Publications

2016

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Zhang, Xuezhi Zhuchenko, Olga Kuspa, Adam Soldati, Thierry (2016) Social amoebae trap and kill bacteria by casting DNA nets. Nat. Commun. 7 10938.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. Zhang, Xuezhi Soldati, Thierry (2016) Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism. Front. Immunol. 7 269.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. Moreau, Dimitri Gruenberg, Jean (2016) Automated Microscopy and High Content Screens (Phenotypic Screens) in Academia Labs. Chimia 70 (12) 878-882.
  43. 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.
  44. Johann, D. Goswami, D. Kruse, Karsten (2016) Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors. Phys. Rev. E 93 062415.
  45. Fritzsche, Marco Erlenkämper, Christoph Moeendarbary, Emade Charras, Guillaume Kruse, Karsten (2016) Actin kinetics shapes cortical network structure and mechanics. Sci. Adv. 2 (4) e1501337.
  46. 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.