Items where Subject is "07 Faculty of Science > Institute of Molecular Life Sciences"

Greber, Urs F; Flatt, Justin W (2019). Adenovirus Entry: From Infection to Immunity. Annual Review of Virology, 6(1):annurev-virology.

Haug, Marion F; Berger, Manuela; Gesemann, Matthias; Neuhauss, Stephan C F (2019). Differential expression of PKCα and -β in the zebrafish retina. Histochemistry and Cell Biology, 151(6):521-530.

Wagner, Johanna; Rapsomaniki, Maria Anna; Chevrier, Stéphane; Anzeneder, Tobias; Langwieder, Claus; Dykgers, August; Rees, Martin; Ramaswamy, Annette; Muenst, Simone; Soysal, Savas Deniz; Jacobs, Andrea; Windhager, Jonas; Silina, Karina; van den Broek, Maries; Dedes, Konstantin Johannes; Rodríguez Martínez, Maria; Weber, Walter Paul; Bodenmiller, Bernd (2019). A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell, 177(5):1330-1345.

Zurkirchen, Luis; Varum, Sandra; Giger, Sonja; Klug, Annika; Häusel, Jessica; Bossart, Raphaël; Zemke, Martina; Cantù, Claudio; Atak, Zeynep Kalender; Zamboni, Nicola; Basler, Konrad; Sommer, Lukas (2019). Yin Yang 1 sustains biosynthetic demands during brain development in a stage-specific manner. Nature Communications, 10:2192.

Jawaid, Ali; Woldemichael, Bisrat T; Kremer, Eloïse A; Laferriere, Florent; Gaur, Niharika; Afroz, Tariq; Polymenidou, Magdalini; Mansuy, Isabelle M (2019). Memory decline and its reversal in aging and neurodegeneration involve miR-183/96/182 biogenesis. Molecular Neurobiology, 56(5):3451-3462.

Villani, Ambra; Benjaminsen, Jørgen; Moritz, Christian; Henke, Katrin; Hartmann, Jonas; Norlin, Nils; Richter, Kerstin; Schieber, Nicole L; Franke, Tilman; Schwab, Yannick; Peri, Francesca (2019). Clearance by Microglia Depends on Packaging of Phagosomes into a Unique Cellular Compartment. Developmental Cell, 49(1):77-88.e7.

Varum, Sandra; Baggiolini, Arianna; Zurkirchen, Luis; Atak, Zeynep Kalender; Cantù, Claudio; Marzorati, Elisa; Bossart, Raphaël; Wouters, Jasper; Häusel, Jessica; Tuncer, Eylül; Zingg, Daniel; Veen, Dominiek; John, Nessy; Balz, Marcel; Levesque, Mitchell P; Basler, Konrad; Aerts, Stein; Zamboni, Nicola; Dummer, Reinhard; Sommer, Lukas (2019). Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation. Cell Stem Cell, 24(4):637-653.e9.

Cianciolo Cosentino, Chiara; Berto, Alessandro; Pelletier, Stéphane; Hari, Michelle; Loffing, Johannes; Neuhauss, Stephan C F; Doye, Valérie (2019). Moderate Nucleoporin 133 deficiency leads to glomerular damage in zebrafish. Scientific Reports, 9:4750.

Caviglia, Sara; Flores-Benitez, David; Lattner, Johanna; Luschnig, Stefan; Brankatschk, Marko (2019). Rabs on the fly: functions of Rab GTPases during development. Small GTPases, 10(2):89-98.

Doumpas, Nikolaos; Lampart, Franziska; Robinson, Mark D; Lentini, Antonio; Nestor, Colm E; Cantù, Claudio; Basler, Konrad (2019). TCF/LEF dependent and independent transcriptional regulation of Wnt/β-catenin target genes. EMBO Journal Online, 38(2):e98873.

Szklarczyk, Damian; Gable, Annika L; Lyon, David; Junge, Alexander; Wyder, Stefan; Huerta-Cepas, Jaime; Simonovic, Milan; Doncheva, Nadezhda T; Morris, John H; Bork, Peer; Jensen, Lars J; von Mering, Christian (2019). STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1):D607-D613.

Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide; Hernández-Plaza, Ana; Forslund, Sofia K; Cook, Helen; Mende, Daniel R; Letunic, Ivica; Rattei, Thomas; Jensen, Lars J; von Mering, Christian; Bork, Peer (2019). eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47(D1):D309-D314.

Villani, Ambra; Peri, Francesca (2019). Microglia: Picky Brain Eaters. Developmental Cell, 48(1):3-4.

Greber, Urs F (2019). Editorial: Physical Virology and the Nature of Virus Infections. In: Greber, Urs F. Physical Virology. Basel, Switzerland: Springer, online.

Gemünden, Michèle. Identification of novel fission yeast cell polarity regulators by mass spectrometry of detergent-resistant membranes. 2019, University of Zurich, Faculty of Science.

Zang, Jingjing; Neuhauss, Stephan C F (2018). The Binding Properties and Physiological Functions of Recoverin. Frontiers in Molecular Neuroscience, 11:473.

Baillon, Ludovic; Germani, Federico; Rockel, Claudia; Hilchenbach, Jochen; Basler, Konrad (2018). Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells. Scientific Reports, 8(1):17712.

Deemyad, Tara; Lüthi, Joel; Spruston, Nelson (2018). Astrocytes integrate and drive action potential firing in inhibitory subnetworks. Nature Communications, 9(1):4336.

Tackmann, Janko; Arora, Natasha; Schmidt, Thomas Sebastian Beedikt; Rodrigues, João Frederico Matias; von Mering, Christian (2018). Ecologically informed microbial biomarkers and accurate classification of mixed and unmixed samples in an extensive cross-study of human body sites. Microbiome, 6:192.

Dyke, Stephanie O M; Linden, Mikael; Lappalainen, Ilkka; De Argila, Jordi Rambla; et al; Baudis, Michael (2018). Registered access: authorizing data access. European Journal of Human Genetics, 26(12):1721-1731.

Berchtold, Doris; Battich, Nico; Pelkmans, Lucas (2018). A Systems-Level Study Reveals Regulators of Membrane-less Organelles in Human Cells. Molecular Cell, 72(6):1035-1049.

Yakimovich, Artur; Witte, Robert; Andriasyan, Vardan; Georgi, Fanny; Greber, Urs F (2018). Label-Free Digital Holo-tomographic Microscopy Reveals Virus-Induced Cytopathic Effects in Live Cells. mSphere, 3(6):e00599-18.

Germani, Federico; Hain, Daniel; Sternlicht, Denise; Moreno, Eduardo; Basler, Konrad (2018). The Toll pathway inhibits tissue growth and regulates cell fitness in an infection-dependent manner. eLife, 7:e39939.

Cantù, Claudio; Felker, Anastasia; Zimmerli, Dario; Prummel, Karin D; Cabello, Elena M; Chiavacci, Elena; Méndez-Acevedo, Kevin M; Kirchgeorg, Lucia; Burger, Sibylle; Ripoll, Jorge; Valenta, Tomas; Hausmann, George; Vilain, Nathalie; Aguet, Michel; Burger, Alexa; Panáková, Daniela; Basler, Konrad; Mosimann, Christian (2018). Mutations in and genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling. Genes and Development, 32(21-22):1443-1458.

Krishnaswamy, Smita; Zivanovic, Nevena; Sharma, Roshan; Pe'er, Dana; Bodenmiller, Bernd (2018). Learning time-varying information flow from single-cell epithelial to mesenchymal transition data. PLoS ONE, 13(10):e0203389.

Carrio-Cordo, Paula; Baudis, Michael (2018). Mountains and Chasms: Surveying the Oncogenomic Publication Landscape. Oncology:Epub ahead of print.

Popovic, Doris; Koch, Birgit; Kueblbeck, Moritz; Ellenberg, Jan; Pelkmans, Lucas (2018). Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. Cell Systems, 7(4):398-411.

Daga, Neha; Eicher, Simone; Kannan, Abhilash; Casanova, Alain; Low, Shyan H; Kreibich, Saskia; Andritschke, Daniel; Emmenlauer, Mario; Jenkins, Jeremy L; Hardt, Wolf-Dietrich; Greber, Urs F; Dehio, Christoph; von Mering, Christian (2018). Growth-restricting effects of siRNA transfections: a largely deterministic combination of off-target binding and hybridization-independent competition. Nucleic Acids Research, 46(18):9309-9320.

Kirchgeorg, Lucia; Felker, Anastasia; van Oostrom, Marek; Chiavacci, Elena; Mosimann, Christian (2018). Cre/lox-controlled spatiotemporal perturbation of FGF signaling in zebrafish. Developmental Dynamics, 247(10):1146-1159.

Bischof, Johannes; Duffraisse, Marilyne; Furger, Edy; Ajuria, Leiore; Giraud, Guillaume; Vanderperre, Solene; Paul, Rachel; Björklund, Mikael; Ahr, Damien; Ahmed, Alexis W; Spinelli, Lionel; Brun, Christine; Basler, Konrad; Merabet, Samir (2018). Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live. eLife, 7:e38853.

Cook, Helen Victoria; Doncheva, Nadezhda Tsankova; Szklarczyk, Damian; von Mering, Christian; Jensen, Lars Juhl (2018). Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. Viruses, 10(10):519.

Roulin, Pascal S; Murer, Luca; Greber, Urs F (2018). A single point mutation in the rhinovirus 2B protein reduces the requirement for phosphatidylinositol 4-kinase class 3beta in viral replication. Journal of Virology, 92(23):e01462-18.

Gut, Gabriele; Herrmann, Markus D; Pelkmans, Lucas (2018). Multiplexed protein maps link subcellular organization to cellular state. Science, 361(6401):eaar7042.

Dona, Margo; Slijkerman, Ralph; Lerner, Kimberly; Broekman, Sanne; Wegner, Jeremy; Howat, Taylor; Peters, Theo; Hetterschijt, Lisette; Boon, Nanda; de Vrieze, Erik; Sorusch, Nasrin; Wolfrum, Uwe; Kremer, Hannie; Neuhauss, Stephan; Zang, Jingjing; Kamermans, Maarten; Westerfield, Monte; Phillips, Jennifer; van Wijk, Erwin (2018). Usherin defects lead to early-onset retinal dysfunction in zebrafish. Experimental Eye Research, 173:148-159.

Neuhauss, Stephan C F (2018). Sensory Biology: How to Structure a Tailor-Made Retina. Current Biology, 28(13):R737-R739.

Rai, Arpan Kumar; Chen, Jia-Xuan; Selbach, Matthias; Pelkmans, Lucas (2018). Kinase-controlled phase transition of membraneless organelles in mitosis. Nature, 559:211-216.

Zingg, Daniel; Debbache, Julien; Peña-Hernández, Rodrigo; Antunes, Ana T; Schaefer, Simon M; Cheng, Phil F; Zimmerli, Dario; Haeusel, Jessica; Calçada, Raquel R; Tuncer, Eylul; Zhang, Yudong; Bossart, Raphaël; Wong, Kwok-Kin; Basler, Konrad; Dummer, Reinhard; Santoro, Raffaella; Levesque, Mitchell P; Sommer, Lukas (2018). EZH2-mediated primary cilium deconstruction drives metastatic melanoma formation. Cancer Cell, 34(1):69-84.

