2012

• Friedrich, Nikolas; Hagedorn, Monica; Soldati-Favre, Dominique; Soldati, Thierry (2012) Prison Break: Pathogens' Strategies To Egress from Host Cells. Microbiol. Mol. Biol. Rev. 76 (4) 707-720.
• Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix; the CycliX consortium, (2012) Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles. PLoS Biol. 10 (11) e1001442.
• Fernandez, Paula; Solenthaler, Max; Spertini, Olivier; Quarroz, Stephane; Rovo, Alicia; Lovey, Pierre-Yves; Leoncini, Leda; Ruault-Jungblut, Sylvie; D?Asaro, Mathilde; Schaad, Olivier; Docquier, Mylène; Descombes, Patrick; Matthes, Thomas; Starczynowski, Daniel T. (2012) Using Digital RNA Counting and Flow Cytometry to Compare mRNA with Protein Expression in Acute Leukemias. PLoS ONE 7 (11) e49010.
• Morlot, Sandrine; Galli, Valentina; Klein, Marius; Chiaruttini, Nicolas; Manzi, John; Humbert, Frédéric; Dinis, Luis; Lenz, Martin; Cappello, Giovanni; Roux, Aurélien (2012) Membrane Shape at the Edge of the Dynamin Helix Sets Location and Duration of the Fission Reaction. Cell 151 (3) 619-629.
• Dieckmann, Régis; Gueho, Aurélie; Monroy, Roger; Ruppert, Thomas; Bloomfield, Gareth; Soldati, Thierry (2012) The Balance in the Delivery of ER Components and the Vacuolar Proton Pump to the Phagosome Depends on Myosin IK in Dictyostelium. Mol. Cell. Proteomics 11 (10) 886-900.
• Skruzny, Michal; Brach, Thorsten; Ciuffa, Rodolfo; Rybina, Sofia; Wachsmuth, Malte; Kaksonen, Marko (2012) Molecular basis for coupling the plasma membrane to the actin cytoskeleton during clathrin-mediated endocytosis. Proc. Natl. Acad. Sci. U. S. A. 109 (38) E2533-E2542.
• Kicheva, Anna; Bollenbach, Tobias; Wartlick, Ortrud; Jülicher, Frank; Gonzalez-Gaitan, Marcos (2012) Investigating the principles of morphogen gradient formation: from tissues to cells. Curr. Opin. Genet. Dev. 22 (6) 527-532.
• Kukulski, Wanda; Schorb, Martin; Kaksonen, Marko; Briggs, John A.G. (2012) Plasma Membrane Reshaping during Endocytosis Is Revealed by Time-Resolved Electron Tomography. Cell 150 (3) 508-520.
• Kukulski, Wanda Schorb, Martin Welsch, Sonja Picco, Andrea Kaksonen, Marko Briggs, John A.G. (2012) Precise, Correlated Fluorescence Microscopy and Electron Tomography of Lowicryl Sections Using Fluorescent Fiducial Markers. Correlative Light and Electron Microscopy Volume 111 (Chapter 13)Ed. Müller-Reichert, Thomas Verkade, PaulMethods in Cell Biology. Elsevier. 235-257.
• Santos, Aline X. S.; Riezman, Howard (2012) Yeast as a model system for studying lipid homeostasis and function. FEBS Lett. 586 (18) 2858-2867.
• Kornmann, Benoît; Roux, Aurélien (2012) Lipids as organizers of cell membranes. EMBO Rep. 13 (8) 667-669.
• Gruenberg, Jean (2012) An MBoC Favorite: Functional interactions between sphingolipids and sterols in biological membranes regulating cell physiology. Mol. Biol. Cell 23 (13) 2402.
• Jarmoszewicz, Katarzyna; Łukasiak, Katarzyna; Riezman, Howard; Kaminska, Joanna; Polymenis, Michael (2012) Rsp5 Ubiquitin Ligase Is Required for Protein Trafficking in Saccharomyces cerevisiae COPI Mutants. PLoS ONE 7 (6) e39582.
• Hornitschek, Patricia; Kohnen, Markus V.; Lorrain, Séverine; Rougemont, Jacques; Ljung, Karin; López-Vidriero, Irene; Franco-Zorrilla, José M.; Solano, Roberto; Trevisan, Martine; Pradervand, Sylvain; Xenarios, Ioannis; Fankhauser, Christian (2012) Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J. 71 (5) 699-711.
