt, Alexander and Claassen, Manfred and Aebersold, Ruedi}, journal={Current Opinion in Chemical Biology}, volume={13}, number={5-6}, pages={510--517}, year={2009}, publisher={Elsevier Current Trends} } @article{claassen2009proteome, title={Proteome coverage prediction with infinite Markov models}, author={Claassen, Manfred and Aebersold, Ruedi and Buhmann, Joachim M}, journal={Bioinformatics}, volume={25}, number={12}, pages={i154--i160}, year={2009}, publisher={Oxford University Press} } @article{schmidt2011absolute, title={Absolute quantification of microbial proteomes at different states by directed mass spectrometry}, author={Schmidt, Alexander and Beck, Martin and Malmstr{\"o}m, Johan and Lam, Henry and Claassen, Manfred and Campbell, David and Aebersold, Ruedi}, journal={Molecular Systems Biology}, volume={7}, number={1}, pages={510}, year={2011}, publisher={John Wiley \& Sons, Ltd Chichester, UK} } @article{beck2011comprehensive, title={Comprehensive proteomics}, author={Beck, Martin and Claassen, Manfred and Aebersold, Ruedi}, journal={Current Opinion in Biotechnology}, volume={22}, number={1}, pages={3--8}, year={2011}, publisher={Elsevier Current Trends} } @article{claassen2011proteome, title={Proteome coverage prediction for integrated proteomics datasets}, author={Claassen, Manfred and Aebersold, Ruedi and Buhmann, Joachim M}, journal={Journal of Computational Biology}, volume={18}, number={3}, pages={283--293}, year={2011}, publisher={Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA} } @article{claassen2012generic, title={Generic comparison of protein inference engines}, author={Claassen, Manfred and Reiter, Lukas and Hengartner, Michael O and Buhmann, Joachim M and Aebersold, Ruedi}, journal={Molecular \& Cellular Proteomics}, volume={11}, number={4}, year={2012}, publisher={Elsevier} } @article{beck2011quantitative, title={The quantitative proteome of a human cell line}, author={Beck, Martin and Schmidt, Alexander and Malmstroem, Johan and Claassen, Manfred and Ori, Alessandro and Szymborska, Anna and Herzog, Franz and Rinner, Oliver and Ellenberg, Jan and Aebersold, Ruedi}, journal={Molecular Systems Biology}, volume={7}, number={1}, pages={549}, year={2011}, publisher={John Wiley \& Sons, Ltd Chichester, UK} } @article{ludwig2012estimation, title={Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry}, author={Ludwig, Christina and Claassen, Manfred and Schmidt, Alexander and Aebersold, Ruedi}, journal={Molecular \& Cellular Proteomics}, volume={11}, number={3}, year={2012}, publisher={Elsevier} } @article{walzthoeni2012false, title={False discovery rate estimation for cross-linked peptides identified by mass spectrometry}, author={Walzthoeni, Thomas and Claassen, Manfred and Leitner, Alexander and Herzog, Franz and Bohn, Stefan and F{\"o}rster, Friedrich and Beck, Martin and Aebersold, Ruedi}, journal={Nature Methods}, volume={9}, number={9}, pages={901--903}, year={2012}, publisher={Nature Publishing Group} } @article{claassen2012inference, title={Inference and validation of protein identifications}, author={Claassen, Manfred}, journal={Molecular \& Cellular Proteomics}, volume={11}, number={11}, pages={1097--1104}, year={2012}, publisher={Elsevier} } @article{schubert2013mtb, title={The Mtb proteome library: a resource of assays to quantify the complete proteome of Mycobacterium tuberculosis}, author={Schubert, Olga T and Mouritsen, Jeppe and Ludwig, Christina and R{\"o}st, Hannes L and Rosenberger, George and Arthur, Patrick K and Claassen, Manfred and Campbell, David S and Sun, Zhi and Farrah, Terry and others}, journal={Cell Host \& Microbe}, volume={13}, number={5}, pages={602--612}, year={2013}, publisher={Cell Press} } @article{claassen2013shooting, title={Shooting movies of signaling network dynamics with multiparametric cytometry}, author={Claassen, Manfred}, journal={Current Topics in Microbiology and Immunology}, pages={177--189}, year={2013}, publisher={Springer, Berlin, Heidelberg} } @article{arvaniti2013markov, title={Markov network structure learning