Marrero-Rodríguez, Daniel; Taniguchi-Ponciano, Keiko; Subramaniam, Malayannan; Hawse, John R; Pitel, Kevin S; Arreola-De la Cruz, Hugo; Huerta-Padilla, Victor; Ponce-Navarrete, Gustavo; Figueroa-Corona, Ma Del Pilar; Gomez-Virgilio, Laura; Martinez-Cuevas, Teresa I; Mendoza-Rodriguez, Monica; Rodriguez-Esquivel, Miriam; Romero-Morelos, Pablo; Ramirez-Salcedo, Jorge; Baudis, Michael; Meraz-Rios, Marco; Jimenez-Vega, Florinda; Salcedo, Mauricio (2018). Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins. Scientific Reports, 8(1):9445.

Berger, Simon; Lattmann, Evelyn; Aegerter-Wilmsen, Tinri; Hengartner, Michael; Hajnal, Alex; deMello, Andrew; Casadevall I Solvas, Xavier (2018). Correction: Long-term C. elegans immobilization enables high resolution developmental studies in vivo. Lab on a chip, 18(12):1802.

Degirmenci, Bahar; Valenta, Tomas; Dimitrieva, Slavica; Hausmann, George; Basler, Konrad (2018). GLI1-expressing mesenchymal cells form the essential Wnt-secreting niche for colon stem cells. Nature, 558(7710):449-453.

Merks, Anne Margarete; Swinarski, Marie; Meyer, Alexander Matthias; Müller, Nicola Victoria; Özcan, Ismail; Donat, Stefan; Burger, Alexa; Gilbert, Stephen; Mosimann, Christian; Abdelilah-Seyfried, Salim; Panáková, Daniela (2018). Planar cell polarity signalling coordinates heart tube remodelling through tissue-scale polarisation of actomyosin activity. Nature Communications, 9(1):2161.

Ros, Oriol; Barrecheguren, Pablo José; Cotrufo, Tiziana; Schaettin, Martina; Roselló-Busquets, Cristina; Vílchez-Acosta, Alba; Hernaiz-Llorens, Marc; Martínez-Marmol, Ramón; Ulloa, Fausto; Stoeckli, Esther T; Araújo, Sofia J; Soriano, Eduardo (2018). A conserved role for Syntaxin-1 in pre- and post-commissural midline axonal guidance in fly, chick, and mouse. PLoS Genetics, 14(6):e1007432.

Spletter, Maria L; Barz, Christiane; Yeroslaviz, Assa; Zhang, Xu; Lemke, Sandra B; Bonnard, Adrien; Brunner, Erich; Cardone, Giovanni; Basler, Konrad; Habermann, Bianca H; Schnorrer, Frank (2018). A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle. eLife, 7:e34058.

Felker, Anastasia; Prummel, Karin D; Merks, Anne M; Mickoleit, Michaela; Brombacher, Eline C; Huisken, Jan; Panáková, Daniela; Mosimann, Christian (2018). Continuous addition of progenitors forms the cardiac ventricle in zebrafish. Nature Communications, 9(1):2001.

Eberle, Patric; Höller, Christian; Müller, Philipp; Suomalainen, Maarit; Greber, Urs F; Eghlidi, Hadi; Poulikakos, Dimos (2018). Single entity resolution valving of nanoscopic species in liquids. Nature Nanotechnology, 13(7):578-582.

Stoeckli, Esther T (2018). Understanding axon guidance: are we nearly there yet? Development, 145(10):dev151415.

Chevrier, Stéphane; Crowell, Helena L; Zanotelli, Vito RT; Engler, Stefanie; Robinson, Mark D; Bodenmiller, Bernd (2018). Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry. Cell Systems, 6(5):612-620.e5.

Berger, Simon; Lattmann, Evelyn; Aegerter-Wilmsen, Tinri; Hengartner, Michael; Hajnal, Alex; deMello, Andrew; Casadevall i Solvas, Xavier (2018). Long-term C. elegans immobilization enables high resolution developmental studies in vivo. Lab on a chip, 18(9):1359-1368.

Haug, Marion F; Gesemann, Matthias; Berger, Manuela; Neuhauss, Stephan C F (2018). Phylogeny and distribution of protein kinase C variants in the zebrafish. Journal of Comparative Neurology, 526(7):1097-1109.

Chaurasia, Soumya; Lehner, Christian F (2018). Dynamics and control of sister kinetochore behavior during the meiotic divisions in Drosophila spermatocytes. PLoS Genetics, 14(5):e1007372.

Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; et al; von Mering, Christian (2018). Unexplored therapeutic opportunities in the human genome. Nature Reviews. Drug Discovery, 17(5):317-332.

Witte, Robert; Andriasyan, Vardan; Georgi, Fanny; Yakimovich, Artur; Greber, Urs F (2018). Concepts in Light Microscopy of Viruses. Viruses, 10(4):E202.

Zimmerli, Dario; Cecconi, Virginia; Valenta, Tomas; Hausmann, George; Cantù, Claudio; Restivo, Gaetana; Hafner, Jürg; Basler, Konrad; van den Broek, Maries (2018). WNT ligands control initiation and progression of human papillomavirus-driven squamous cell carcinoma. Oncogene, 37(27):3753-3762.

Schulz, Daniel; Zanotelli, Vito Riccardo Tomaso; Fischer, Jana Raja; Schapiro, Denis; Engler, Stefanie; Lun, Xiao-Kang; Jackson, Hartland Warren; Bodenmiller, Bernd (2018). Correction: Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Systems, 6(4):531.

Pelissier Vatter, Fanny A; Schapiro, Denis; Chang, Hang; Borowsky, Alexander D; Lee, Jonathan K; Parvin, Bahram; Stampfer, Martha R; LaBarge, Mark A; Bodenmiller, Bernd; Lorens, James B (2018). High-Dimensional Phenotyping Identifies Age-Emergent Cells in Human Mammary Epithelia. Cell Reports, 23(4):1205-1219.

Catena, Raúl; Montuenga, Luis M; Bodenmiller, Bernd (2018). Ruthenium counterstaining for imaging mass cytometry. Journal of Pathology, 244(4):479-484.

Wang, I-Hsuan; Burckhardt, Christoph J; Yakimovich, Artur; Greber, Urs F (2018). Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton. Viruses, 10(4):1-31.

Stichling, Nicole; Suomalainen, Maarit; Flatt, Justin W; Schmid, Markus; Pacesa, Martin; Hemmi, Silvio; Jungraithmayr, Wolfgang; Maler, Mareike D; Freudenberg, Marina A; Plückthun, Andreas; May, Tobias; Köster, Mario; Fejer, György; Greber, Urs F (2018). Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor. PLoS Pathogens, 14(3):e1006914.

Lötzerich, Mark; Roulin, Pascal S; Boucke, Karin; Witte, Robert; Georgiev, Oleg; Greber, Urs F (2018). Rhinovirus 3C protease suppresses apoptosis and triggers caspase-independent cell death. Cell Death and Disease, 9(3):272.

Lidsky, Peter V; Lukyanov, Konstantin A; Misra, Tvisha; Handke, Björn; Mishin, Alexander S; Lehner, Christian F (2018). A genetically encoded fluorescent probe for imaging of oxygenation gradients in living. Development, 145(4):dev156257.

Rapsomaniki, Maria Anna; Lun, Xiao-Kang; Woerner, Stefan; Laumanns, Marco; Bodenmiller, Bernd; Martínez, María Rodríguez (2018). CellCycleTRACER accounts for cell cycle and volume in mass cytometry data. Nature Communications, 9(1):632.

Naharros, Irene Ojeda; Cristian, Flavia B; Zang, Jingjing; Gesemann, Matthias; Ingham, Philip W; Neuhauss, Stephan C F; Bachmann-Gagescu, Ruxandra (2018). The ciliopathy protein TALPID3/KIAA0586 acts upstream of Rab8 activation in zebrafish photoreceptor outer segment formation and maintenance. Scientific Reports, 8:2211.

Schmid, Markus; Ernst, Patrick; Honegger, Annemarie; Suomalainen, Maarit; Zimmermann, Martina; Braun, Lukas; Stauffer, Sarah; Thom, Cristian; Dreier, Birgit; Eibauer, Matthias; Kipar, Anja; Vogel, Viola; Greber, Urs F; Medalia, Ohad; Plückthun, Andreas (2018). Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control. Nature Communications, 9(1):450.

de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas (2018). Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens. Molecular Systems Biology, 14(1):e8064.

Wentzel, Corinna; Delvendahl, Igor; Sydlik, Sebastian; Georgiev, Oleg; Müller, Martin (2018). Dysbindin links presynaptic proteasome function to homeostatic recruitment of low release probability vesicles. Nature Communications:9:267.

Degirmenci, Bahar; Hausmann, George; Valenta, Tomas; Basler, Konrad (2018). Wnt Ligands as a Part of the Stem Cell Niche in the Intestine and the Liver. Progress in molecular biology and translational science, 153:1-19.

Puri, Sahil. Approaching zebrafish (Danio rerio) caudal fin regeneration from a biomechanical perspective. 2018, University of Zurich, Faculty of Science.

Strauss, Justin Eric. Characterization of genes linked to human intellectual disability through functional analyses in the developing nervous system. 2018, University of Zurich, Faculty of Science.

Asadollahi, Reza; Strauss, Justin E; Zenker, Martin; Beuing, Oliver; Edvardson, Simon; Elpeleg, Orly; Strom, Tim M; Joset, Pascal; Niedrist, Dunja; Otte, Christine; Oneda, Beatrice; Boonsawat, Paranchai; Azzarello-Burri, Silvia; Bartholdi, Deborah; Papik, Michael; Zweier, Markus; Haas, Cordula; Ekici, Arif B; Baumer, Alessandra; Boltshauser, Eugen; Steindl, Katharina; Nothnagel, Michael; Schinzel, Albert; Stoeckli, Esther T; Rauch, Anita (2018). Clinical and experimental evidence suggest a link between KIF7 and C5orf42-related ciliopathies through Sonic Hedgehog signaling. European Journal of Human Genetics, 26(2):197-209.

Heimlicher, Maria Barbara. Cytoplasmic freezing: exploring a newly discovered extreme immobilisation of the cytoplasmic content of the fission yeast Schizosaccharomyces pombe. 2018, University of Zurich, Faculty of Science.

Zimmerli, Dario. Elucidating the roles of Wnt-secretion and β-catenin's interaction partners in development and disease. 2018, University of Zurich, Faculty of Science.

Manzella, Gabriele. Exploiting precision medicine in rhabdomyosarcoma. 2018, University of Zurich, Faculty of Science.

Kamkina, Polina. Genetic and molecular characterization of new genes which influence germline apoptosis in C. elegans. 2018, University of Zurich, Faculty of Science.

Sbalzarini, Ivo F; Greber, Urs F (2018). How Computational Models Enable Mechanistic Insights into Virus Infection. In: Yamauchi, Yohei. Influenza Virus. New York, NY: Springer, 609-631.

Byczkowicz, Niklas; Ritzau-Jost, Andreas; Delvendahl, Igor; Hallermann, Stefan (2018). How to maintain active zone integrity during high-frequency transmission. Neuroscience Research, 127:61-69.

Keim, Jennifer. Interplay between different forms of synaptic plasticity at the Drosophila neuromuscular junction. 2018, University of Zurich, Faculty of Science.

Phelps, Ian G; Dempsey, Jennifer C; Grout, Megan E; Isabella, Christine R; Tully, Hannah M; Doherty, Dan; Bachmann-Gagescu, Ruxandra (2018). Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity. Genetics in Medicine, 20(2):223-233.

Hock, Eva-Maria. Mechanisms of disease initation in FUS and TDP-43 proteinopathies. 2018, University of Zurich, Faculty of Science.

