Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy. by Nicolas Guex, Eugenia Migliavacca, Ioannis Xenarios

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Towards mouse genetic-specific RNA-sequencing read mapping. by Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis Xenarios

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Comparison of strategies to detect epistasis from eQTL data. by Karen Kapur, Thierry Schüpbach, Ioannis Xenarios, Zoltán Kutalik, Sven Bergmann

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Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth by Martial Sankar, Kaisa Nieminen, Laura Ragni, Ioannis Xenarios, Christian S Hardtke

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Dissection of the macrophage response towards infection by the Leishmania-viral endosymbiont duo and dynamics of the type I interferon response by Amel Bekkar, Nathalie Isorce, Tiia Snäkä, Stéphanie Claudinot, Chantal Desponds, Dmitry Kopelyanskiy, Florence Prével, Marta Reverte, Ioannis Xenarios, Ioannis Xenarios, Nicolas Fasel, Filipa Teixeira

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Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs. by Xuezhi Zhang, Karl-Heinz Krause, Ioannis Xenarios, Thierry Soldati, Brigitte Boeckmann

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Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor by Tiia Snäkä, Amel Bekkar, Chantal Desponds, Florence Prével, Stéphanie Claudinot, Nathalie Isorce, Filipa Teixeira, Coline Grasset, Ioannis Xenarios, Ioannis Xenarios, Isabel C. Lopez-Mejia, Lluis Fajas, Nicolas Fasel

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TIE-2 expressing monocytes in human cancers by Riccardo Turrini, Angélique Pabois, Ioannis Xenarios, George Coukos, Jean-François Delaloye, Marie-Agnès Doucey

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Predicting combinations of immunomodulators to enhance dendritic cell-based vaccination based on a hybrid experimental and computational platform by Rita Ahmed, Isaac Crespo, Sandra Tuyaerts, Amel Bekkar, Michele Graciotti, Ioannis Xenarios, Lana E. Kandalaft

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Virosaurus A Reference to Explore and Capture Virus Genetic Diversity by Anne Gleizes, Florian Laubscher, Nicolas Guex, Christian Iseli, Thomas Junier, Samuel Cordey, Jacques Fellay, Ioannis Xenarios, Laurent Kaiser, Philippe Le Mercier

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An integrated ontology resource to explore and study host-virus relationships. by Patrick Masson, Chantal Hulo, Edouard de Castro, Rebecca Foulger, Sylvain Poux, Alan Bridge, Jane Lomax, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

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DynaStI: A Dynamic Retention Time Database for Steroidomics by Santiago Codesido, Giuseppe Marco Randazzo, Fabio Lehmann, Víctor González-Ruiz, Arnaud García, Ioannis Xenarios, Robin Liechti, Alan Bridge, Julien Boccard, Serge Rudaz

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The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection. by Chantal Hulo, Patrick Masson, Edouard de Castro, Andrea H Auchincloss, Rebecca Foulger, Sylvain Poux, Jane Lomax, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier

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Neutrophils and Snail Orchestrate the Establishment of a Pro-tumor Microenvironment in Lung Cancer by Julien Faget, Svenja Groeneveld, Gael Boivin, Martial Sankar, Nadine Zangger, Miguel Garcia, Nicolas Guex, Inti Zlobec, Loïc Steiner, Alessandra Piersigilli, Ioannis Xenarios, Etienne Meylan

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A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle by Christian Linke, Anastasia Chasapi, Alberto González-Novo, Istabrak Al Sawad, Silvia Tognetti, Edda Klipp, Mart Loog, Sylvia Krobitsch, Francesc Posas, Ioannis Xenarios, Matteo Barberis

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An anti-influenza combined therapy assessed by single cell RNA-sequencing by Chiara Medaglia, Ilya Kolpakov, Arnaud Charles-Antoine Zwygart, Yong Zhu, Samuel Constant, Song Huang, Valeria Cagno, Emmanouil T. Dermitzakis, Francesco Stellacci, Ioannis Xenarios, Caroline Tapparel

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Deciphering the Dynamic Transcriptional and Post-transcriptional Networks of Macrophages in the Healthy Heart and after Myocardial Injury by Wencke Walter, Laura Alonso-Herranz, Verdiana Trappetti, Isaac Crespo, Mark Ibberson, Marta Cedenilla, Anna Karaszewska, Vanessa Núñez, Ioannis Xenarios, Alicia G. Arroyo, Fátima Sánchez-Cabo, Mercedes Ricote

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Scaling up data curation using deep learning: An application to literature triage in genomic variation resources. by Kyubum Lee, Maria Livia Famiglietti, Aoife McMahon, Chih-Hsuan Wei, Jacqueline Ann Langdon MacArthur, Sylvain Poux, Lionel Breuza, Alan Bridge, Fiona Cunningham, Ioannis Xenarios, Zhiyong Lu

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A systems genetics resource and analysis of sleep regulation in the mouse. by Shanaz Diessler, Maxime Jan, Yann Emmenegger, Nicolas Guex, Benita Middleton, Debra J Skene, Mark Ibberson, Frederic Burdet, Lou Götz, Marco Pagni, Martial Sankar, Robin Liechti, Charlotte N Hor, Ioannis Xenarios, Paul Franken

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Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform by Adrian Egli, Dominique S. Blanc, Gilbert Greub, Peter M. Keller, Vladimir Lazarevic, Aitana Lebrand, Stephen Leib, Richard A. Neher, Vincent Perreten, Alban Ramette, Jacques Schrenzel, Roger Stephan, Karoline Wagner, Daniel Wüthrich, Ioannis Xenarios

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