via ensemble-of-forests models}, author={Arvaniti, Eirini and Claassen, Manfred}, journal={arXiv}, year={2013} } @article{mitov2013fused, title={A fused elastic net logistic regression model for multi-task binary classification}, author={Mitov, Venelin and Claassen, Manfred}, journal={arXiv}, year={2013} } @article{de2015computational, title={Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics}, author={de Vargas Roditi, Laura and Claassen, Manfred}, journal={Current Opinion in Biotechnology}, volume={34}, pages={9--15}, year={2015}, publisher={Elsevier Current Trends} } @article{gawinecka2015proteomic, title={Proteomic profiling of aortic tissue-derived secretome towards biomarkers for acute aortic dissection}, author={Gawinecka, J and Reiser, H and Sch{\"o}nrath, F and Falk, V and Arvaniti, E and Claassen, M and von Eckardstein, A}, journal={Atherosclerosis}, volume={241}, number={1}, pages={e185--e186}, year={2015}, publisher={Elsevier} } @article{arvaniti2017sensitive, title={Sensitive detection of rare disease-associated cell subsets via representation learning}, author={Arvaniti, Eirini and Claassen, Manfred}, journal={Nature Communications}, volume={8}, number={1}, pages={1--10}, year={2017}, publisher={Nature Publishing Group} } @article{feigelman2016exact, title={Exact Bayesian lineage tree-based inference identifies Nanog negative autoregulation in mouse embryonic stem cells}, author={Feigelman, Justin and Ganscha, Stefan and Hastreiter, Simon and Schwarzfischer, Michael and Filipczyk, Adam and Schroeder, Timm and Theis, Fabian J and Marr, Carsten and Claassen, Manfred}, journal={bioRxiv}, pages={053231}, year={2016}, publisher={Cold Spring Harbor Laboratory} } @article{sib2016sib, title={The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases}, author={SIB Swiss Institute of Bioinformatics Members}, journal={Nucleic Acids Research}, volume={44}, number={D1}, pages={D27--D37}, year={2016}, publisher={Oxford University Press} } @article{curkic2016epitope, title={Epitope-tagged autotransporters as single-cell reporters for gene expression by a Salmonella Typhimurium wbaP mutant}, author={Curki{\'c}, Ismeta and Sch{\"u}tz, Monika and Oberhettinger, Philipp and Diard, M{\'e}d{\'e}ric and Claassen, Manfred and Linke, Dirk and Hardt, Wolf-Dietrich}, journal={Plos One}, volume={11}, number={5}, pages={e0154828}, year={2016}, publisher={Public Library of Science San Francisco, CA USA} } @article{feigelman2016matleap, title={matLeap: A fast adaptive Matlab-ready tau-leaping implementation suitable for Bayesian inference}, author={Feigelman, Justin and Ganscha, Stefan and Claassen, Manfred}, journal={arXiv}, year={2016} } @article{feigelman2016analysis, title={Analysis of cell lineage trees by exact Bayesian inference identifies negative autoregulation of Nanog in mouse embryonic stem cells}, author={Feigelman, Justin and Ganscha, Stefan and Hastreiter, Simon and Schwarzfischer, Michael and Filipczyk, Adam and Schroeder, Timm and Theis, Fabian J and Marr, Carsten and Claassen, Manfred}, journal={Cell Systems}, volume={3}, number={5}, pages={480--490}, year={2016}, publisher={Cell Press} } @article{klimovskaia2016sparse, title={Sparse regression based structure learning of stochastic reaction networks from single cell snapshot time series}, author={Klimovskaia, Anna and Ganscha, Stefan and Claassen, Manfred}, journal={PLoS Computational Biology}, volume={12}, number={12}, pages={e1005234}, year={2016}, publisher={Public Library of Science San Francisco, CA USA} } @article{gawinecka2016comprehensive, title={Comprehensive molecular profiling in acute aortic dissection: seeking diagnostic biomarkers: DGKL-P110}, author={Gawinecka, J and Reiser, H and Sch{\"o}nrath, F and Arvaniti, E and Claassen, M and Falk, V and von Eckardstein, A}, journal={Clinical Chemistry and Laboratory Medicine}, volume={54}, number={10}, year={2016} } @article{leuenberger2017cell, title={Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability}, author={Leuenberger, Pascal and Ganscha, Stefan and Kahraman, Abdullah