Publications

2015

  1. Gerstenmaier, Lilli Pilla, Rachel Herrmann, Lydia Herrmann, Hendrik Prado, Monica Villafano, Geno J. Kolonko, Margot Reimer, Rudolph Soldati, Thierry King, Jason S. Hagedorn, Monica (2015) The autophagic machinery ensures nonlytic transmission of mycobacteria. Proc. Natl. Acad. Sci. USA 112 (7) E687-E692.
  2. Wilson-Zbinden, Caroline dos Santos, Aline Xavier da Silveira Stoffel-Studer, Ingrid van der Vaart, Aniek Hofmann, Kay Reggiori, Fulvio Riezman, Howard Kraft, Claudine Peter, Matthias (2015) Autophagy Competes for a Common Phosphatidylethanolamine Pool with Major Cellular PE-Consuming Pathways in Saccharomyces cerevisiae. Genetics 199 (2) 475-485.
  3. Kressmann, Sabine Campos, Claudia Castanon, Irinka Fürthauer, Maximilian González-Gaitán, Marcos (2015) Directional Notch trafficking in Sara endosomes during asymmetric cell division in the spinal cord. Nat. Cell Biol. 17 (3) 333-339.
  4. Saleem, Mohammed Morlot, Sandrine Hohendahl, Annika Manzi, John Lenz, Martin Roux, Aurélien (2015) A balance between membrane elasticity and polymerization energy sets the shape of spherical clathrin coats. Nat. Commun. 6 6249.
  5. Ounzain, Samir Micheletti, Rudi Beckmann, Tal Schroen, Blanche Alexanian, Michael Pezzuto, Iole Crippa, Stefania Nemir, Mohamed Sarre, Alexandre Johnson, Rory Dauvillier, Jérôme Burdet, Frédéric Ibberson, Mark Guigó, Roderic Xenarios, Ioannis Heymans, Stephane Pedrazzini, Thierry (2015) Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur. Heart J. 36 (6) 353-368.
  6. Morgat, Anne Axelsen, Kristian B. Lombardot, Thierry Alcántara, Rafael Aimo, Lucila Zerara, Mohamed Niknejad, Anne Belda, Eugeni Hyka-Nouspikel, Nevila Coudert, Elisabeth Redaschi, Nicole Bougueleret, Lydie Steinbeck, Christoph Xenarios, Ioannis Bridge, Alan (2015) Updates in Rhea—a manually curated resource of biochemical reactions. Nucleic Acids Res. 43 (D1) D459-D464.
  7. Mitchell, Alex Chang, Hsin-Yu Daugherty, Louise Fraser, Matthew Hunter, Sarah Lopez, Rodrigo McAnulla, Craig McMenamin, Conor Nuka, Gift Pesseat, Sebastien Sangrador-Vegas, Amaia Scheremetjew, Maxim Rato, Claudia Yong, Siew-Yit Bateman, Alex Punta, Marco Attwood, Teresa K. Sigrist, Christian J. A. Redaschi, Nicole Rivoire, Catherine Xenarios, Ioannis Kahn, Daniel Guyot, Dominique Bork, Peer Letunic, Ivica Gough, Julian Oates, Matt Haft, Daniel Huang, Hongzhan Natale, Darren A. Wu, Cathy H. Orengo, Christine Sillitoe, Ian Mi, Huaiyu Thomas, Paul D. Finn, Robert D. (2015) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43 (D1) D213-D221.
  8. Pedruzzi, Ivo Rivoire, Catherine Auchincloss, Andrea H. Coudert, Elisabeth Keller, Guillaume de Castro, Edouard Baratin, Delphine Cuche, Béatrice A. Bougueleret, Lydie Poux, Sylvain Redaschi, Nicole Xenarios, Ioannis Bridge, Alan (2015) HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res. 43 (D1) D1064-D1070.
  9. The Gene Ontology Consortium*, (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res. 43 (D1) D1049-D1056.
  10. Naldi, Aurélien Monteiro, Pedro T. Müssel, Christoph Kestler, Hans A. Thieffry, Denis Xenarios, Ioannis Saez-Rodriguez, Julio Helikar, Tomas Chaouiya, Claudine (2015) Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 31 (7) 1154-1159.
  11. Wachowicz, Paulina Chasapi, Anastasia Krapp, Andrea Cano del Rosario, Elena Schmitter, Daniel Sage, Daniel Unser, Michael Xenarios, Ioannis Rougemont, Jacques Simanis, Viesturs (2015) Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN. J. Cell Sci. 128 (4) 741-754.