Staib, Matthias. Mechanisms of pavlovian aversive conditioning in human auditory cortex. 2018, University of Zurich, Faculty of Science.

D'Agati, Gianluca. Modeling of developmental and tumorigenic lesions of the zebrafish notochord. 2018, University of Zurich, Faculty of Science.

Germani, Federico; Bergantinos, Cora; Johnston, Laura A (2018). Mosaic Analysis in Drosophila. Genetics, 208(2):473-490.

Crameri, Michel; Bauer, Michael; Caduff, Nicole; Walker, Raphael; Steiner, Fiona; Franzoso, Francesca D; Gujer, Cornelia; Boucke, Karin; Kucera, Talissa; Zbinden, Andrea; Münz, Christian; Fraefel, Cornel; Greber, Urs F; Pavlovic, Jovan (2018). MxB is an interferon-induced restriction factor of human herpesviruses. Nature Communications, 9(1):1980.

Heller, Davide Martin. Network consistency applied to developmental biology and molecular evolution. 2018, University of Zurich, Faculty of Science.

Andriasyan, Vardan. Quantitative and predictive analyses of adenovirus egress from infected cells based on live cell imaging and machine learning. 2018, University of Zurich, Faculty of Science.

Schulz, Daniel; Zanotelli, Vito Riccardo Tomaso; Fischer, Jana Raja; Schapiro, Denis; Engler, Stefanie; Lun, Xiao-Kang; Jackson, Hartland Warren; Bodenmiller, Bernd (2018). Simultaneous multiplexed imaging of mRNA and proteins with subcellular resolution in breast cancer tissue samples by mass cytometry. Cell Systems, 6(1):25-36.e5.

Lun, Xiaokang. Single-cell analysis reveals protein abundance-dependent signaling network modulations. 2018, University of Zurich, Faculty of Science.

Maxeiner, Sabrina. The C. elegans RAS/MAPK and WNT signalling pathways are modified by polymorphic genes and molecular oxygen. 2018, University of Zurich, Faculty of Science.

Haag, Andrea. The CHORD containing protein CHP-1 regulates RTK/RAS/MAPK and Wnt signaling during vulval development. 2018, University of Zurich, Faculty of Science.

Soneson, Charlotte; Robinson, Mark D (2018). Towards unified quality verification of synthetic count data with countsimQC. Bioinformatics, 34(4):691-692.

Lehnherr, André. Tracing the evolutionary history of the SLC1 gene family. 2018, University of Zurich, Faculty of Science.

Degirmenci, Bahar. Wnt-secreting stem cell niche drives intestinal renewal, regeneration and cancer. 2018, University of Zurich, Faculty of Science.

Gao, Bo; Huang, Qingyao; Baudis, Michael (2018). segment_liftover : a Python tool to convert segments between genome assemblies. F1000Research, 7:319.

Ojeda Naharros, Irene; Gesemann, Matthias; Mateos, José M; Barmettler, Gery; Forbes, Austin; Ziegler, Urs; Neuhauss, Stephan C F; Bachmann-Gagescu, Ruxandra (2017). Loss-of-function of the ciliopathy protein Cc2d2a disorganizes the vesicle fusion machinery at the periciliary membrane and indirectly affects Rab8-trafficking in zebrafish photoreceptors. PLoS Genetics, 13(12):e1007150.

Omasits, Ulrich; Varadarajan, Adithi R; Schmid, Michael; Goetze, Sandra; Melidis, Damianos; Bourqui, Marc; Nikolayeva, Olga; Québatte, Maxime; Patrignani, Andrea; Dehio, Christoph; Frey, Juerg E; Robinson, Mark D; Wollscheid, Bernd; Ahrens, Christian H (2017). An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Research, 27(12):2083-2095.

Myachina, Faina; Bosshardt, Fritz; Bischof, Johannes; Kirschmann, Moritz; Lehner, Christian F (2017). Drosophila β-Tubulin 97EF is upregulated at low temperature and stabilizes microtubules. Development, 144(24):4573-4587.

Regev, Aviv; Teichmann, Sarah A; Lander, Eric S; Amit, Ido; Benoist, Christophe; Birney, Ewan; Bodenmiller, Bernd; et al (2017). The Human Cell Atlas. eLife, 6:e27041.

Leonardi, Irina; Gerstgrasser, Alexandra; Schmidt, Thomas S B; Nicholls, Flora; Tewes, Bernhard; Greinwald, Roland; von Mering, Christian; Rogler, Gerhard; Frey-Wagner, Isabelle (2017). Preventive Trichuris suis ova (TSO) treatment protects immunocompetent rabbits from DSS colitis but may be detrimental under conditions of immunosuppression. Scientific Reports, 7(1):16500.

Sauerwald, Julia. Impacts of surrounding tissues on FGF-dependent vessel ingrowth during Drosophila airway development. 2017, University of Zurich, Faculty of Science.

Mitsiadis, Thimios A; Pagella, Pierfrancesco; Cantù, Claudio (2017). Early determination of the periodontal domain by the wnt-antagonist Frzb/Sfrp3. Frontiers in Physiology, 8:936.

Mateos, José M; Barmettler, Gery; Doehner, Jana; Ojeda Naharros, Irene; Guhl, Bruno; Neuhauss, Stephan C F; Kaech, Andres; Bachmann-Gagescu, Ruxandra; Ziegler, Urs (2017). Correlative super-resolution and electron microscopy to resolve protein localization in zebrafish retina. Journal of Visualized Experiments (Jove), 129:e56113.

Roubinet, Chantal; Tsankova, Anna; Pham, Tri Thanh; Monnard, Arnaud; Caussinus, Emmanuel; Affolter, Markus; Cabernard, Clemens (2017). Spatio-temporally separated cortical flows and spindle geometry establish physical asymmetry in fly neural stem cells. Nature Communications, 8(1):1383.

Norris, Megan L; Pauli, Andrea; Gagnon, James A; Lord, Nathan D; Rogers, Katherine W; Mosimann, Christian; Zon, Leonard I; Schier, Alexander F (2017). Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling. eLife, 6:e22626.

Mackay, Alan; Burford, Anna; Carvalho, Diana; Izquierdo, Elisa; Fazal-Salom, Janat; Taylor, Kathryn R; Bjerke, Lynn; Clarke, Matthew; Vinci, Mara; Nandhabalan, Meera; Temelso, Sara; Popov, Sergey; Molinari, Valeria; Raman, Pichai; Waanders, Angela J; Han, Harry J; Gupta, Saumya; Marshall, Lynley; Zacharoulis, Stergios; Vaidya, Sucheta; Mandeville, Henry C; Bridges, Leslie R; Martin, Andrew J; Al-Sarraj, Safa; Chandler, Christopher; Ng, Ho-Keung; Li, Xingang; Mu, Kun; Trabelsi, Saoussen; Brahim, Dorra H'mida-Ben; Baudis, Michael; Jones, Chris; et al (2017). Integrated molecular meta-analysis of 1,000 pediatric high-grade and diffuse intrinsic pontine glioma. Cancer Cell, 32(4):520-537.e5.

D'Agati, Gianluca; Beltre, Rosanna; Sessa, Anna; Burger, Alexa; Zhou, Yi; Mosimann, Christian; White, Richard M (2017). A defect in the mitochondrial protein Mpv17 underlies the transparent casper zebrafish. Developmental Biology, 430(1):11-17.

Stainier, Didier Y R; Raz, Erez; Lawson, Nathan D; Ekker, Stephen C; Burdine, Rebecca D; Eisen, Judith S; Ingham, Philip W; Schulte-Merker, Stefan; Yelon, Deborah; Weinstein, Brant M; Mullins, Mary C; Wilson, Stephen W; Ramakrishnan, Lalita; Amacher, Sharon L; Neuhauss, Stephan C F; Meng, Anming; Mochizuki, Naoki; Panula, Pertti; Moens, Cecilia B (2017). Guidelines for morpholino use in zebrafish. PLoS Genetics, 13(10):e1007000.

Item, Flurin; Wueest, Stephan; Lemos, Vera; Stein, Sokrates; Lucchini, Fabrizio C; Denzler, Rémy; Fisser, Muriel C; Challa, Tenagne D; Pirinen, Eija; Kim, Youngsoo; Hemmi, Silvio; Gulbins, Erich; Gross, Atan; O'Reilly, Lorraine A; Stoffel, Markus; Auwerx, Johan; Konrad, Daniel (2017). Fas cell surface death receptor controls hepatic lipid metabolism by regulating mitochondrial function. Nature Communications, 8:480.

Sterken, Mark G; van Bemmelen van der Plaat, Linda; Riksen, Joost A G; Rodriguez, Miriam; Schmid, Tobias; Hajnal, Alex; Kammenga, Jan E; Snoek, Basten L (2017). Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans. G3 : Genes, Genomes, Genetics, 7(9):3185-3193.

Becker, Eugenia; Schmidt, Thomas S B; Bengs, Susan; Poveda, Lucy; Opitz, Lennart; Atrott, Kirstin; Stanzel, Claudia; Biedermann, Luc; Rehman, Ateequr; Jonas, Daniel; von Mering, Christian; Rogler, Gerhard; Frey-Wagner, Isabelle (2017). Effects of oral antibiotics and isotretinoin on the murine gut microbiota. International Journal of Antimicrobial Agents, 50(3):342-351.

Niklaus, Stephanie; Neuhauss, Stephan C F (2017). Genetic approaches to retinal research in zebrafish. Journal of Neurogenetics, 31(3):70-87.

Franz, Alexandra; Brunner, Erich; Basler, Konrad (2017). Generation of genome-modified Drosophila cell lines using SwAP. Fly, 11(4):303-311.

Pacesa, Martin; Hendrickx, Rodinde; Bieri, Manuela; Flatt, Justin W; Greber, Urs F; Hemmi, Silvio (2017). Small-size recombinant adenoviral hexon protein fragments for the production of virus-type specific antibodies. Virology Journal, 14(1):158-171.

Ochoa-Espinosa, Amanda; Harmansa, Stefan; Caussinus, Emmanuel; Affolter, Markus (2017). Myosin II is not required for Drosophila tracheal branch elongation and cell intercalation. Development, 144(16):2961-2968.

Rodrigues, João F Matias; Schmidt, Thomas Sebastian Benedikt; Tackmann, Janko; von Mering, Christian (2017). MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics, 33(23):3808-3810.

Yang, Qiutan; Roiz, Daniel; Mereu, Louisa; Daube, Michael; Hajnal, Alex (2017). The Invading Anchor Cell Induces Lateral Membrane Constriction during Vulval Lumen Morphogenesis in C. elegans. Developmental Cell, 42(3):271-285.e3.

Van den Berge, Koen; Soneson, Charlotte; Robinson, Mark D; Clement, Lieven (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology, 18(1):151.

Huerta-Cepas, Jaime; Forslund, Kristoffer; Coelho, Luis Pedro; Szklarczyk, Damian; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2017). Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Molecular Biology and Evolution, 34(8):2115-2122.

Maler, Mareike D; Nielsen, Peter J; Stichling, Nicole; Cohen, Idan; Ruzsics, Zsolt; Wood, Connor; Engelhard, Peggy; Suomalainen, Maarit; Gyory, Ildiko; Huber, Michael; Müller-Quernheim, Joachim; Schamel, Wolfgang W A; Gordon, Siamon; Jakob, Thilo; Martin, Stefan F; Jahnen-Dechent, Willi; Greber, Urs F; Freudenberg, Marina A; Fejer, György (2017). Key role of the scavenger receptor MARCO in mediating adenovirus infection and subsequent innate responses of macrophages. mBio, 8(4):e00670-17.