and Cappelletti, Valentina and Boersema, Paul J and von Mering, Christian and Claassen, Manfred and Picotti, Paola}, journal={Science}, volume={355}, number={6327}, year={2017}, publisher={American Association for the Advancement of Science} } @article{zampieri2017nontargeted, title={Nontargeted metabolomics reveals the multilevel response to antibiotic perturbations}, author={Zampieri, Mattia and Zimmermann, Michael and Claassen, Manfred and Sauer, Uwe}, journal={Cell Reports}, volume={19}, number={6}, pages={1214--1228}, year={2017}, publisher={Cell Press} } @article{kuehne2017metabolic, title={Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data}, author={Kuehne, Andreas and Mayr, Urs and S{\'e}vin, Daniel C and Claassen, Manfred and Zamboni, Nicola}, journal={PLoS Computational Biology}, volume={13}, number={6}, pages={e1005577}, year={2017}, publisher={Public Library of Science} } @article{macnair2019tree, title={Tree-ensemble analysis assesses presence of multifurcations in single cell data}, author={Macnair, Will and De Vargas Roditi, Laura and Ganscha, Stefan and Claassen, Manfred}, journal={Molecular Systems Biology}, volume={15}, number={3}, pages={e8552}, year={2019} } @article{ventura2018tgf, title={TGF-\beta induces oncofetal fibronectin that, in turn, modulates TGF-\beta superfamily signaling in endothelial cells}, author={Ventura, Elisa and Weller, Michael and Macnair, Will and Eschbach, Katja and Beisel, Christian and Cordazzo, Cinzia and Claassen, Manfred and Zardi, Luciano and Burghardt, Isabel}, journal={Journal of Cell Science}, volume={131}, number={1}, pages={jcs209619}, year={2018}, publisher={The Company of Biologists Ltd} } @article{arvaniti2018automated, title={Automated Gleason grading of prostate cancer tissue microarrays via deep learning}, author={Arvaniti, Eirini and Fricker, Kim S and Moret, Michael and Rupp, Niels and Hermanns, Thomas and Fankhauser, Christian and Wey, Norbert and Wild, Peter J and Rueschoff, Jan H and Claassen, Manfred}, journal={Scientific Reports}, volume={8}, number={1}, pages={1--11}, year={2018}, publisher={Nature Publishing Group} } @article{sajic2018similarities, title={Similarities and differences of blood N-glycoproteins in five solid carcinomas at localized clinical stage analyzed by sWATH-MS}, author={Sajic, Tatjana and Liu, Yansheng and Arvaniti, Eirini and Surinova, Silvia and Williams, Evan G and Schiess, Ralph and H{\"u}ttenhain, Ruth and Sethi, Atul and Pan, Sheng and Brentnall, Teresa A and others}, journal={Cell Reports}, volume={23}, number={9}, pages={2819--2831}, year={2018}, publisher={Cell Press} } @article{ganscha2018supervised, title={Supervised learning on synthetic data for reverse engineering gene regulatory networks from experimental time-series}, author={Ganscha, Stefan and Fortuin, Vincent and Horn, Max and Arvaniti, Eirini and Claassen, Manfred}, journal={bioRxiv}, pages={356477}, year={2018}, publisher={Cold Spring Harbor Laboratory} } @article{taylor2020dynamic, title={Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming}, author={Taylor-King, Jake P and Riseth, Asbj{\o}rn N and Macnair, Will and Claassen, Manfred}, journal={PLoS Computational Biology}, volume={16}, number={1}, pages={e1007491}, year={2020}, publisher={Public Library of Science San Francisco, CA USA} } @article{shi2018dynamics, title={The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling}, author={Shi, Chun-Lin and Von Wangenheim, Daniel and Herrmann, Ullrich and Wildhagen, Mari and Kulik, Ivan and Kopf, Andreas and Ishida, Takashi and Olsson, Vilde and Anker, Mari Kristine and Albert, Markus and others}, journal={Nature Plants}, volume={4}, number={8}, pages={596--604}, year={2018}, publisher={Nature Publishing Group} } @article{arvaniti2018coupling, title={Coupling weak and strong supervision for classification of prostate cancer histopathology images}, author={Arvaniti, Eirini and Claassen, Manfred}, journal={arXiv}, year={2018} } @article{arvaniti2019automated, title={Automated Gleason grading of prostate cancer