  12. Loubéry, Sylvain Seum, Carole Moraleda, Ana Daeden, Alicia Fürthauer, Maximilian Gonzalez-Gaitan, Marcos (2015) [Erratum] Uninflatable and Notch Control the Targeting of Sara Endosomes during Asymmetric Division. Curr. Biol. 25 (6) 817-818.
  13. Barisch, Caroline Paschke, Peggy Hagedorn, Monica Maniak, Markus Soldati, Thierry (2015) Lipid droplet dynamics at early stages of Mycobacterium marinum infection in Dictyostelium. Cell. Microbiol. 17 (9) 1332-1349.
  14. Dikoglu, Esra Alfaiz, Ali Gorna, Maria Bertola, Deborah Chae, Jong Hee Cho, Tae-Joon Derbent, Murat Alanay, Yasemin Guran, Tulay Kim, Ok-Hwa Llerenar Jr, Juan C. Yamamoto, Guillerme Superti-Furga, Giulio Reymond, Alexandre Xenarios, Ioannis Stevenson, Brian Campos-Xavier, Belinda Bonafé, Luisa Superti-Furga, Andrea Unger, Sheila (2015) Mutations in LONP1, a mitochondrial matrix protease, cause CODAS syndrome. Am. J. Med. Genet. 167 (7) 1501-1509.
  15. Guex, Nicolas Crespo, Isaac Bron, Sylvian Ifticene-Treboux, Assia Faes-van\'t Hull, Eveline Kharoubi, Solange Liechti, Robin Werffeli, Patricia Ibberson, Mark Majo, Francois Nicolas, Michäel Laurent, Julien Garg, Abhishek Zaman, Khalil Lehr, Hans-Anton Stevenson, Brian J. Rüegg, Curzio Coukos, George Delaloye, Jean-François Xenarios, Ioannis Doucey, Marie-Agnès Mac Gabhann, Feilim (2015) Angiogenic Activity of Breast Cancer Patients’ Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches. PLoS Comput Biol 11 (3) e1004050.
  16. Barisch, Caroline López-Jiménez, Ana T. Soldati, Thierry (2015) Live Imaging of Mycobacterium marinum Infection in Dictyostelium discoideum. Mycobacteria Protocols Vol. 1285 (Chapter 23)Ed. Parish, Tanya Roberts, David M.Methods in Molecular Biology. Springer. (New York). 369-385.
  17. Harrison, Christopher F. Kicka, Sébastien Kranjc, Agata Finsel, Ivo Chiriano, Gianpaolo Ouertatani-Sakouhi, Hajer Soldati, Thierry Scapozza, Leonoardo Hilbi, Hubert (2015) Adrenergic antagonists restrict replication of Legionella. Microbiol. 161 (7) 1392-1406.
  18. Overduin, Michael Rajesh, Sandya Gruenberg, Jean Lenoir, Marc (2015) Secondary structure and 1H, 13C, 15N resonance assignments of the endosomal sorting protein sorting nexin 3. Biomol. NMR Assign. 9 (2) 355-358.
  19. Scott, Cameron C. Vossio, Stefania Vacca, Fabrizio Snijder, Berend Larios, Jorge Schaad, Olivier Guex, Nicolas Kuznetsov, Dmitry Martin, Olivier Chambon, Marc Turcatti, Gerardo Pelkmans, Lucas Gruenberg, Jean (2015) Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. EMBO Rep. 16 (6) 741-752.
  20. Scott, Cameron C. Vossio, Stefania Vacca, Fabrizio Snijder, Berend Larios, Jorge Schaad, Olivier Guex, Nicolas Kuznetsov, Dmitry Martin, Olivier Chambon, Marc Turcatti, Gerardo Pelkmans, Lucas Gruenberg, Jean (2015) Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. EMBO Rep. 16 (6) 741-752.
  21. Harrison, Christopher F. Chiriano, Gianpaolo Finsel, Ivo Manske, Christian Hoffmann, Christine Steiner, Bernhard Kranjc, Agata Patthey-Vuadens, Ophelie Kicka, Sebastien Trofimov, Valentin Ouertatani-Sakhoui, Hajer Soldati, Thierry Scapozza, Leonardo Hilbi, Hubert (2015) Amoebae-based screening reveals a novel family of compounds restricting intracellular Legionella pneumophila. ACS Infect. Dis. 1 (7) 327-338.
