Publications

2015

  • 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.
  • , 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.
  • 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.
  • 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.
  • 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.
  • Aumeier, Charlotte; Polinski, Ellen; Menzel, Diedrik (2015) Actin, actin-related proteins and profilin in diatoms: A comparative genomic analysis. Mar. Genomics 23 133-142.
  • Gonzalez-Gaitan, Marcos; Roux, Aurélien (2015) When cell biology meets theory. J. Cell Biol. 210 (7) 1041-1045.
  • 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.
  • 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.
  • Johann, D.; Goswami, D.; Kruse, Karsten (2015) Generation of Stable Overlaps between Antiparallel Filaments. Phys. Rev. Lett. 115 art. num. 118103.
  • 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.
  • 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.
  • Doucey, Marie-Agnès; Xenarios, Ioannis (2015) Toward a rational design of combination therapy in cancer. OncoImmunology 4 (11) e1046674.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Picco, Andrea; Mund, Markus; Ries, Jonas; Nédélec, François; Kaksonen, Marko (2015) Visualizing the functional architecture of the endocytic machinery. eLife 4 e04535.
  • 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.
  • 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.
  • Manzano-Lopez, Javier; Perez-Linero, Ana M.; Aguilera-Romero, Auxiliadora; Martin, Maria E.; Okano, Tatsuki; Silva, Daniel Varon; Seeberger, Peter H.; Riezman, Howard; Funato, Kouichi; Goder, Veit; Wellinger, Ralf E.; Muñiz, Manuel (2015) COPII Coat Composition Is Actively Regulated by Luminal Cargo Maturation. Curr. Biol. 25 (2) 152-162.
  • 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.
  • 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.
  • 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.
  • 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.
  • The Gene Ontology Consortium*, (2015) Gene Ontology Consortium: going forward. Nucleic Acids Res. 43 (D1) D1049-D1056.
  • 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.
  • 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.
  • 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.