tissue microarrays via deep learning}, author={Arvaniti, Eirini and Fricker, Kim S and Moret, Michael and Rupp, Niels and Hermanns, Thomas and Fankhauser, Christian and Wey, Norbert and Wild, Peter J and Ruschoff, Jan H and Claassen, Manfred}, journal={Scientific Reports}, volume={9}, year={2019}, publisher={Nature Publishing Group} } @article{galli2019gm, title={GM-CSF and CXCR4 define a T helper cell signature in multiple sclerosis}, author={Galli, Edoardo and Hartmann, Felix J and Schreiner, Bettina and Ingelfinger, Florian and Arvaniti, Eirini and Diebold, Martin and Mrdjen, Dunja and van der Meer, Franziska and Krieg, Carsten and Al Nimer, Faiez and others}, journal={Nature Medicine}, volume={25}, number={8}, pages={1290--1300}, year={2019}, publisher={Nature Publishing Group} } @article{yalcinkaya2019unravelling, title={Unravelling The Structure-Function-Relationships Of High Density Lipoproteins (Hdl) By A Systems Biological Approach}, author={Yalcinkaya, M and Cardner, M and Goetze, S and Luca, E and Balasz, M and Hunjadi, M and Ritsch, A and Hartung, J and Landmesser, U and Liebisch, G and others}, journal={Atherosclerosis}, volume={287}, pages={e20--e21}, year={2019}, publisher={Elsevier} } @article{yalcinkaya2019structure, title={Structure-function Relationships of HDL in Diabetes and Coronary Heart Disease}, author={Yalcinkaya, Mustafa and Cardner, Mathias and Goetze, Sandra and Luca, Edlira and Bal{\'a}z, Miroslav and Hunjadi, Monika and Hartung, Johannes and Kr{\"a}nkel, Nicolle and Shemet, Andrej and Radosavljevic, Silvija and others}, journal={Clinical Chemistry and Laboratory Medicine}, volume={57}, number={9}, year={2019} } @article{cardner2020structure, title={Structure-function relationships of HDL in diabetes and coronary heart disease}, author={Cardner, Mathias and Yalcinkaya, Mustafa and Goetze, Sandra and Luca, Edlira and Balaz, Miroslav and Hunjadi, Monika and Hartung, Johannes and Shemet, Andrej and Kr{\"a}nkel, Nicolle and Radosavljevic, Silvija and others}, journal={JCI insight}, volume={5}, number={1}, year={2020}, publisher={American Society for Clinical Investigation} } @article{gawinecka2017comprehensive, title={Comprehensive molecular profiling in acute aortic dissection: seeking diagnostic biomarkers: FV12}, author={Gawinecka, Joanna and Sch{\"o}nrath, Felix and Reiser, Hans and Arvaniti, Eirini and Claassen, Manfred and von Eckardstein, Arnold}, journal={Clinical Chemistry and Laboratory Medicine}, volume={55}, number={11}, year={2017} } @article{mosbacher2020positive, title={Positive feedback induces switch between distributive and processive phosphorylation of Hog1}, author={Mosbacher, Maximilian and Lee, Sung Sik and Peter, Matthias and Claassen, Manfred}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{bues2020deterministic, title={Deterministic scRNA-seq of individual intestinal organoids reveals new subtypes and coexisting distinct stem cell pools}, author={Bues, Johannes and Bio{\v{c}}anin, Marjan and Pezoldt, Joern and Dainese, Riccardo and Chrisnandy, Antonius and Rezakhani, Saba and Saelens, Wouter and Gupta, Revant and Russeil, Julie and Saeys, Yvan and others}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{grogg2020automated, title={Automated Gleason grading of whole slide prostatectomy images}, author={Grogg, J and Arvaniti, E and Gretser, S and Smith, K and Sulser, T and Hermanns, T and Wild, PJ and Fankhauser, CD and Claassen, M}, journal={European Urology Open Science}, volume={19}, pages={e581}, year={2020}, publisher={Elsevier} } @article{sandu2020landscape, title={Landscape of exhausted virus-specific CD8 T cells in chronic LCMV infection}, author={Sandu, Ioana and Cerletti, Dario and Oetiker, Nathalie and Borsa, Mariana and Wagen, Franziska and Spadafora, Ilaria and Welten, Suzanne PM and Stolz, Ugne and Oxenius, Annette and Claassen, Manfred}, journal={Cell Reports}, volume={32}, number={8}, pages={108078}, year={2020}, publisher={Cell Press} } @article{sandu2020exhausted, title={Exhausted CD8+ T cells exhibit low and strongly