  22. Aimo, Lucila Liechti, Robin Nouspikel, Nevila Niknejad, Anne Gleizes, Anne Gotz, Lou Kuznetsov, Dmitry David, Fabrice P. A. van der Gout, Gisou Riezman, Howard Bougueleret, Lydie Xenarios, Ioannis Bridge, Alan (2015) The SwissLipids knowledgebase for lipid biology. Bioinformatics 31 (17) 2860-2866.
  23. Aimo, Lucila Liechti, Robin Nouspikel, Nevila Niknejad, Anne Gleizes, Anne Gotz, Lou Kuznetsov, Dmitry David, Fabrice P. A. van der Gout, Gisou Riezman, Howard Bougueleret, Lydie Xenarios, Ioannis Bridge, Alan (2015) The SwissLipids knowledgebase for lipid biology. Bioinformatics 31 (17) 2860-2866.
  24. Suresh, Harsha Garadi da Silveira dos Santos, Aline Xavier Kukulski, Wanda Tyedmers, Jens Riezman, Howard Bukau, Bernd Mogk, Axel (2015) Prolonged starvation drives reversible sequestration of lipid biosynthetic enzymes and organelle reorganization in Saccharomyces cerevisiae. Mol. Biol. Cell 26 (9) 1601-1615.
  25. Barbier de Reuille, Pierre Routier-Kierzkowska, Anne-Lise Kierzkowski, Daniel Bassel, George W. Schüpbach, Thierry Tauriello, Gerardo Bajpai, Namrata Strauss, Sören Weber, Alain Kiss, Annamaria Burian, Agata Hofhuis, Hugo Sapala, Aleksandra Lipowczan, Marcin Heimlicher, Maria B. Robinson, Sarah Bayer, Emmanuelle M. Basler, Konrad Koumoutsakos, Petros Roeder, Adrienne H. K. Aegerter-Wilmsen, Tinri Nakayama, Naomi Tsiantis, Miltos Hay, Angela Kwiatkowska, Dorota Xenarios, Ioannis Kuhlemeier, Cris Smith, Richard S. (2015) MorphoGraphX: A platform for quantifying morphogenesis in 4D. eLife 4 e05864.
  26. Schaper, Elke Korsunsky, Alexander Messina, Antonio Murri, Riccardo Pečerska, Jūlija Stockinger, Heinz Zoller, Stefan Xenarios, Ioannis Anisimova, Maria (2015) TRAL: Tandem repeat annotation library. Bioinformatics 31 (18) 3051-3053.
  27. Frechin, Mathieu Stoeger, Thomas Daetwyler, Stephan Gehin, Charlotte Battich, Nico Damm, Eva-Maria Stergiou, Lilli Riezman, Howard Pelkmans, Lucas (2015) Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour. Nature 523 (7558) 88-91.
  28. Xie, Xiaojiang Gutiérrez, Agustín Trofimov, Valentin Szilagyi, Istvan Soldati, Thierry Bakker, Eric (2015) Potassium Sensitive Optical Nanosensors Containing Voltage Sensitive Dyes. CHIMIA 69 (4) 196-198.
  29. Boeckmann, Brigitte Marcet-Houben, Marina Rees, Jonathan A. Forslund, Kristoffer Huerta-Cepas, Jaime Muffato, Matthieu Yilmaz, Pelin Xenarios, Ioannis Bork, Peer Lewis, Suzanna E. Gabaldón, Toni (2015) Quest for Orthologs entails Quest for Tree of Life: in Search of the Gene Stream. Genome Biol. Evol. 7 (7) 1988-1999.
  30. Chasapi, Anastasia Wachowicz, Paulina Niknejad, Anne Collin, Philippe Krapp, Andrea Cano, Elena Simanis, Viesturs Xenarios, Ioannis Toda, Takashi (2015) An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation. PLoS ONE 10 (8) e0134214.
  31. Blom, Tomas Li, Shiqian Dichlberger, Andrea Bäck, Nils Kim, Young Ah Loizides-Mangold, Ursula Riezman, Howard Bittman, Robert Ikonen, Elina (2015) LAPTM4B facilitates late endosomal ceramide export to control cell death pathways. Nat. Chem. Biol. 11 (10) 799-806.
  32. Toruń, Anna Szymańska, Ewelina Castanon, Irinka Wolińska-Nizioł, Lidia Bartosik, Anna Jastrzębski, Kamil Miętkowska, Magdalena González-Gaitán, Marcos Miaczynska, Marta Königshoff, Melanie (2015) Endocytic Adaptor Protein Tollip Inhibits Canonical Wnt Signaling. PLoS ONE 10 (6) e0130818.
