Publications

2016

  • Moreau, Dimitri; Gruenberg, Jean (2016) Automated Microscopy and High Content Screens (Phenotypic Screens) in Academia Labs. Chimia 70 (12) 878-882.
  • Soleimanpour, Saeideh; Colom, Adai; Derivery, Emmanuel; Gonzalez-Gaitan, Marcos; Roux, Aurelien; Sakai, Naomi; Matile, Stefan (2016) Headgroup Engineering in Mechanosensitive Membrane Probes. Chem. Commun. 52 (100) 14450-14453.
  • Dhingra, Madhur S.; Artois, Jean; Robinson, Timothy P.; Linard, Catherine; Chaiban, Celia; Xenarios, Ioannis; Engler, Robin; Liechti, Robin; Kuznetsov, Dimitry; Xiao, Xiangming; Von Dobschuetz, Sophie; Claes, Filip; Newman, Scott H.; Dauphin, Gwenaëlle; Gilbert, Marius (2016) Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation. eLife , 10.7554/eLife.19571.
  • Rodrigues, Tania; Krawczyk, Michal; Skowronska-Krawczyk, Dorota; Matter-Sadzinski, Lidia; Matter, Jean-Marc (2016) Delayed neurogenesis with respect to eye growth shapes the pigeon retina for high visual acuity. Development 143 4701-4712.
  • Bonny, Mike; Hui, Xin; Schweizer, Julia; Kaestner, Lars; Zeug, André; Kruse, Karsten; Lipp, Peter (2016) C2-domain mediated nano-cluster formation increases calcium signaling efficiency. Sci. Rep. 6 art. num. 36028.
  • Loviglio, Maria Nicla; Beck, Christine R.; White, Janson J.; Leleu, Marion; Harel, Tamar; Guex, Nicolas; Niknejad, Anne; Bi, Weimin; Chen, Edward S.; Crespo, Isaac; Yan, Jiong; Charng, Wu-Lin; Gu, Shen; Fang, Ping; Coban-Akdemir, Zeynep; Shaw, Chad A.; Jhangiani, Shalini N.; Muzny, Donna M.; Gibbs, Richard A.; Rougemont, Jacques; Xenarios, Ioannis; Lupski, James R.; Reymond, Alexandre (2016) Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Med. 8 (1) 105.
  • Aumeier, Charlotte; Schaedel, Laura; Gaillard, Jérémie; John, Karin; Blanchoin, Laurent; Théry, Manuel (2016) Self-repair promotes microtubule rescue. Nat. Cell Biol. 18 (10) 1054-1064.
  • Dorier, Julien; Crespo, Isaac; Niknejad, Anne; Liechti, Robin; Ebeling, Martin; Xenarios, Ioannis (2016) Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method. BMC Bioinf. 75 (6) 066701.
  • Antonny, Bruno; Burd, Christopher; De Camilli, Pietro; Chen, Elizabeth; Daumke, Oliver; Faelber, Katja; Ford, Marijn; Frolov, Vadim A.; Frost, Adam; Hinshaw, Jenny E.; Kirchhausen, Tom; Kozlov, Michael M.; Lenz, Martin; Low, Harry H.; McMahon, Harvey; Merrifield, Christien; Pollard, Thomas D.; Robinson, Phillip J.; Roux, Aurélien; Schmid, Sandra (2016) Membrane fission by dynamin: what we know and what we need to know. EMBO J. 35 (21) 2270-2284.
  • Megyeri, Márton; Riezman, Howard; Schuldiner, Maya; Futerman, Anthony H. (2016) Making Sense of the Yeast Sphingolipid Pathway. J. Mol. Biol. 428 (24 Part A) 4765-4775.
  • Buckley, Catherine M.; Gopaldass, Navin; Bosmani, Cristina; Johnston, Simon A.; Soldati, Thierry; Insall, Robert H.; King, Jason S. (2016) WASH drives early recycling from macropinosomes and phagosomes to maintain surface phagocytic receptors. Proc. Natl. Acad. Sci. USA 113 (40) E5906-E5915.
  • Muriel, Olivia; Tomas, Alejandra; Scott, Cameron C.; Gruenberg, Jean (2016) Moesin and cortactin control actin-dependent multivesicular endosome biogenesis. Mol. Biol. Cell 27 (21) 3305-3316.