• Pons, Véronique; Ustunel, Cansel; Rolland, Corinne; Torti, Eleonora; Parton, Robert G.; Gruenberg, Jean; Johannes, Ludger (2012) SNX12 Role in Endosome Membrane Transport. PLoS ONE 7 (6) e38949.
• Kobayashi, Tomonori; Komatsu, Toru; Kamiya, Mako; Campos, Cláudia; González-Gaitán, Marcos; Terai, Takuya; Hanaoka, Kenjiro; Nagano, Tetsuo; Urano, Yasuteru (2012) Highly Activatable and Environment-Insensitive Optical Highlighters for Selective Spatiotemporal Imaging of Target Proteins. J. Am. Chem. Soc. 134 (27) 11153-11160.
• Tollis, Sylvain Gopaldass, Navin Soldati, Thierry Endres, Robert G. (2012) How One Cell Eats Another: Principles of Phagocytosis. Systems Microbiology: Current Topics and Applications (Chapter 6)Ed. Robertson, Brian D. Wren, Brendan W.Caister Academic Press. (Norfolk). 97-128.
• Artimo, Panu; Jonnalagedda, Manohar; Arnold, Konstantin; Baratin, Delphine; Csardi, Gabor; de Castro, Edouard; Duvaud, Séverine; Flegel, Volker; Fortier, Arnaud; Gasteiger, Elisabeth; Grosdidier, Aurélien; Hernandez, Céline; Ioannidis, Vassilios; Kuznetsov, Dmitry; Liechti, Robin; Moretti, Sébastien; Mostaguir, Khaled; Redaschi, Nicole; Rossier, Grégoire; Xenarios, Ioannis; Stockinger, Heinz (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 40 (W1) W597-W603.
• Loizides-Mangold, Ursula; David, Fabrice P. A.; Nesatyy, Victor J.; Kinoshita, Taroh; Riezman, Howard (2012) Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. J. Lipid Res. 53 (8) 1522-1534.
• Epstein, Sharon; Castillon, Guillaume A.; Qin, Yongmei; Riezman, Howard (2012) An essential function of sphingolipids in yeast cell division. Mol. Microbiol. 84 (6) 1018-1032.
• Snijder, Berend; Sacher, Raphael; Rämö, Pauli; Liberali, Prisca; Mench, Karin; Wolfrum, Nina; Burleigh, Laura; Scott, Cameron C.; Verheije, Monique H.; Mercer, Jason; Moese, Stefan; Heger, Thomas; Theusner, Kristina; Jurgeit, Andreas; Lamparter, David; Balistreri, Giuseppe; Schelhaas, Mario; De Haan, Cornelis A. M.; Marjomäki, Varpu; Hyypiä, Timo; Rottier, Peter J. M.; Sodeik, Beate; Marsh, Mark; Gruenberg, Jean; Amara, Ali; Greber, Urs; Helenius, Ari; Pelkmans, Lucas (2012) Single-cell analysis of population context advances RNAi screening at multiple levels. Mol. Syst. Biol. 8:579 18 pp.
• Soldati, Thierry; Neyrolles, Olivier (2012) Mycobacteria and the Intraphagosomal Environment: Take It With a Pinch of Salt(s)!. Traffic 13 (8) 1042-1052.
• Berchtold, Doris; Piccolis, Manuele; Chiaruttini, Nicolas; Riezman, Isabelle; Riezman, Howard; Roux, Aurélien; Walther, Tobias C.; Loewith, Robbie (2012) Plasma membrane stress induces relocalization of Slm proteins and activation of TORC2 to promote sphingolipid synthesis. Nat. Cell Biol. 14 (5) 542-547.
• Alonso Doval, David; Fin, Andrea; Takahashi-Umebayashi, Miwa; Riezman, Howard; Roux, Aurelien; Sakai, Naomi; Matile, Stefan (2012) Amphiphilic Dynamic NDI and PDI Probes:  Imaging Microdomains in Giant Unilamellar Vesicles. Org. Biomol. Chem. 10 (30) 6087-6093.
• Klionsky, Daniel J.; Abdalla, Fabio C.; Abeliovich, Hagai; Abraham, Robert T.; ..., ; Soldati, Thierry; et al., (2012) Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8 (4) 445-544.