Dev Singh, Kapil; Milstein, Stuart; Zheng, Xue; Keller, Martin; Grossmann, Jonas; Roschitzki, Bernd; Hengartner, Michael O (2017). Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS ONE, 12(7):e0182270.

Marty, Florian; Rago, Gianluca; Smith, Donald F; Gao, Xiaoli; Eijkel, Gert B; MacAleese, Luke; Bonn, Mischa; Brunner, Erich; Basler, Konrad; Heeren, Ron M A (2017). Combining ToF-SIMS imaging mass spectrometry and CARS microspectroscopy reveals lipid patterns reminiscent of gene expression patterns in the wing imaginal disc of Drosophila melanogaster. Analytical Chemistry, 89(18):9664-9670.

Neve, Anuja; Kumar, Karthiga Santhana; Tripolitsioti, Dimitra; Grotzer, Michael A; Baumgartner, Martin (2017). Investigation of brain tissue infiltration by medulloblastoma cells in an ex vivo model. Scientific Reports, 7(1):5297.

Van De Weghe, Julie C; Rusterholz, Tamara D S; Latour, Brooke; Grout, Megan E; Aldinger, Kimberly A; Shaheen, Ranad; Dempsey, Jennifer C; Maddirevula, Sateesh; Cheng, Yong-Han H; Phelps, Ian G; Gesemann, Matthias; Goel, Himanshu; Birk, Ohad S; Alanzi, Talal; Rawashdeh, Rifaat; Khan, Arif O; Bamshad, Michael J; Nickerson, Deborah A; Neuhauss, Stephan C F; Dobyns, William B; Alkuraya, Fowzan S; Roepman, Ronald; Bachmann-Gagescu, Ruxandra; Doherty, Dan (2017). Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. American Journal of Human Genetics, 101(1):23-36.

Heinze, Svenia D; Kohlbrenner, Tea; Ippolito, Domenica; Meccariello, Angela; Burger, Alexa; Mosimann, Christian; Saccone, Giuseppe; Bopp, Daniel (2017). CRISPR-Cas9 targeted disruption of the yellow ortholog in the housefly identifies the brown body locus. Scientific Reports, 7(1):e1-e9.

Sanchez Bosch, Pablo; Ziukaite, Ruta; Alexandre, Cyrille; Basler, Konrad; Vincent, Jean-Paul B (2017). Dpp controls growth and patterning in Drosophila wing precursors through distinct modes of action. eLife, 6:e22546.

Herdman, Chelsea; Mars, Jean-Clement; Stefanovsky, Victor Y; Tremblay, Michel G; Sabourin-Felix, Marianne; Lindsay, Helen; Robinson, Mark D; Moss, Tom (2017). A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genetics, 13(7):e1006899.

Yakimovich, Artur; Huttunen, Moona; Zehnder, Benno; Coulter, Lesley J; Gould, Victoria; Schneider, Christoph; Kopf, Manfred; McInnes, Colin J; Greber, Urs F; Mercer, Jason (2017). Inhibition of Poxvirus Gene Expression and Genome Replication by Bisbenzimide Derivatives. Journal of Virology:00838-17.

Sugano, Yuya; Cianciolo Cosentino, Chiara; Loffing-Cueni, Dominique; Neuhauss, Stephan C. F; Loffing, Johannes (2017). Comparative transcriptomic analysis identifies evolutionarily conserved gene products in the vertebrate renal distal convoluted tubule. Pflügers Archiv : European Journal of Physiology, 469(7-8):859-867.

Ostapchuk, Philomena; Suomalainen, Maarit; Zheng, Yueting; Boucke, Karin; Greber, Urs F; Hearing, Patrick (2017). The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection. PLoS Pathogens, 13(6):e1006455.

Niklaus, Stephanie; Cadetti, Lucia; Vom Berg-Maurer, Colette M; Lehnherr, André; Hotz, Adriana L; Forster, Ian C; Gesemann, Matthias; Neuhauss, Stephan C F (2017). Shaping of signal transmission at the photoreceptor synapse by EAAT2 glutamate transporters. eNeuro, 4(3):e0339.

Kirla, Krishna Tulasi; Niklaus, Stephanie; Kraemer, Thomas; Groh, Ksenia; Schirmer, Kristin; Neuhauss, Stephan (2017). Cocaine Accumulation in Zebrafish Eyes Leads to Augmented Amplitudes in the Electroretinogram. Matters:1-4.

Zimmerli, Dario; Hausmann, George; Cantù, Claudio; Basler, Konrad (2017). Pharmacological interventions in the Wnt pathway: Inhibition of Wnt secretion versus disrupting the protein-protein interfaces of nuclear factors. British Journal of Pharmacology, 174(24):4600-4610.

Wang, I-Hsuan; Burckhardt, Christoph J; Yakimovich, Artur; Morf, Matthias K; Greber, Urs F (2017). The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport. Journal of Cell Science, 130(13):2185-2195.

Sharma, Akash; Heinze, Svenia D; Wu, Yanli; Kohlbrenner, Tea; Morilla, Ian; Brunner, Claudia; Wimmer, Ernst A; van de Zande, Louis; Robinson, Mark D; Beukeboom, Leo W; Bopp, Daniel (2017). Male sex in houseflies is determined byMdmd, a paralog of the generic splice factor geneCWC22. Science, 356(6338):642-645.

Flatt, Justin W; Greber, Urs F (2017). Viral mechanisms for docking and delivering at nuclear pore complexes. Seminars in Cell & Developmental Biology, 68:59-71.

Blyszczuk, Przemyslaw; Müller-Edenborn, Björn; Valenta, Tomas; Osto, Elena; Stellato, Mara; Behnke, Silvia; Glatz, Katharina; Basler, Konrad; Lüscher, Thomas F; Distler, Oliver; Eriksson, Urs; Kania, Gabriela (2017). Transforming growth factor-β-dependent Wnt secretion controls myofibroblast formation and myocardial fibrosis progression in experimental autoimmune myocarditis. European Heart Journal, 38(18):1413-1425.

Rot, Gregor; Wang, Zhen; Huppertz, Ina; Modic, Miha; Lenče, Tina; Hallegger, Martina; Haberman, Nejc; Curk, Tomaž; von Mering, Christian; Ule, Jernej (2017). High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Reports, 19(5):1056-1067.

Prasad, Vibhu; Suomalainen, Maarit; Hemmi, Silvio; Greber, Urs F (2017). Cell Cycle-Dependent Kinase Cdk9 Is a Postexposure Drug Target against Human Adenoviruses. ACS Infectious Diseases, 3(6):398-405.

Chiavacci, Elena; Kirchgeorg, Lucia; Felker, Anastasia; Burger, Alexa; Mosimann, Christian (2017). Early frameshift alleles of zebrafish tbx5a that fail to develop the heartstrings phenotype. Matters:1-7.

Hockman, Dorit; Burns, Alan J; Schlosser, Gerhard; Gates, Keith P; Jevans, Benjamin; Mongera, Alessandro; Fisher, Shannon; Unlu, Gokhan; Knapik, Ela W; Kaufman, Charles K; Mosimann, Christian; Zon, Leonard I; Lancman, Joseph J; Dong, P Duc S; Lickert, Heiko; Tucker, Abigail S; Baker, Clare V H (2017). Evolution of the hypoxia-sensitive cells involved in amniote respiratory reflexes. eLife, 6:e21231.

Franz, Alexandra; Shlyueva, Daria; Brunner, Erich; Stark, Alexander; Basler, Konrad (2017). Probing the canonicity of the Wnt/Wingless signaling pathway. PLoS Genetics, 13(4):e1006700.

Himmels, Patricia; Paredes, Isidora; Adler, Heike; Karakatsani, Andromachi; Luck, Robert; Marti, Hugo H; Ermakova, Olga; Rempel, Eugen; Stoeckli, Esther T; Ruiz de Almodóvar, Carmen (2017). Motor neurons control blood vessel patterning in the developing spinal cord. Nature Communications, 8:14583.

Mathews, Kristina Wehr; Cavegn, Margrith; Zwicky, Monica (2017). Sexual Dimorphism of Body Size Is Controlled by Dosage of the X-Chromosomal Gene Myc and by the Sex-Determining Gene tra in Drosophila. Genetics, 205(3):1215-1228.

Marinova, Zoya; Maercker, Andreas; Küffer, Andreas; Robinson, Mark D; Wojdacz, Tomasz K; Walitza, Susanne; Grünblatt, Edna; Burri, Andrea (2017). DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma. BMC Medical Genetics, 18(1):21.

Leuenberger, Pascal; Ganscha, Stefan; Kahraman, Abdullah; Cappelletti, Valentina; Boersema, Paul J; von Mering, Christian; Claassen, Manfred; Picotti, Paola (2017). Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science, 355(6327):1-13.

Feigelman, Rounak; Kahlert, Christian R; Baty, Florent; Rassouli, Frank; Kleiner, Rebekka L; Kohler, Philipp; Brutsche, Martin H; von Mering, Christian (2017). Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome, 5(1):20.

Cantù, Claudio; Pagella, Pierfrancesco; Shajiei, Tania D; Zimmerli, Dario; Valenta, Tomas; Hausmann, George; Basler, Konrad; Mitsiadis, Thimios A (2017). A cytoplasmic role of Wnt/β-catenin transcriptional cofactors Bcl9, Bcl9l, and Pygopus in tooth enamel formation. Science Signaling, 10(465):eaah4598.

Gays, Dafne; Hess, Christopher; Camporeale, Annalisa; Ala, Ugo; Provero, Paolo; Mosimann, Christian; Santoro, Massimo M (2017). An exclusive cellular and molecular network governs intestinal smooth muscle cell differentiation in vertebrates. Development, 144(3):464-478.

Lun, Xiao-Kang; Zanotelli, Vito R T; Wade, James D; Schapiro, Denis; Tognetti, Marco; Dobberstein, Nadine; Bodenmiller, Bernd (2017). Influence of node abundance on signaling network state and dynamics analyzed by mass cytometry. Nature Biotechnology, 35(2):164-172.

Walser, Michael; Umbricht, Christoph Alois; Fröhli, Erika; Nanni, Paolo; Hajnal, Alex (2017). β-Integrin de-phosphorylation by the Density-Enhanced Phosphatase DEP-1 attenuates EGFR signaling in C. elegans. PLoS Genetics, 13(1):e1006592.

Stoeckli, Esther (2017). Where does axon guidance lead us? F1000Research, 6:78.

Neuhauss, Stephan C F (2017). Olfaction: how fish catch a whiff. Current Biology, 27(2):57-58.

Sauerwald, Julia; Soneson, Charlotte; Robinson, Mark D; Luschnig, Stefan (2017). Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila. Development, 144(4):657-663.

Sendoel, Ataman; Dunn, Joshua G; Rodriguez, Edwin H; Naik, Shruti; Gomez, Nicholas C; Hurwitz, Brian; Levorse, John; Dill, Brian D; Schramek, Daniel; Molina, Henrik; Weissman, Jonathan S; Fuchs, Elaine (2017). Translation from unconventional 5′ start sites drives tumour initiation. Nature, 541(7638):494-499.

Greber, Urs F; Bartenschlager, Ralf (2017). An expanded view of viruses. FEMS Microbiology Reviews, 41(1):1-4.

Schmidt, Thomas Sebastian Benedikt; Matias Rodrigues, João Frederico; von Mering, Christian (2017). A family of interaction-adjusted indices of community similarity. The ISME journal, 11(3):791-807.