  • Van Voorhis, Wesley C.; Adams, John H.; Adelfio, Roberto; Ahyong, Vida; Akabas, Myles H.; Alano, Pietro; Alday, Aintzane; Alemán Resto, Yesmalie; Alsibaee, Aishah; Alzualde, Ainhoa; Andrews, Katherine T.; Avery, Simon V.; Avery, Vicky M.; Ayong, Lawrence; Baker, Mark; Baker, Stephen; Ben Mamoun, Choukri; Bhatia, Sangeeta; Bickle, Quentin; Bounaadja, Lotfi; Bowling, Tana; Bosch, Jürgen; Boucher, Lauren E.; Boyom, Fabrice F.; Brea, Jose; Brennan, Marian; Burton, Audrey; Caffrey, Conor R.; Camarda, Grazia; Carrasquilla, Manuela; Carter, Dee; Belen Cassera, Maria; Chih-Chien Cheng, Ken; Chindaudomsate, Worathad; Chubb, Anthony; Colon, Beatrice L.; Colón-López, Daisy D.; Corbett, Yolanda; Crowther, Gregory J.; Cowan, Noemi; D\'Alessandro, Sarah; Le Dang, Na; Delves, Michael; DeRisi, Joseph L.; Du, Alan Y.; Duffy, Sandra; Abd El-Salam El-Sayed, Shimaa; Ferdig, Michael T.; Fernández Robledo, José A.; Fidock, David A.; Florent, Isabelle; Fokou, Patrick V. T.; Galstian, Ani; Gamo, Francisco Javier; Gokool, Suzanne; Gold, Ben; Golub, Todd; Goldgof, Gregory M.; Guha, Rajarshi; Guiguemde, W. Armand; Gural, Nil; Guy, R. Kiplin; Hansen, Michael A. E.; Hanson, Kirsten K.; Hemphill, Andrew; Hooft van Huijsduijnen, Rob; Horii, Takaaki; Horrocks, Paul; Hughes, Tyler B.; Huston, Christopher; Igarashi, Ikuo; Ingram-Sieber, Katrin; Itoe, Maurice A.; Jadhav, Ajit; Naranuntarat Jensen, Amornrat; Jensen, Laran T.; Jiang, Rays H. Y.; Kaiser, Annette; Keiser, Jennifer; Ketas, Thomas; Kicka, Sebastien; Kim, Sunyoung; Kirk, Kiaran; Kumar, Vidya P.; Kyle, Dennis E.; Lafuente, Maria Jose; Landfear, Scott; Lee, Nathan; Lee, Sukjun; Lehane, Adele M.; Li, Fengwu; Little, David; Liu, Liqiong; Llinás, Manuel; Loza, Maria I.; Lubar, Aristea; Lucantoni, Leonardo; Lucet, Isabelle; Maes, Louis; Mancama, Dalu; Mansour, Nuha R.; March, Sandra; McGowan, Sheena; Medina Vera, Iset; Meister, Stephan; Mercer, Luke; Mestres, Jordi; Mfopa, Alvine N.; Misra, Raj N.; Moon, Seunghyun; Moore, John P.; Morais Rodrigues da Costa, Francielly; Müller, Joachim; Muriana, Arantza; Nakazawa Hewitt, Stephen; Nare, Bakela; Nathan, Carl; Narraidoo, Nathalie; Nawaratna, Sujeevi; Ojo, Kayode K.; Ortiz, Diana; Panic, Gordana; Papadatos, George; Parapini, Silvia; Patra, Kailash; Pham, Ngoc; Prats, Sarah; Plouffe, David M.; Poulsen, Sally-Ann; Pradhan, Anupam; Quevedo, Celia; Quinn, Ronald J.; Rice, Christopher A.; Abdo Rizk, Mohamed; Ruecker, Andrea; St. Onge, Robert; Salgado Ferreira, Rafaela; Samra, Jasmeet; Robinett, Natalie G.; Schlecht, Ulrich; Schmitt, Marjorie; Silva Villela, Filipe; Silvestrini, Francesco; Sinden, Robert; Smith, Dennis A.; Soldati, Thierry; Spitzmüller, Andreas; Stamm, Serge Maximilian; Sullivan, David J.; Sullivan, William; Suresh, Sundari; Suzuki, Brian M.; Suzuki, Yo; Swamidass, S. Joshua; Taramelli, Donatella; Tchokouaha, Lauve R. Y.; Theron, Anjo; Thomas, David; Tonissen, Kathryn F.; Townson, Simon; Tripathi, Abhai K.; Trofimov, Valentin; Udenze, Kenneth O.; Ullah, Imran; Vallieres, Cindy; Vigil, Edgar; Vinetz, Joseph M.; Voong Vinh, Phat; Vu, Hoan; Watanabe, Nao-aki; Weatherby, Kate; White, Pamela M.; Wilks, Andrew F.; Winzeler, Elizabeth A.; Wojcik, Edward; Wree, Melanie; Wu, Wesley; Yokoyama, Naoaki; Zollo, Paul H. A.; Abla, Nada; Blasco, Benjamin; Burrows, Jeremy; Laleu, Benoît; Leroy, Didier; Spangenberg, Thomas; Wells, Timothy; Willis, Paul A.; Phillips, Margaret A. (2016) Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLoS Pathog. 12 (7) e1005763.