• Orchard, Sandra; Kerrien, Samuel; Abbani, Sara; Aranda, Bruno; Bhate, Jignesh; Bidwell, Shelby; Bridge, Alan; Briganti, Leonardo; Brinkman, Fiona; Cesareni, Gianni; Chatr-aryamontri, Andrew; Chautard, Emilie; Chen, Carol; Dumousseau, Marine; Goll, Johannes; Hancock, Robert; Hannick, Linda I.; Jurisica, Igor; Khadake, Jyoti; Lynn, David J.; Mahadevan, Usha; Perfetto, Livia; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Salwinski, Lukasz; Stümpflen, Volker; Tyers, Mike; Uetz, Peter; Xenarios, Ioannis; Hermjakob, Henning (2012) Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Meth. 9 (4) 345-350.
• Jungo, Florence; Bougueleret, Lydie; Xenarios, Ioannis; Poux, Sylvain (2012) The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon 60 (4) 551-557.
• Burge, Sarah; Attwood, Teresa K.; Bateman, Alex; Berardini, Tanya Z.; Cherry, Michael; O'Donovan, Claire; Xenarios, loannis; Gaudet, Pascale (2012) Biocurators and Biocuration: surveying the 21st century challenges. Database bar059.
• Brankatschk, Ben; Wichert, Sven P.; Johnson, Shem D.; Schaad, Olivier; Rossner, Moritz J.; Gruenberg, Jean (2012) Regulation of the EGF Transcriptional Response by Endocytic Sorting. Sci. Signaling 5 (215) ra21.
• Epstein, Sharon; Kirkpatrick, Clare L.; Castillon, Guillaume A.; Muniz, Manuel; Riezman, Isabelle; David, Fabrice P. A.; Wollheim, Claes B.; Riezman, Howard (2012) Activation of the unfolded protein response pathway causes ceramide accumulation in yeast and INS-1E insulinoma cells. J. Lipid Res. 53 (3) 412-420.
• Lima, Wanessa C.; Leuba, Florence; Soldati, Thierry; Cosson, Pierre (2012) Mucolipin controls lysosome exocytosis in Dictyostelium. J. Cell Sci. 125 (9) 2315-2322.
• Essid, Miriam; Gopaldass, Navin; Yoshida, Kunito; Merrifield, Christien; Soldati, Thierry (2012) Rab8a regulates the exocyst-mediated kiss-and-run discharge of the Dictyostelium contractile vacuole. Mol. Biol. Cell 23 (7) 1267-1282.
• Bissig, Christin Johnson, Shem Gruenberg, Jean (2012) Studying Lipids Involved in the Endosomal Pathway. Lipids Volume 108 (Chapter 2)Methods in Cell Biology. Elsevier. 19-46.
• Jennemann, Richard; Rabionet, Mariona; Gorgas, Karin; Epstein, Sharon; Dalpke, Alexander; Rothermel, Ulrike; Bayerle, Aline; van der Hoeven, Franciscus; Imgrund, Silke; Kirsch, Joachim; Nickel, Walter; Willecke, Klaus; Riezman, Howard; Grone, Hermann-Josef; Sandhoff, Roger (2012) Loss of ceramide synthase 3 causes lethal skin barrier disruption. Hum. Mol. Genet. 21 (3) 586-608.
• Wartlick, Ortrud; Mumcu, Peer; Julicher, Frank; Gonzalez-Gaitan, Marcos (2012) Response to Comment on “Dynamics of Dpp Signaling and Proliferation Control”. Science 335 (6067) 401.
• Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral-Zettler, Linda; Begley, Kimberly; Booth, Tim; Bougueleret, Lydie; Burns, Gully; Chapman, Brad; Clark, Tim; Coleman, Lee-Ann; Copeland, Jay; Das, Sudeshna; de Daruvar, Antoine; de Matos, Paula; Dix, Ian; Edmunds, Scott; Evelo, Chris T.; Forster, Mark J.; Gaudet, Pascale; Gilbert, Jack; Goble, Carole; Griffin, Julian L.; Jacob, Daniel; Kleinjans, Jos; Harland, Lee; Haug, Kenneth; Hermjakob, Henning; Sui, Shannan J. Ho; Laederach, Alain; Liang, Shaoguang; Marshall, Stephen; McGrath, Annette; Merrill, Emily; Reilly, Dorothy; Roux, Magali; Shamu, Caroline E.; Shang, Catherine A.; Steinbeck, Christoph; Trefethen, Anne; Williams-Jones, Bryn; Wolstencroft, Katherine; Xenarios, Ioannis; Hide, Winston (2012) Toward interoperable bioscience data. Nat. Genet. 44 (2) 121-126.