Misra, Tvisha; Baccino-Calace, Martin; Meyenhofer, Felix; Rodriguez-Crespo, David; Akarsu, Hatice; Armenta-Calderón, Ricardo; Gorr, Thomas A; Frei, Christian; Cantera, Rafael; Egger, Boris; Luschnig, Stefan (2017). A genetically encoded biosensor for visualizing hypoxia responses in vivo. Biology Open, 6(2):296-304.

Harmansa, Stefan; Alborelli, Ilaria; Bieli, Dimitri; Caussinus, Emmanuel; Affolter, Markus (2017). A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila. eLife, 6:e22549.

de Ramon Francàs, Gemma; Alther, Tobias; Stoeckli, Esther T (2017). Calsyntenins are expressed in a dynamic and partially overlapping manner during neural development. Frontiers in Neuroanatomy, 11:76.

Franzoso, Francesca D; Seyffert, Michael; Vogel, Rebecca; Yakimovich, Artur; de Andrade Pereira, Bruna; Meier, Anita F; Sutter, Sereina O; Tobler, Kurt; Vogt, Bernd; Greber, Urs F; Büning, Hildegard; Ackermann, Mathias; Fraefel, Cornel (2017). Cell cycle-dependent expression of AAV2 Rep in HSV-1 co-infections gives rise to a mosaic of cells replicating either AAV2 or HSV-1. Journal of Virology:JVI.00357-17.

Eder, Dominik; Basler, Konrad; Aegerter, Christof M (2017). Challenging FRET-based E-Cadherin force measurements in Drosophila. Scientific Reports, 7:13692.

Nowicka, Malgorzata; Krieg, Carsten; Weber, Lukas M; Hartmann, Felix J; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P; Robinson, Mark D (2017). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research, 6:748.

Blattner, Ariane C; Aguilar-Rodríguez, José; Kränzlin, Marcella; Wagner, Andreas; Lehner, Christian F (2017). Drosophila Nnf1 paralogs are partially redundant for somatic and germ line kinetochore function. Chromosoma, 126(1):145-163.

Chaurasia, Soumya. Dynamics of the meiotic division in Drosophila males. 2017, University of Zurich, Faculty of Science.

Eder, Dominik; Aegerter, Christof; Basler, Konrad (2017). Forces controlling organ growth and size. Mechanisms of development, 144:53-61.

Meccariello, Angela; Monti, Simona Maria; Romanelli, Alessandra; Colonna, Rita; Primo, Pasquale; Inghilterra, Maria Grazia; Del Corsano, Giuseppe; Ramaglia, Antonio; Iazzetti, Giovanni; Chiarore, Antonia; Patti, Francesco; Heinze, Svenia D; Salvemini, Marco; Lindsay, Helen; Chiavacci, Elena; Burger, Alexa; Robinson, Mark D; Mosimann, Christian; Bopp, Daniel; Saccone, Giuseppe (2017). Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes. Scientific Reports, 7(1):e1-e11.

Pagella, Pierfrancesco; Cantù, Claudio; Mitsiadis, Thimios A (2017). Linking dental pathologies and cancer via Wnt signalling. OncoTarget, 8(59):99213-99214.

Junge, Alexander; Refsgaard, Jan C; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T; Jensen, Lars Juhl; Gorodkin, Jan (2017). RAIN: RNA-protein Association and Interaction Networks. Database, 2017:1-9.

Barrecheguren, Pablo José; Ros, Oriol; Cotrufo, Tiziana; Kunz, Beat; Soriano, Eduardo; Ulloa, Fausto; Stoeckli, Esther T; Araújo, Sofia J (2017). SNARE proteins play a role in motor axon guidance in vertebrates and invertebrates. Developmental Neurobiology, 77(8):963-974.

Frei, Jeannine A; Stoeckli, Esther T (2017). SynCAMs - From axon guidance to neurodevelopmental disorders. Molecular and Cellular Neurosciences, 81:41-48.

de Ramon Francàs, Gemma; Zuñiga, Nikole R; Stoeckli, Esther T (2017). The spinal cord shows the way - How axons navigate intermediate targets. Developmental Biology, 432(1):43-52.

Martella, Andrea; Sepe, Rosa M; Silvestri, Cristoforo; Zang, Jingjing; Fasano, Giulia; Carnevali, Oliana; De Girolamo, Paolo; Neuhauss, Stephan C F; Sordino, Paolo; Di Marzo, Vincenzo (2016). Important role of endocannabinoid signaling in the development of functional vision and locomotion in zebrafish. FASEB Journal, 30(12):4275-4288.

Myachina, Faina. Characterization of Drosophila betaTub9EF, a beta-tubulin paralog up-regulated at low temperature. 2016, University of Zurich, Faculty of Science.

Weber, Lukas M; Robinson, Mark D (2016). Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data. Cytometry. Part A, 89(12):1084-1096.

Hartmann, Felix J; Bernard-Valnet, Raphaël; Quériault, Clémence; Mrdjen, Dunja; Weber, Lukas M; Galli, Edoardo; Krieg, Carsten; Robinson, Mark D; Nguyen, Xuan-Hung; Dauvilliers, Yves; Liblau, Roland S; Becher, Burkhard (2016). High-dimensional single-cell analysis reveals the immune signature of narcolepsy. Journal of Experimental Medicine, 213(12):2621-2633.

Delvendahl, Igor; Hallermann, Stefan (2016). The cerebellar mossy fiber synapse as a model for high-frequency transmission in the mammalian CNS. Trends in Neurosciences, 39(11):722-737.

Hawkins, Edwin D; Duarte, Delfim; Akinduro, Olufolake; Khorshed, Reema A; Passaro, Diana; Nowicka, Malgorzata; Straszkowski, Lenny; Scott, Mark K; Rothery, Steve; Ruivo, Nicola; Foster, Katie; Waibel, Michaela; Johnstone, Ricky W; Harrison, Simon J; Westerman, David A; Quach, Hang; Gribben, John; Robinson, Mark D; Purton, Louise E; Bonnet, Dominique; Lo Celso, Cristina (2016). T-cell acute leukaemia exhibits dynamic interactions with bone marrow microenvironments. Nature, 538(7626):518-522.

Toggweiler, Janine; Willecke, Maria; Basler, Konrad (2016). The transcription factor Ets21C drives tumor growth by cooperating with AP-1. Scientific Reports, 6:34725.

Subasic, Deni; Stoeger, Thomas; Eisenring, Seline; Matia-González, Ana M; Imig, Jochen; Zheng, Xue; Xiong, Lei; Gisler, Pascal; Eberhard, Ralf; Holtackers, René; Gerber, André P; Pelkmans, Lucas; Hengartner, Michael O (2016). Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes and Development, 30(19):2213-2225.

Roiz, Daniel; Escobar-Restrepo, Juan Miguel; Leu, Philipp; Hajnal, Alex (2016). The C. elegans hox gene lin-39 controls cell cycle progression during vulval development. Developmental Biology, 418(1):124-34.

Malmersjö, Seth; Di Palma, Serena; Diao, Jiajie; Lai, Ying; Pfuetzner, Richard A; Wang, Austin L; McMahon, Moira A; Hayer, Arnold; Porteus, Matthew; Bodenmiller, Bernd; Brunger, Axel T; Meyer, Tobias (2016). Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion. EMBO Journal Online, 35(16):1810-1821.

Glasauer, Stella M K; Wäger, Robert; Gesemann, Matthias; Neuhauss, Stephan C F (2016). mglur6b:EGFP Transgenic zebrafish suggest novel functions of metabotropic glutamate signaling in retina and other brain regions. Journal of Comparative Neurology, 524(12):2363-2378.

Dolowschiak, Tamas; Mueller, Anna Angelika; Pisan, Lynn Joanna; Feigelman, Rounak; Felmy, Boas; Sellin, Mikael Erik; Namineni, Sukumar; Nguyen, Bidong Dinh; Wotzka, Sandra Yvonne; Heikenwalder, Mathias; von Mering, Christian; Mueller, Christoph; Hardt, Wolf-Dietrich (2016). IFN-γ Hinders Recovery from Mucosal Inflammation during Antibiotic Therapy for Salmonella Gut Infection. Cell Host & Microbe, 20(2):238-249.

Luisoni, Stefania; Bauer, Michael; Prasad, Vibhu; Boucke, Karin; Papadopoulos, Chrisovalantis; Meyer, Hemmo; Hemmi, Silvio; Suomalainen, Maarit; Greber, Urs F (2016). Endosomophagy clears disrupted early endosomes but not virus particles during virus entry into cells. Matters:online.

Hock, Eva-Maria; Polymenidou, Magdalini (2016). Prion-like propagation as a pathogenic principle in frontotemporal dementia. Journal of Neurochemistry, 138 Supp:163-183.

Caviglia, Sara; Brankatschk, Marko; Fischer, Elisabeth J; Eaton, Suzanne; Luschnig, Stefan (2016). Staccato/Unc-13-4 controls secretory lysosome-mediated lumen fusion during epithelial tube anastomosis. Nature Cell Biology, 18(7):727-739.

Trost, Martina; Blattner, Ariane C; Leo, Stefano; Lehner, Christian F (2016). Drosophila dany is essential for transcriptional control and nuclear architecture in spermatocytes. Development, 143(14):2664-2676.

Green, Victoria A; Pelkmans, Lucas (2016). A Systems Survey of Progressive Host-Cell Reorganization during Rotavirus Infection. Cell Host & Microbe, 20(1):107-120.

Lindsay, Helen; Burger, Alexa; Biyong, Berthin; Felker, Anastasia; Hess, Christopher; Zaugg, Jonas; Chiavacci, Elena; Anders, Carolin; Jinek, Martin; Mosimann, Christian; Robinson, Mark D (2016). CrispRVariants charts the mutation spectrum of genome engineering experiments. Nature Biotechnology, 34(7):701-702.

Glashauser, Jade. Visualization and analysis of membrane dynamics during epithelial tube. 2016, University of Zurich, Faculty of Science.

Burger, Alexa; Lindsay, Helen; Felker, Anastasia; Hess, Christopher; Anders, Carolin; Chiavacci, Elena; Zaugg, Jonas; Weber, Lukas M; Catena, Raul; Jinek, Martin; Robinson, Mark D; Mosimann, Christian (2016). Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development, 143(11):2025-2037.

De Lella Ezcurra, Ana Laura; Bertolin, Agustina Paola; Kim, Kevin; Katz, Maximiliano Javier; Gándara, Lautaro; Misra, Tvisha; Luschnig, Stefan; Perrimon, Norbert; Melani, Mariana; Wappner, Pablo (2016). miR-190 Enhances HIF-Dependent Responses to Hypoxia in Drosophila by Inhibiting the Prolyl-4-hydroxylase Fatiga. PLoS Genetics, 12(5):e1006073.

Makushok, T; Alves, P; Huisman, S M; Kijowski, A R; Brunner, D (2016). Sterol-rich membrane domains define fission yeast cell polarity. Cell, 165(5):1182-1196.

Cho, Young-Suk; Do, Manh-Hung; Kwon, Se-Young; Moon, Changjong; Kim, Kwonseop; Lee, Keesook; Lee, Sang-Jin; Hemmi, Silvio; Joo, Young-Eun; Kim, Min Soo; Jung, Chaeyong (2016). Efficacy of CD46-targeting chimeric Ad5/35 adenoviral gene therapy for colorectal cancers. OncoTarget, 7(25):38210-38223.

