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.