• Jaiswal, Pundrik; Soldati, Thierry; Thewes, Sascha; Baskar, Ramamurthy (2012) Regulation of aggregate size and pattern by adenosine and caffeine in cellular slime molds. BMC Dev. Biol. 12 (1) 5.
• Sorre, Benoît; Callan-Jones, Andrew; Manzi, John; Goud, Bruno; Prost, Jacques; Bassereau, Patricia; Roux, Aurélien (2012) Nature of curvature coupling of amphiphysin with membranes depends on its bound density. Proc. Natl. Acad. Sci. U. S. A. 109 (1) 173-178.
• Saurat, Jean-Hilaire; Kaya, Guerkan; Saxer-Sekulic, Nikolina; Pardo, Bruno; Becker, Minerva; Fontao, Lionel; Mottu, Florence; Carraux, Pierre; Pham, Xuan-Cuong; Barde, Caroline; Fontao, Fabienne; Zennegg, Markus; Schmid, Peter; Schaad, Olivier; Descombes, Patrick; Sorg, Olivier (2012) The Cutaneous Lesions of Dioxin Exposure: Lessons from the Poisoning of Victor Yushchenko. Toxicol. Sci. 125 (1) 310-317.
• Nikolaev, Sergey I.; Rimoldi, Donata; Iseli, Christian; Valsesia, Armand; Robyr, Daniel; Gehrig, Corinne; Harshman, Keith; Guipponi, Michel; Bukach, Olesya; Zoete, Vincent; Michielin, Olivier; Muehlethaler, Katja; Speiser, Daniel; Beckmann, Jacques S.; Xenarios, Ioannis; Halazonetis, Thanos D.; Jongeneel, C. Victor; Stevenson, Brian J.; Antonarakis, Stylianos E (2012) Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat. Genet. 44 (2) 133-139.
• The Gene Ontology Consortium, (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res. 40 (D1) D559-D564.
• Alcántara, Rafael; Axelsen, Kristian B.; Morgat, Anne; Belda, Eugeni; Coudert, Elisabeth; Bridge, Alan; Cao, Hong; de Matos, Paula; Ennis, Marcus; Turner, Steve; Owen, Gareth; Bougueleret, Lydie; Xenarios, Ioannis; Steinbeck, Christoph (2012) Rhea—a manually curated resource of biochemical reactions. Nucleic Acids Res. 40 (D1) D754-D760.
• Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf (2012) The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40 (D1) D565-D570.
• Morgat, Anne; Coissac, Eric; Coudert, Elisabeth; Axelsen, Kristian B.; Keller, Guillaume; Bairoch, Amos; Bridge, Alan; Bougueleret, Lydie; Xenarios, Ioannis; Viari, Alain (2012) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res. 40 (D1) D761-D769.
• The UniProt Consortium, (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40 (D1) D71-D75.
• Gopaldass, Navin; Patel, Devang; Kratzke, Ramona; Dieckmann, Regis; Hausherr, Stéphanie; Hagedorn, Monica; Monroy, Roger; Krüger, Julia; Neuhaus, Eva M.; Hoffmann, Eik; Hille, Katja; Kuznetsov, Sergei A.; Soldati, Thierry (2012) Dynamin A, Myosin IB and Abp1 Couple Phagosome Maturation to F-Actin Binding. Traffic 13 (1) 120-130.
• Falguières, Thomas; Castle, David; Gruenberg, Jean (2012) Regulation of the MVB Pathway by SCAMP3. Traffic 13 (1) 131-142.
• Garg, Abhishek Mohanram, Kartik De Micheli, Giovanni Xenarios, Ioannis (2012) Implicit Methods for Qualitative Modeling of Gene Regulatory Networks. Gene Regulatory Networks Vol. 786Ed. Deplancke, Bart Gheldof, NeleMethods in Molecular Biology. Humana Press. 397-343.