Mansouri, Maysam; Bellon-Echeverria, Itxaso; Rizk, Aurélien; Ehsaei, Zahra; Cianciolo Cosentino, Chiara; Silva, Catarina S; Xie, Ye; Boyce, Frederick M; Davis, M Wayne; Neuhauss, Stephan C F; Taylor, Verdon; Ballmer-Hofer, Kurt; Berger, Imre; Berger, Philipp (2016). Highly efficient baculovirus-mediated multigene delivery in primary cells. Nature Communications, 7:11529.

Cantù, Claudio; Zimmerli, Dario; Basler, Konrad (2016). Unexpected survival of mice carrying a mutation in Pygo2 that strongly reduces its binding to Bcl9/9l. Matters Select:1-5.

Catena, Raúl; Özcan, Alaz; Zivanovic, Nevena; Bodenmiller, Bernd (2016). Enhanced multiplexing in mass cytometry using osmium and ruthenium tetroxide species. Cytometry. Part A, 89(5):491-497.

Altenhoff, Adrian M; et al (2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5):425-430.

Segerer, Stephan; Sugano, Yuya; Lindenmeyer, Maja T; Auberger, Ines; Ziegler, Urs; Cohen, Clemens D; Neuhauss, Stephan C F; Loffing, Johannes (2016). The Authors Reply. Kidney International, 89(5):1161-1162.

Glasauer, Stella; Neuhauss, Stephan (2016). Expression of CaBP transcripts in retinal bipolar cells of developing and adult zebrafish. Matters:1-4.

Bodenmiller, Bernd (2016). Multiplexed epitope-based tissue imaging for discovery and healthcare applications. Cell Systems, 2(4):225-238.

Blattner, Ariane C; Chaurasia, Soumya; McKee, Bruce D; Lehner, Christian F (2016). Separase is required for homolog and sister disjunction during drosophila melanogaster male meiosis, but not for biorientation of sister centromeres. PLoS Genetics, 12(4):e1005996.

Valenta, Tomas; Degirmenci, Bahar; Moor, Andreas E; Herr, Patrick; Zimmerli, Dario; Moor, Matthias B; Hausmann, George; Cantù, Claudio; Aguet, Michel; Basler, Konrad (2016). Wnt ligands secreted by subepithelial mesenchymal cells are essential for the survival of intestinal stem cells and gut homeostasis. Cell Reports, 15:1-8.

Schmidt, Katharina; Keiser, Simon; Günther, Viola; Georgiev, Oleg; Hirsch, Hans H; Schaffner, Walter; Bethge, Tobias (2016). Transcription enhancers as major determinants of SV40 polyomavirus growth efficiency and host cell tropism. Journal of General Virology, 97(7):1597-1603.

Felker, Anastasia; Nieuwenhuize, Susan; Dolbois, Aymeric; Blazkova, Kristyna; Hess, Christopher; Low, Larry W L; Burger, Sibylle; Samson, Natasha; Carney, Tom J; Bartunek, Petr; Nevado, Cristina; Mosimann, Christian (2016). In vivo performance and properties of tamoxifen metabolites for CreERT2 control. PLoS ONE, 11(4):e0152989.

Schmidt, Katharina; Steiner, Kurt; Petrov, Boyan; Georgiev, Oleg; Schaffner, Walter (2016). Short-lived mammals (shrew, mouse) have a less robust metal-responsive transcription factor than humans and bats. Biometals, 29(3):423-432.

Soneson, Charlotte; Robinson, Mark D (2016). iCOBRA: open, reproducible, standardized and live method benchmarking. Nature Methods, 13(4):283.

Trost, Martina; Blattner, Ariane C; Lehner, Christian F (2016). Regulated protein depletion by the auxin-inducible degradation system in Drosophila melanogaster. Fly, 10(1):35-46.

Gschweitl, Michaela; Ulbricht, Anna; Barnes, Christopher A; Enchev, Radoslav I; Stoffel-Studer, Ingrid; Meyer-Schaller, Nathalie; Huotari, Jatta; Yamauchi, Yohei; Greber, Urs F; Helenius, Ari; Peter, Matthias (2016). A SPOPL/Cullin-3 ubiquitin ligase complex regulates endocytic trafficking by targeting EPS15 at endosomes. eLife, 5:e13841.

Alther, Tobias A; Domanitskaya, Elena; Stoeckli, Esther T (2016). Calsyntenin 1-mediated trafficking of axon guidance receptors regulates the switch in axonal responsiveness at a choice point. Development, 143(6):994-1004.

Stoeger, Thomas; Battich, Nico; Pelkmans, Lucas (2016). Passive Noise Filtering by Cellular Compartmentalization. Cell, 164(6):1151-1161.

Felker, A; Mosimann, C (2016). Contemporary zebrafish transgenesis with Tol2 and application for Cre/lox recombination experiments. In: Detrich, H William; Westerfield, Monte; Zon, Leonard I. The Zebrafish : Genetics, Genomics, and Transcriptomics. Amsterdam: Elsevier, 219-244.

Ochsenbein, Alexandra M; Karaman, Sinem; Proulx, Steven T; Berchtold, Michaela; Jurisic, Giorgia; Stoeckli, Esther T; Detmar, Michael (2016). Endothelial cell-derived semaphorin 3A inhibits filopodia formation by blood vascular tip cells. Development, 143(4):589-594.

Yamauchi, Yohei; Greber, Urs F (2016). Principles of virus uncoating: cues and the snooker ball. Traffic, 17(6):569-592.

Greber, Urs F (2016). Virus and host mechanics support membrane penetration and cell entry. Journal of Virology, 90(8):3802-3805.

Kaufman, C K; Mosimann, C; Fan, Z P; Yang, S; Thomas, A J; Ablain, J; Tan, J L; Fogley, R D; van Rooijen, E; Hagedorn, E J; Ciarlo, C; White, R M; Matos, D A; Puller, A-C; Santoriello, C; Liao, E C; Young, R A; Zon, L I (2016). A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science, 351(6272):aad2197.

Soneson, Charlotte; Matthes, Katarina L; Nowicka, Malgorzata; Law, Charity W; Robinson, Mark D (2016). Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage. Genome Biology, 17:12.

Heller, Davide; Hoppe, Andreas; Restrepo, Simon; Gatti, Lorenzo; Tournier, Alexander L; Tapon, Nicolas; Basler, Konrad; Mao, Yanlan (2016). EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics. Developmental Cell, 36(1):103-116.

Henninger, Jonathan; Santoso, Buyung; Hans, Stefan; Durand, Ellen; Moore, Jessica; Mosimann, Christian; Brand, Michael; Traver, David; Zon, Leonard (2016). Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development. Nature Cell Biology, 19(1):17-27.

Yakimovich, Artur; Yakimovich, Yauhen; Schmid, Michael; Mercer, Jason; Sbalzarini, Ivo F; Greber, Urs F (2016). Infectio: a Generic Framework for Computational Simulation of Virus Transmission between Cells. mSphere, 1(1):e00078-15.

Szklarczyk, Damian; Santos, Alberto; von Mering, Christian; Jensen, Lars Juhl; Bork, Peer; Kuhn, Michael (2016). STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Research, 44(D1):D380-D384.

Stockinger, Heinz; Palagi, Patricia M; Durinx, Christine; Baudis, Michael; von Mering, Christian; Szövényi, Peter; et al (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Research, 44(D1):D27-37.

Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer; Cook, Helen; Heller, Davide; Walter, Mathias C; Rattei, Thomas; Mende, Daniel R; Sunagawa, Shinichi; Kuhn, Michael; Jensen, Lars Juhl; von Mering, Christian; Bork, Peer (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research, 44(D1):D286-D293.

Mittag, Sonnhild; Valenta, Tomas; Weiske, Jörg; Bloch, Laura; Klingel, Susanne; Gradl, Dietmar; Wetzel, Franziska; Chen, Yuan; Petersen, Iver; Basler, Konrad; Huber, Otmar (2016). A novel role for the tumour suppressor Nitrilase1 modulating the Wnt/β-catenin signalling pathway. Cell Discovery, 2:15039.

Fehr, A; Ruetten, M; Seth-Smith, H; Nufer, Lisbeth; Voegtlin, A; Lehner, Angelika; Greub, Gilbert; Crosier, P; Neuhauss, S C F; Vaughan, Lloyd (2016). A zebrafish model for Chlamydia infection with the obligate intracellular pathogen Waddlia chondrophila. Frontiers in Microbiology:7:1829.

Catena, Raúl; Özcan, Alaz; Jacobs, Andrea; Chevrier, Stephane; Bodenmiller, Bernd (2016). AirLab: a cloud-based platform to manage and share antibody-based single-cell research. Genome Biology, 17(1):142.

Pasakarnis, Laurynas; Frei, Erich; Caussinus, Emmanuel; Affolter, Markus; Brunner, Damian (2016). Amnioserosa cell constriction but not epidermal actin cable tension autonomously drives dorsal closure. Nature Cell Biology, 18(11):1161-1172.

Toggweiler, Janine. Analysing Tumor Growth in Drosophila: Defining a Role for the Transcription Factor Ets21C. 2016, University of Zurich, Faculty of Science.

Burri, Andrea; Marinova, Zoya; Robinson, Mark D; Kühnel, Brigitte; Waldenberger, Melanie; Wahl, Simone; Kunze, Sonja; Gieger, Christian; Livshits, Gregory; Williams, Frances (2016). Are epigenetic factors implicated in chronic widespread pain? PLoS ONE, 11(11):e0165548.

Avilés, Evelyn C; Stoeckli, Esther T (2016). Canonical wnt signaling is required for commissural axon guidance. Developmental Neurobiology, 76(2):190-208.

Restrepo, Simon; Zartman, Jeremiah J; Basler, Konrad (2016). Cultivation and Live Imaging of Drosophila Imaginal Discs. Methods in Molecular Biology, 1478:203-213.

Nowicka, Malgorzata; Robinson, Mark D (2016). DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Research, 5:1356.

Jenny, Fabian H; Basler, Konrad (2016). Drosophila DDX3/Belle exerts its function outside of the Wnt/Wingless signaling pathway. PLoS ONE, 11(12):e0166862.

Restrepo, Simon; Basler, Konrad (2016). Drosophila wing imaginal discs respond to mechanical injury via slow InsP3R-mediated intercellular calcium waves. Nature Communications, 7:12450.

Mackay, Alan; Burford, Anna; Salom, Janat Fazal; et al; Baudis, Michael (2016). Hg-95integrated molecular meta-analysis of 1000 paediatric high grade glioma and dipg. Neuro-Oncology, 18(suppl 3):iii70.3-iii70.

Baillon, Ludovic. Identification of careless - a Gene Involved in Cell Competition in Drosophila melanogaster. 2016, University of Zurich, Faculty of Science.

Rot, Gregor. Integrative Approaches for Studying Regulatory Principles of Alternative Polyadenylation. 2016, University of Zurich, Faculty of Science.

Zafar, Sadia; Parviainen, Suvi; Siurala, Mikko; Hemminki, Otto; Havunen, Riikka; Tähtinen, Siri; Bramante, Simona; Vassilev, Lotta; Wang, Hongjie; Lieber, Andre; Hemmi, Silvio; de Gruijl, Tanja; Kanerva, Anna; Hemminki, Akseli (2016). Intravenously usable fully serotype 3 oncolytic adenovirus coding for CD40L as an enabler of dendritic cell therapy. OncoImmunology:e1265717.