  33. Romanova-Michaelides, Maria Aguilar-Hidalgo, Daniel Jülicher, Frank Gonzalez-Gaitan, Marcos (2015) The wing and the eye: a parsimonious theory for scaling and growth control?. Wiley Interdiscip. Rev.: Dev. Biol. 4 (6) 591-608.
  34. Xie, Xiaojiang Gutierrez, Agustin Trofimov, Valentin Szilágyi, István Soldati, Thierry Bakker, Eric (2015) Charged Solvatochromic Dyes as Signal Transducers in pH Independent Fluorescent and Colorimetric Ion Selective Nanosensors. Anal. Chem. 87 (19) 9954-9959.
  35. Avinoam, Ori Schorb, Martin Beese, Carsten J. Briggs, John A. G. Kaksonen, Marko (2015) Endocytic sites mature by continuous bending and remodeling of the clathrin coat. Science 348 (6241) 1369-1372.
  36. Skruzny, Michal Desfosses, Ambroise Prinz, Simone Dodonova, Svetlana O. Gieras, Anna Uetrecht, Charlotte Jakobi, Arjen J. Abella, Marc Hagen, Wim J.H. Schulz, Joachim Meijers, Rob Rybin, Vladimir Briggs, John A.G. Sachse, Carsten Kaksonen, Marko (2015) An Organized Co-assembly of Clathrin Adaptors Is Essential for Endocytosis. Dev. Cell 33 (2) 150-162.
  37. Dan Dunn, Joe Alvarez, Luis A. J. Zhang, Xuezhi Soldati, Thierry (2015) Reactive oxygen species and mitochondria: A nexus of cellular homeostasis. Redox Biol. 6 472-485.
  38. Gonzalez-Gaitan, Marcos Roux, Aurélien (2015) When cell biology meets theory. J. Cell Biol. 210 (7) 1041-1045.
  39. Gonzalez-Gaitan, Marcos Roux, Aurélien (2015) When cell biology meets theory. J. Cell Biol. 210 (7) 1041-1045.
  40. Picco, Andrea Mund, Markus Ries, Jonas Nédélec, François Kaksonen, Marko (2015) Visualizing the functional architecture of the endocytic machinery. eLife 4 e04535.
  41. Lukinavičius, Gražvydas Blaukopf, Claudia Pershagen, Elias Schena, Alberto Reymond, Luc Derivery, Emmanuel Gonzalez-Gaitan, Marcos D’Este, Elisa Hell, Stefan W. Wolfram Gerlich, Daniel Johnsson, Kai (2015) SiR–Hoechst is a far-red DNA stain for live-cell nanoscopy. Nat. Commun. 6 8497.
  42. Johnson, Shem Gruenberg, Jean (2015) The pathway of VSV entry into cells. Biology and Pathogenesis of Rhabdo- and Filoviruses (Chapter 3)Ed. Pattnaik, Asit K. Whitt, Michael A.World Scientific. 33-47.
  43. Chiaruttini, Nicolas Redondo-Morata, Lorena Colom, Adai Humbert, Frédéric Lenz, Martin Scheuring, Simon Roux, Aurélien (2015) Relaxation of Loaded ESCRT-III Spiral Springs Drives Membrane Deformation. Cell 163 (4) 866-879.
  44. Derivery, Emmanuel Seum, Carole Daeden, Alicia Loubéry, Sylvain Holtzer, Laurent Jülicher, Frank Gonzalez-Gaitan, Marcos (2015) Polarized endosome dynamics by spindle asymmetry during asymmetric cell division. Nature 528 (7581) 280-285.
  45. Höglinger, Doris Haberkant, Per Aguilera-Romero, Auxiliadora Riezman, Howard Porter, Forbes D. Platt, Frances M. Galione, Antony Schultz, Carsten (2015) Intracellular sphingosine releases calcium from lysosomes. eLife 4 e10616.
  46. Doucey, Marie-Agnès Xenarios, Ioannis (2015) Toward a rational design of combination therapy in cancer. OncoImmunology 4 (11) e1046674.
  47. , SIB Swiss Institute of Bioinformatics Members (2015) The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Res. 44 (D1) D27-D37.
  48. Johann, D. Goswami, D. Kruse, Karsten (2015) Generation of Stable Overlaps between Antiparallel Filaments. Phys. Rev. Lett. 115 art. num. 118103.