  • Artois, Jean; Newman, Scott H.; Dhingra, Madhur S.; Chaiban, Celia; Linard, Catherine; Cattoli, Giovanni; Monne, Isabella; Fusaro, Alice; Xenarios, Ioannis; Engler, Robin; Liechti, Robin; Kuznetsov, Dmitri; Pham, Thanh Long; Nguyen, Tung; Pham, Van Dong; Castellan, David; Von Dobschuetz, Sophie; Claes, Filip; Dauphin, Gwenaëlle; Inui, Ken; Gilbert, Marius (2016) Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors. Sci. Rep. 6 30316.
  • Delincé, Matthieu Jean-Hubert; Bureau, Jean-Baptiste; López-Jiménez, Ana Teresa; Cosson, Pierre; Soldati, Thierry; McKinney, John (2016) A microfluidic cell-trapping device for single-cell tracking of host-microbe interactions. Lab Chip 16 (17) 3276-3285.
  • Zhang, Xuezhi; Soldati, Thierry (2016) Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism. Front. Immunol. 7 269.
  • Wollrab, Viktoria; Thiagarajan, Raghavan; Wald, Anne; Kruse, Karsten; Riveline, Daniel (2016) Still and rotating myosin clusters determine cytokinetic ring constriction. Nat. Commun. 7 art. num. 11860.
  • Kukulski, Wanda; Picco, Andrea; Specht, Tanja; Briggs, John A. G.; Kaksonen, Marko (2016) Clathrin modulates vesicle scission, but not invagination shape, in yeast endocytosis. eLife 5 e16036.
  • Johann, D.; Goswami, D.; Kruse, Karsten (2016) Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors. Phys. Rev. E 93 062415.
  • Hohendahl, Annika; Roux, Aurélien; Galli, Valentina (2016) Structural insights into the centronuclear myopathy-associated functions of BIN1 and dynamin 2. J. Struct. Biol. 196 (1) 37-47.
  • Sikorska, Natalia; Lemus, Leticia; Aguilera-Romero, Auxiliadora; Manzano-Lopez, Javier; Riezman, Howard; Muñiz, Manuel; Goder, Veit (2016) Limited ER quality control for GPI-anchored proteins. J. Cell Biol. 269 (6) 19695-704.
  • Bertipaglia, Chiara; Schneider, Sarah; Jakobi, Arjen J.; Tarafder, Abul K.; Bykov, Yury S.; Picco, Andrea; Kukulski, Wanda; Kosinski, Jan; Hagen, Wim J. H.; Ravichandran, Arvind C.; Wilmanns, Matthias; Kaksonen, Marko; Briggs, John A. G.; Sachse, Carsten (2016) Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. EMBO Rep. 17 (7) 1044-1060.
  • Degueurce, Gwendoline; D\'Errico, Ilenia; Pich, Christine; Ibberson, Mark; Schütz, Frédéric; Montagner, Alexandra; Sgandurra, Marie; Mury, Lionel; Jafari, Paris; Boda, Akash; Meunier, Julien; Rezzonico, Roger; Brembilla, Nicolò Costantino; Hohl, Daniel; Kolios, Antonios; Hofbauer, Günther; Xenarios, Ioannis; Michalik, Liliane (2016) Identification of a novel PPARβ/δ/miR‐21‐3p axis in UV‐induced skin inflammation. EMBO Mol Med. e201505384.
  • Rodius, Sophie; Androsova, Ganna; Götz, Lou; Liechti, Robin; Crespo, Isaac; Merz, Susanne; Nazarov, Petr V.; de Klein, Niek; Jeanty, Céline; González-Rosa, Juan M.; Muller, Arnaud; Bernardin, Francois; Niclou, Simone P.; Vallar, Laurent; Mercader, Nadia; Ibberson, Mark; Xenarios, Ioannis; Azuaje, Francisco (2016) Analysis of the dynamic co-expression network of heart regeneration in the zebrafish. Sci. Rep. 6 26822.