Eshwar, Athmanya K; Tall, Ben D; Gangiredla, Jayanthi; Gopinath, Gopal R; Patel, Isha R; Neuhauss, Stephan C F; Stephan, Roger; Lehner, Angelika (2016). Linking genomo- and pathotype: Exploiting the Zebrafish embryo model to investigate the divergent virulence potential among cronobacter spp. PLoS ONE, 11(6):e0158428.

Eder, Dominik. Mechanical Forces in Growth Regulation – Challenging Force Measurements and Force Manipulations in the Drosophila Wing Imaginal Disc. 2016, University of Zurich, Faculty of Science.

Feigelman, Rounak. Metagenomic Analysis of Lung and Oral Microbial Communities Using Whole Genome Shotgun Sequencing. 2016, University of Zurich, Faculty of Science.

Kamkina, Polina; Snoek, L Basten; Grossmann, Jonas; Volkers, Rita J M; Sterken, Mark G; Daube, Michael; Roschitzki, Bernd; Fortes, Claudia; Schlapbach, Ralph; Roth, Alexander; von Mering, Christian; Hengartner, Michael O; Schrimpf, Sabine P; Kammenga, Jan E (2016). Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans. Molecular & Cellular Proteomics, 15(5):1670-1680.

Singh, Kapil Dev; Roschitzki, Bernd; Snoek, L. Basten; Grossmann, Jonas; Zheng, Xue; Elvin, Mark; Kamkina, Polina; Schrimpf, Sabine P; Poulin, Gino B; Kammenga, Jan E; Hengartner, Michael O (2016). Natural genetic variation influences protein abundances in C. elegans developmental signalling pathways. PLoS ONE, 11(3):e0149418.

Raddi, Najat; Vigant, Frédéric; Wagner-Ballon, Oriane; Giraudier, Stéphane; Custers, Jerome; Hemmi, Silvio; Benihoud, Karim (2016). Pseudotyping serotype 5 adenovirus with the fiber from other serotypes uncovers a key role of the fiber protein in adenovirus 5-induced thrombocytopenia. Human Gene Therapy, 27(2):193-201.

Franceschini, Andrea; Lin, Jianyi; von Mering, Christian; Jensen, Lars Juhl (2016). SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics, 32(7):1085-1087.

Baumann, Lisa; Ros, Albert; Rehberger, Kristina; Neuhauss, Stephan C F; Segner, Helmut (2016). Thyroid disruption in zebrafish (Danio rerio) larvae: Different molecular response patterns lead to impaired eye development and visual functions. Aquatic Toxicology, 172:44-55.

Caussinus, Emmanuel; Affolter, Markus (2016). deGradFP: A System to Knockdown GFP-Tagged Proteins. Methods in Molecular Biology, 1478:177-187.

Riascos-Bernal, Dario F; Chinnasamy, Prameladevi; Cao, Longyue Lily; Dunaway, Charlene M; Valenta, Tomas; Basler, Konrad; Sibinga, Nicholas E S (2016). β-Catenin C-terminal signals suppress p53 and are essential for artery formation. Nature Communications, 7:12389.

Kulic, Iva; et al; Robinson, M D (2015). Loss of the Notch effector RBPJ promotes tumorigenesis. Journal of Experimental Medicine, 212(1):37-52.

Harmansa, Stefan; Hamaratoglu, Fisun; Affolter, Markus; Caussinus, Emmanuel (2015). Dpp spreading is required for medial but not for lateral wing disc growth. Nature, 527(7578):317-227.

Bilgin Sonay, Tugce; Carvalho, Tiago; Robinson, Mark D; Greminger, Maja P; Krützen, Michael; Comas, David; Highnam, Gareth; Mittelman, David; Sharp, Andrew; Marques-Bonet, Tomàs; Wagner, Andreas (2015). Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Research, 25(11):1591-1599.

Sugano, Yuya; Lindenmeyer, Maja T; Auberger, Ines; Ziegler, Urs; Segerer, Stephan; Cohen, Clemens D; Neuhauss, Stephan C F; Loffing, Johannes (2015). The Rho-GTPase binding protein IQGAP2 is required for the glomerular filtration barrier. Kidney International, 88(5):1047-1056.

Carrella, Sabrina; D'Agostino, Ylenia; Barbato, Sara; Huber-Reggi, Sabina P; Salierno, Francesco G; Manfredi, Anna; Neuhauss, Stephan C F; Banfi, Sandro; Conte, Ivan (2015). miR-181a/b control the assembly of visual circuitry by regulating retinal axon specification and growth. Developmental Neurobiology, 75(11):1252-1267.

Moor, Andreas E; Anderle, Pascale; Cantù, Claudio; Rodriguez, Patrick; Wiedemann, Norbert; Baruthio, Frédérique; Deka, Jürgen; André, Sylvie; Valenta, Tomas; Moor, Matthias B; Győrffy, Balázs; Barras, David; Delorenzi, Mauro; Basler, Konrad; Aguet, Michel (2015). BCL9/9L-β-catenin signaling is associated with poor outcome in colorectal cancer. EBioMedicine, 2(12):1932-1943.

Dona, Margo; Bachmann-Gagescu, Ruxandra; Texier, Yves; Toedt, Grischa; Hetterschijt, Lisette; Tonnaer, Edith L; Peters, Theo A; van Beersum, Sylvia E C; Bergboer, Judith G M; Horn, Nicola; de Vrieze, Erik; Slijkerman, Ralph W N; van Reeuwijk, Jeroen; Flik, Gert; Keunen, Jan E; Ueffing, Marius; Gibson, Toby J; Roepman, Ronald; Boldt, Karsten; Kremer, Hannie; van Wijk, Erwin (2015). NINL and DZANK1 co-function in vesicle transport and are essential for photoreceptor development in Zebrafish. PLoS Genetics, 11(10):e1005574.

Zhou, Xiaobei; Robinson, Mark D (2015). Do count-based differential expression methods perform poorly when genes are expressed in only one condition? Genome Biology, 16(222):online.

Bachmann-Gagescu, Ruxandra; Dona, Margo; Hetterschijt, Lisette; Tonnaer, Edith; Peters, Theo; de Vrieze, Erik; Mans, Dorus A; van Beersum, Sylvia E C; Phelps, Ian G; Arts, Heleen H; Keunen, Jan E; Ueffing, Marius; Roepman, Ronald; Boldt, Karsten; Doherty, Dan; Moens, Cecilia B; Neuhauss, Stephan C F; Kremer, Hannie; van Wijk, Erwin (2015). The ciliopathy protein CC2D2A Associates with NINL and functions in RAB8-MICAL3-regulated vesicle trafficking. PLoS Genetics, 11(10):e1005575.

Ortega-Esteban, Alvaro; Bodensiek, Kai; San Martín, Carmen; Suomalainen, Maarit; Greber, Urs F; de Pablo, Pedro J; Schaap, Iwan A T (2015). Fluorescence Tracking of Genome Release during the Mechanical Unpacking of Single Viruses. ACS Nano:1-28.

Stoeger, Thomas; Battich, Nico; Herrmann, Markus D; Yakimovich, Yauhen; Pelkmans, Lucas (2015). Computer vision for image-based transcriptomics. Methods, 85:44-53.

Bachmann-Gagescu, Ruxandra; Phelps, Ian G; Dempsey, Jennifer C; Sharma, Vivek A; Ishak, Gisele E; Boyle, Evan A; Wilson, Meredith; Marques Lourenço, Charles; Arslan, Mutluay; Shendure, Jay; Doherty, Dan (2015). KIAA0586 is mutated in Joubert syndrome. Human Mutation, 36(9):831-835.

Wang, Mingcong; Herrmann, Christina J; Simonovic, Milan; Szklarczyk, Damian; von Mering, Christian (2015). Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics, 15(18):3163-3168.

Mosimann, Christian; Panáková, Daniela; Werdich, Andreas A; Musso, Gabriel; Burger, Alexa; Lawson, Katy L; Carr, Logan A; Nevis, Kathleen R; Sabeh, M. Khaled; Zhou, Yi; Davidson, Alan J; DiBiase, Anthony; Burns, Caroline E; Burns, C Geoffrey; MacRae, Calum A; Zon, Leonard I (2015). Chamber identity programs drive early functional partitioning of the heart. Nature Communications, 6:8146.

Gut, Gabriele; Tadmor, Michelle D; Pe'er, Dana; Pelkmans, Lucas; Liberali, Prisca (2015). Trajectories of cell-cycle progression from fixed cell populations. Nature Methods, 12(10):951-954.

Zang, Jingjing; Keim, Jennifer; Kastenhuber, Edda; Gesemann, Matthias; Neuhauss, Stephan C F (2015). Recoverin depletion accelerates cone photoresponse recovery. Open Biology, 5(8):150086.

Bologna, Serena; Altmannova, Veronika; Valtorta, Emanuele; Koenig, Christiane; Liberali, Prisca; Gentili, Christian; Anrather, Dorothea; Ammerer, Gustav; Pelkmans, Lucas; Krejci, Lumir; Ferrari, Stefano (2015). Sumoylation regulates EXO1 stability and processing of DNA damage. Cell Cycle, 14(15):2439-2450.

Bachmann-Gagescu, R; Dempsey, J C; Phelps, I G; O'Roak, B J; Knutzen, D M; Rue, T C; Ishak, G E; Isabella, C R; Gorden, N; Adkins, J; Boyle, E A; de Lacy, N; O'Day, D; Alswaid, A; Ramadevi A, R; Lingappa, L; Lourenço, C; Martorell, L; Garcia-Cazorla, À; Ozyürek, H; Haliloğlu, G; Tuysuz, B; Topçu, M; Chance, P; Parisi, M A; Glass, I A; Shendure, J; Doherty, D (2015). Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. Journal of Medical Genetics, 52(8):514-522.

Subasic, Deni; Brümmer, Anneke; Wu, Yibo; Pinto, Sérgio Morgado; Imig, Jochen; Keller, Martin; Jovanovic, Marko; Lightfoot, Helen Louise; Nasso, Sara; Goetze, Sandra; Brunner, Erich; Hall, Jonathan; Aebersold, Ruedi; Zavolan, Mihaela; Hengartner, Michael O (2015). Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family inC. elegans. Genome Research, 25(11):1680-1691.

Flatt, Justin W; Greber, Urs F (2015). Misdelivery at the nuclear pore complex-stopping a virus dead in its tracks. Cells, 4(3):277-296.

Hall, Benjamin A; Piterman, Nir; Hajnal, Alex; Fisher, Jasmin (2015). Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling. Biophysical Journal, 109(2):428-438.

Gopal, Suhasini R; Chen, Daniel H-C; Chou, Shih-Wei; Zang, Jingjing; Neuhauss, Stephan C F; Stepanyan, Ruben; McDermott, Brian M; Alagramam, Kumar N (2015). Zebrafish models for the mechanosensory hair cell dysfunction in Usher syndrome 3 reveal that Clarin-1 is an essential hair bundle protein. Journal of Neuroscience, 35(28):10188-10201.

Luisoni, Stefania; Suomalainen, Maarit; Boucke, Karin; Tanner, Lukas B; Wenk, Markus R; Guan, Xue Li; Grzybek, Michał; Coskun, Ünal; Greber, Urs F (2015). Co-option of membrane wounding enables virus penetration into cells. Cell Host & Microbe, 18(1):75-85.

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.