inhibited TCR signaling during chronic LCMV infection}, author={Sandu, Ioana and Cerletti, Dario and Claassen, Manfred and Oxenius, Annette}, journal={Nature Communications}, volume={11}, number={1}, pages={1--11}, year={2020}, publisher={Nature Publishing Group} } @article{merk2020genome, title={Genome-wide CRISPR and small-molecule screens uncover targetable dependencies in ATRT}, author={Merk, Daniel J and Hirsch, Sophie and Tsiami, Foteini and Walter, Bianca and Haeusser, Lara A and Babaei, Sepideh and Admar, Jakob and Casadei, Nicolas and Roggia, Cristiana and Spohn, Michael and others}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{cerletti2020fate, title={Fate trajectories of CD8+ T cells in chronic LCMV infection}, author={Cerletti, Dario and Sandu, Ioana and Gupta, Revant and Oxenius, Annette and Claassen, Manfred}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{gupta2020cytopath, title={Cytopath: Simulation based inference of differentiation trajectories from RNA velocity fields}, author={Gupta, Revant and Cerletti, Dario and Gut, Gilles and Oxenius, Annette and Claassen, Manfred}, journal={bioRxiv}, year={2020}, publisher={Cold Spring Harbor Laboratory} } @article{wirsching2021negative, title={Negative allosteric modulators of metabotropic glutamate receptor 3 target the stem-like phenotype of glioblastoma}, author={Wirsching, Hans-Georg and Silginer, Manuela and Ventura, Elisa and Macnair, Will and Burghardt, Isabel and Claassen, Manfred and Gatti, Silvia and Wichmann, J{\"u}rgen and Riemer, Claus and Schneider, Hannah and others}, journal={Molecular Therapy-Oncolytics}, volume={20}, pages={166--174}, year={2021}, publisher={Elsevier} } @article{canepa2021identification, title={Identification of ALP+/CD73+ defining markers for enhanced osteogenic potential in human adipose-derived mesenchymal stromal cells by mass cytometry}, author={Canepa, Daisy D and Casanova, Elisa A and Arvaniti, Eirini and Tosevski, Vinko and M{\"a}rsmann, Sonja and Eggerschwiler, Benjamin and Halvachizadeh, Sascha and Buschmann, Johanna and Barth, Andr{\'e} A and Plock, Jan A and others}, journal={Stem Cell Research \& Therapy}, volume={12}, number={1}, pages={1--16}, year={2021}, publisher={BioMed Central} } @article{garrido2021visualizing, title={Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder}, author={Garrido, Quentin and Damrich, Sebastian and J{\"a}ger, Alexander and Cerletti, Dario and Claassen, Manfred and Najman, Laurent and Hamprecht, Fred}, journal={arXiv}, year={2021} } @article{pfister2021nash, title={NASH limits anti-tumour surveillance in immunotherapy-treated HCC}, author={Pfister, Dominik and N{\'u}{\~n}ez, Nicol{\'a}s Gonzalo and Pinyol, Roser and Govaere, Olivier and Pinter, Matthias and Szydlowska, Marta and Gupta, Revant and Qiu, Mengjie and Deczkowska, Aleksandra and Weiner, Assaf and others}, journal={Nature}, volume={592}, number={7854}, pages={450--456}, year={2021}, publisher={Nature Publishing Group} } @article{kopf2021latent, title={Latent representation learning in biology and translational medicine}, author={Kopf, Andreas and Claassen, Manfred}, journal={Patterns}, volume={2}, number={3}, pages={100198}, year={2021}, publisher={Elsevier} } @article{kreutmair2021distinct, title={Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia}, author={Kreutmair, Stefanie and Unger, Susanne and N{\'u}{\~n}ez, Nicol{\'a}s Gonzalo and Ingelfinger, Florian and Alberti, Chiara and De Feo, Donatella and Krishnarajah, Sinduya and Kauffmann, Manuel and Friebel, Ekaterina and Babaei, Sepideh and others}, journal={Immunity}, year={2021}, publisher={Cell Press} } @article{kopf2021mixture, title={Mixture-of-Experts Variational Autoencoder for clustering and generating from similarity-based representations on single cell data}, author={Kopf, Andreas and Fortuin, Vincent and Somnath, Vignesh Ram and Claassen, Manfred}, journal={PLoS Computational Biology}, volume={17}, number={6}, pages={e1009086}, year={2021}, publisher={Public Library of Science San Francisco, CA USA} } , , .