  • Holtzer, Laurent; Oleinich, Igor; Anzola, Marcello; Lindberg, Eric; Sadhu, Kalyan K.; Gonzalez-Gaitan, Marcos; Winssinger, Nicolas (2016) Nucleic Acid Templated Chemical Reaction in a Live Vertebrate. ACS Cent. Sci. 2 (6) 394-400.
  • Gueho, Aurélie; Bosmani, Cristina; Gopaldass, Navin; Molle, Virginie; Soldati, Thierry; Letourneur, François (2016) Dictyostelium EHD associates with Dynamin and participates in phagosome maturation. J. Cell Sci. 129 2354-2367.
  • Savoglidis, Georgios; da Silveira dos Santos, Aline Xavier; Riezman, Isabelle; Angelino, Paolo; Riezman, Howard; Hatzimanikatis, Vassily (2016) A method for analysis and design of metabolism using metabolomics data and kinetic models: application on lipidomics using a novel kinetic model of sphingolipid metabolism. Metab. Eng. 37 46-62.
  • Druce, Megan; Hulo, Chantal; Masson, Patrick; Sommer, Paula; Xenarios, Ioannis; Le Mercier, Philippe; De Oliveira, Tulio (2016) Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. Database 2016 baw045.
  • Zufferey, Anne; Ibberson, Mark; Reny, Jean-Luc; Nolli, S?verine; Schvartz, Domitille; Docquier, Myl?ne; Xenarios, Ioannis; Sanchez, Jean-Charles; Fontana, Pierre (2016) New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach. Hum Genet 101 (43) 130-414.
  • Altenhoff, Adrian M.; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A.; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P.; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Jensen, Lars Juhl; Martin, Maria J.; Muffato, Matthieu; Altenhoff, Adrian M.; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P.; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Lecompte, Odile; Xenarios, Ioannis; Sjölander, Kimmen; Martin, Maria J.; Muffato, Matthieu; Gabaldón, Toni; Lewis, Suzanna E.; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe; Gabaldón, Toni; Lewis, Suzanna E.; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe (2016) Standardized benchmarking in the quest for orthologs. Nat. Methods 13 425-430.
  • Fritzsche, Marco; Erlenkämper, Christoph; Moeendarbary, Emade; Charras, Guillaume; Kruse, Karsten (2016) Actin kinetics shapes cortical network structure and mechanics. Sci. Adv. 2 (4) e1501337.
  • Alessandri, Kevin; Feyeux, Maxime; Gurchenkov, Basile; Delgado, Christophe; Trushko, Anastasiya; Krause, Karl-Heinz; Vignjevic, Danijela; Nassoy, Pierre; Roux, Aurélien (2016) A 3D printed microfluidic device for production of functionalized hydrogel microcapsules for culture and differentiation of human Neuronal Stem Cells (hNSC). Lab Chip 16 (9) 1593-1604.
  • Lugli, Natalia; Kamileri, Irene; Keogh, Adrian; Malinka, Thomas; Sarris, Michalis E.; Talianidis, Iannis; Schaad, Olivier; Candinas, Daniel; Stroka, Deborah; Halazonetis, Thanos D. (2016) R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders. EMBO Rep. 17 (5) 769-779.
  • Crespo, Isaac; Doucey, Marie-Agnès; Xenarios, Ioannis (2016) Social networks help to infer causality in the tumor microenvironment. BMC Res. Notes 9 (1) 1-10.
  • Zhang, Xuezhi; Zhuchenko, Olga; Kuspa, Adam; Soldati, Thierry (2016) Social amoebae trap and kill bacteria by casting DNA nets. Nat. Commun. 7 10938.
  • Zufferey, Anne; Ibberson, Mark; Reny, Jean-Luc; Nolli, Séverine; Schvartz, Domitille; Docquier, Mylène; Xenarios, Ioannis; Sanchez, Jean-Charles; Fontana, Pierre (2016) New molecular insights into modulation of platelet reactivity in aspirin-treated patients using a network-based approach. Hum. Genet. 135 (4) 403-414.
  • Crippa, Stefania; Nemir, Mohamed; Ounzain, Samir; Ibberson, Mark; Berthonneche, Corinne; Sarre, Alexandre; Boisset, Gaëlle; Maison, Damien; Harshman, Keith; Xenarios, Ioannis; Diviani, Dario; Schorderet, Daniel; Pedrazzini, Thierry (2016) Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways. Cardiovasc. Res. 110 (1) 73-84.
  • Wallabregue, Antoine; Moreau, Dimitri; Sherin, Peter; Moneva Lorente, Pau; Jarolímová, Zdeňka; Bakker, Eric; Vauthey, Eric; Gruenberg, Jean; Lacour, Jérôme (2016) Selective Imaging of Late Endosomes with a pH-Sensitive Diazaoxatriangulene Fluorescent Probe. J. Am. Chem. Soc. 138 (6) 1752-1755.
  • Mamińska1, Agnieszka; Bartosik, Anna; Banach-Orłowska, Magdalena; Pilecka, Iwona; Jastrzębski, Kamil; Zdżalik-Bielecka, Daria; Castanon, Irinka; Poulain, Morgane; Neyen, Claudine; Wolińska-Nizioł, Lidia; Toruń, Anna; Szymańska, Ewelina; Kowalczyk, Agata; Piwocka, Katarzyna; Simonsen, Anne; Stenmark, Harald; Fürthauer, Maximilian; González-Gaitán, Marcos; Miaczynska, Marta (2016) ESCRT proteins restrict constitutive NF-κB signaling by trafficking cytokine receptors. Sci. Signaling 9 (411) ra8.
  • Slepikas, Liudas; Chiriano, Gianpaolo; Perozzo, Remo; Tardy, Sébastien; Kranjc-Pietrucci, Agata; Patthey-Vuadens, Ophélie; Ouertatani-Sakouhi, Hajer; Kicka, Sébastien; Harrison, Christopher F.; Scrignari, Tiziana; Perron, Karl; Hilbi, Hubert; Soldati, Thierry; Cosson, Pierre; Tarasevicius, Eduardas; Scapozza, Leonardo (2016) In silico driven design and synthesis of rhodanine derivatives as novel antibacterials targeting the enoyl reductase InhA. J. Med. Chem. 59 (24) 10917-10928.
  • Boutet, Emmanuel Lieberherr, Damien Tognolli, Michael Schneider, Michel Bansal, Parit Bridge, Alan J. Poux, Sylvain Bougueleret, Lydie Xenarios, Ioannis (2016) UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Plant Bioinformatics Volume 1374Ed. Edwards, DavidMethods in Molecular Biology. Springer. (New-York). 23-54.
  • Garcia, Alba Alfonso; Pfisterer, Simon G.; Riezman, Howard; Ikonen, Elina; Potma, Eric O. (2016) D38-cholesterol as a Raman active probe for imaging intracellular cholesterol storage. J. Biomed. Opt. 21 (6) 061003.
  • Reny, Jean-Luc; Fontana, Pierre; Hochholzer, Willibald; Neumann, Franz Josef; ten Berg, Jurriën; Janssen, Paul W.; Geisler, Tobias; Gawaz, Meinrad; Marcucci, Rossella; Gori, Anna-Maria; Cuisset, Thomas; Alessi, Marie-Christine; Berdagué, Philippe; Gurbel, Paul A.; Yong, Gerald; Angiolillo, Dominick J.; Aradi, Daniel; Beigel, Roy; Campo, Gianluca; Combescure, Christophe (2016) Vascular risk levels affect the predictive value of platelet reactivity for the occurrence of MACE in patients on clopidogrel. Systematic review and meta-analysis of individual patient data.. Thromb. Haemostasis 115 (4) 844-855.
  • Alfaiz, Ali Abdullah; Müller, Verena; Boutry-Kryza, Nadia; Ville, Dorothée; Guex, Nicolas; de Bellescize, Julitta; Rivier, Clotilde; Labalme, Audrey; des Portes, Vincent; Edery, Patrick; Till, Marianne; Xenarios, Ioannis; Sanlaville, Damien; Herrmann, Johannes M.; Lesca, Gaétan; Reymond, Alexandre (2016) West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1. Eur. J. Hum. Genet. 24 1001-1008.
  • Muñiz, Manuel; Riezman, Howard (2016) Trafficking of glycosylphosphatidyl inositol anchored proteins from the endoplasmic reticulum to the cell surface. J. Lipid Res. 57 352-360.
  • Bron, Sylvian; Henry, Luc; Faes-van\'t Hull, Eveline; Turrini, Riccardo; Vanhecke, Dominique; Guex, Nicolas; Ifticene-Treboux, Assia; Marina Iancu, Emanuela; Semilietof, Aikaterini; Rufer, Nathalie; Lehr, Hans-Anton; Xenarios, Ioannis; Coukos, George; Delaloye, Jean-François; Doucey, Marie-Agnès (2016) TIE-2-expressing monocytes are lymphangiogenic and associate specifically with lymphatics of human breast cancer. OncoImmunology 5 (2) e1073882.