Thompson, Owen A; Snoek, L Basten; Nijveen, Harm; Sterken, Mark G; Volkers, Rita J M; Brenchley, Rachel; Van't Hof, Arjen; Bevers, Roel P J; Cossins, Andrew R; Yanai, Itai; Hajnal, Alex; Schmid, Tobias; Perkins, Jaryn D; Spencer, David; Kruglyak, Leonid; Andersen, Erik C; Moerman, Donald G; Hillier, LaDeana W; Kammenga, Jan E; Waterston, Robert H (2015). Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856. Genetics, 200(3):975-989.

Andersen, Ditte S; Colombani, Julien; Palmerini, Valentina; Chakrabandhu, Krittalak; Boone, Emilie; Röthlisberger, Michael; Toggweiler, Janine; Basler, Konrad; Mapelli, Marina; Hueber, Anne-Odile; Léopold, Pierre (2015). The Drosophila TNF receptor Grindelwald couples loss of cell polarity and neoplastic growth. Nature, 522(7557):482-486.

Conte, Ivan; Hadfield, Kristen D; Barbato, Sara; Carrella, Sabrina; Pizzo, Mariateresa; Bhat, Rajeshwari S; Carissimo, Annamaria; Karali, Marianthi; Porter, Louise F; Urquhart, Jill; Hateley, Sofie; O'Sullivan, James; Manson, Forbes D C; Neuhauss, Stephan C F; Banfi, Sandro; Black, Graeme C M (2015). MiR-204 is responsible for inherited retinal dystrophy associated with ocular coloboma. Proceedings of the National Academy of Sciences of the United States of America, 112(25):3236-3245.

Byri, Sunitha; Misra, Tvisha; Syed, Zulfeqhar A; Bätz, Tilmann; Shah, Jimit; Boril, Lukas; Glashauser, Jade; Aegerter-Wilmsen, Tinri; Matzat, Till; Moussian, Bernard; Uv, Anne; Luschnig, Stefan (2015). The Triple-Repeat Protein Anakonda Controls Epithelial Tricellular Junction Formation in Drosophila. Developmental Cell, 33(4):1-14.

Walser, M; Hajnal, A; Escobar-Restrepo, Juan M (2015). FRAP analysis of LET-23::GFP in the vulval epithelial cells of living caenorhabditis elegans larvae. Bio-protocol, 5(11):e1489.

Schmid, Tobias; Hajnal, Alex (2015). Signal transduction during C. elegans vulval development: a NeverEnding story. Current Opinion in Genetics & Development, 32:1-9.

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 Reports, 16(6):741-752.

Fehr, Alexander; Eshwar, Athmanya K; Neuhauss, Stephan Cf; Ruetten, Maja; Lehner, Angelika; Vaughan, Lloyd (2015). Evaluation of zebrafish as a model to study the pathogenesis of the opportunistic pathogen Cronobacter turicensis. Emerging Microbes and Infections, 4(5):e29.

Schmid, Tobias; Snoek, L Basten; Fröhli, Erika; van der Bent, M Leontien; Kammenga, Jan; Hajnal, Alex (2015). Systemic regulation of RAS/MAPK signaling by the serotonin metabolite 5-HIAA. PLoS Genetics, 11(5):e1005236.

Schmid, Corina A; Robinson, Mark D; Scheifinger, Nicole A; Müller, Sebastian; Cogliatti, Sergio; Tzankov, Alexandar; Müller, Anne (2015). DUSP4 deficiency caused by promoter hypermethylation drives JNK signaling and tumor cell survival in diffuse large B cell lymphoma. Journal of Experimental Medicine:1-18.

Schertel, Claus; Albarca, Monica; Rockel-Bauer, Claudia; Kelley, Nicholas W; Bischof, Johannes; Hens, Korneel; van Nimwegen, Erik; Basler, Konrad; Deplancke, Bart (2015). A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome Research, 25(4):514-523.

Schaffner, Walter (2015). Enhancers, enhancers - from their discovery to today's universe of transcription enhancers. Biological Chemistry, 396(4):311-327.

Siebourg-Polster, Juliane; Mudrak, Daria; Emmenlauer, Mario; Rämö, Pauli; Dehio, Christoph; Greber, Urs; Fröhlich, Holger; Beerenwinkel, Niko (2015). NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Computational Biology, 11(4):e1004078.

Baker, Emma K; Taylor, Scott; Gupte, Ankita; Chalk, Alistair M; Bhattacharya, Shreya; Green, Alanna C; Martin, T John; Strbenac, Dario; Robinson, Mark D; Purton, Louise E; Walkley, Carl R (2015). Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma. Bone, 73:223-232.

Briona, Lisa K; Poulain, Fabienne E; Mosimann, Christian; Dorsky, Richard I (2015). Wnt/β-catenin signaling is required for radial glial neurogenesis following spinal cord injury. Developmental Biology, 403(1):15-21.

Müller, Martin; Genç, Özgür; Davis, Graeme W (2015). RIM-Binding Protein Links Synaptic Homeostasis to the Stabilization and Replenishment of High Release Probability Vesicles. Neuron, 85(5):1056-1069.

Keiser, Simon; Schmidt, Katharina; Bethge, Tobias; Steiger, Julia; Hirsch, Hans H; Schaffner, Walter; Georgiev, Oleg (2015). Emergence of infectious simian virus 40 whose AT tract in the replication origin/early promoter region is substituted by cellular or viral DNAs. Journal of General Virology, 96:601-606.

Bethge, Tobias; Hachemi, Helen A; Manzetti, Julia; Gosert, Rainer; Schaffner, Walter; Hirsch, Hans H (2015). Sp1 sites in the noncoding control region of BK polyomavirus are key regulators of bidirectional viral early and late gene expression. Journal of Virology, 89(6):3396-3411.

Haug, Marion F; Gesemann, Matthias; Lazović, Viktor; Neuhauss, Stephan C F (2015). Eumetazoan cryptochrome phylogeny and evolution. Genome Biology and Evolution, 7(2):601-619.

Davis, Graeme W; Müller, Martin (2015). Homeostatic Control of Presynaptic Neurotransmitter Release. Annual Review of Physiology, 77(1):251-270.

Gillers, Benjamin S; Chiplunkar, Aditi; Aly, Haytham; Valenta, Tomas; Basler, Konrad; Christoffels, Vincent M; Efimov, Igor R; Boukens, Bastiaan J; Rentschler, Stacey (2015). Canonical wnt signaling regulates atrioventricular junction programming and electrophysiological properties. Circulation Research, 116(3):398-406.

Butko, E; Distel, M; Pouget, C; Weijts, B; Kobayashi, I; Ng, K; Mosimann, C; Poulain, F E; McPherson, A; Ni, C-W; Stachura, D L; Del Cid, N; Espin-Palazon, R; Lawson, N D; Dorsky, R; Clements, W K; Traver, D (2015). Gata2b is a restricted early regulator of hemogenic endothelium in the zebrafish embryo. Development, 142(6):1050-1061.

Luisoni, Stefania. Lipid Requirements for Adenovirus Infection. 2015, University of Zurich, Faculty of Science.

Szklarczyk, Damian; Franceschini, Andrea; Wyder, Stefan; Forslund, Kristoffer; Heller, Davide; Huerta-Cepas, Jaime; Simonovic, Milan; Roth, Alexander; Santos, Alberto; Tsafou, Kalliopi P; Kuhn, Michael; Bork, Peer; Jensen, Lars J; von Mering, Christian (2015). STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(Database i):D447-52.

Cai, Haoyang; Gupta, Saumya; Rath, Prisni; Ai, Ni; Baudis, Michael (2015). arrayMap 2014: an updated cancer genome resource. Nucleic Acids Research, 43:D825-D830.

LeClaire, Lawrence L; Rana, Manish; Baumgartner, Martin; Barber, Diane L (2015). The Nck-interacting kinase NIK increases Arp2/3 complex activity by phosphorylating the Arp2 subunit. Journal of Cell Biology, 208(2):161-170.

Ingold, Esther; Vom Berg-Maurer, Colette M; Burckhardt, Christoph J; Lehnherr, André; Rieder, Philip; Keller, Philip J; Stelzer, Ernst H; Greber, Urs F; Neuhauss, Stephan C F; Gesemann, Matthias (2015). Proper migration and axon outgrowth of zebrafish cranial motoneuron subpopulations require the cell adhesion molecule MDGA2A. Biology Open, 4(2):146-154.

Jenny, Fabian Heinz; Basler, Konrad (2015). Powerful Drosophila screens that paved the wingless pathway. Fly, 8(4):218-225.

Gu, Lei; Frommel, Sandra C; Oakes, Christopher C; Simon, Ronald; Grupp, Katharina; Gerig, Cristina Y; Bär, Dominik; Robinson, Mark D; Baer, Constance; Weiss, Melanie; Gu, Zuguang; Schapira, Matthieu; Kuner, Ruprecht; Sültmann, Holger; Provenzano, Maurizio; Yaspo, Marie-Laure; Brors, Benedikt; Korbel, Jan; Schlomm, Thorsten; Sauter, Guido; Eils, Roland; Plass, Christoph; Santoro, Raffaella (2015). BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature Genetics, 47(1):22-30.

Galluzzi, L; Bravo-San Pedro, J M; Vitale, I; et al (2015). Essential versus accessory aspects of cell death: recommendations of the NCCD 2015. Cell Death and Differentiation, 22(1):58-73.

Draganova, Kalina; Zemke, Martina; Zurkirchen, Luis; Valenta, Tomas; Cantù, Claudio; Okoniewski, Michal; Schmid, Marie-Theres; Hoffmans, Raymond; Götz, Magdalena; Basler, Konrad; Sommer, Lukas (2015). Wnt/β-catenin signaling regulates sequential fate decisions of murine cortical precursor cells. Stem Cells, 33(1):170-182.

Georgiopoulou, Stavroula. Assessment of the Role of Endothelial mTORC2 in FGF2-induced Angiogenesis in vivo. 2015, University of Zurich, Faculty of Medicine.

Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K (2015). Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes. Systematic and Applied Microbiology, 38(5):330-339.

Robinson, Mark D; Pelizzola, Mattia (2015). Computational epigenomics: challenges and opportunities. Frontiers in Genetics, 6:88.

Locke, Warwick J; Zotenko, Elena; Stirzaker, Clare; Robinson, Mark D; Hinshelwood, Rebecca A; Stone, Andrew; Reddel, Roger R; Huschtscha, Lily I; Clark, Susan J (2015). Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clinical Epigenetics, 7(1):52.

Brox, Dominik; Comba, Peter; Herten, Dirk-Peter; Kimmle, Esther; Morgen, Michael; Rühl, Carmen L; Rybina, Arina; Stephan, Holger; Storch, Golo; Wadepohl, Hubert (2015). CuII-selective bispidine–dye conjugates. Journal of Inorganic Biochemistry, 148:78-83.

Lebert, Dorothée; Louwagie, Mathilde; Goetze, Sandra; Picard, Guillaume; Ossola, Reto; Duquesne, Caroline; Basler, Konrad; Ferro, Myriam; Rinner, Oliver; Aebersold, Ruedi; Garin, Jérôme; Mouz, Nicolas; Brunner, Erich; Brun, Virginie (2015). DIGESTIF: A universal quality standard for the control of bottom-up proteomics experiments. Journal of Proteome Research, 14(2):787-803.

Soneson, Charlotte; Love, Michael I; Robinson, Mark D (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4:1521.

Stutz, Katrin; Kaech, Andres; Aebi, Markus; Künzler, Markus; Hengartner, Michael O (2015). Disruption of the C. elegans intestinal brush border by the fungal lectin CCL2 phenocopies dietary lectin toxicity in mammals. PLoS ONE, 10(6):e0129381.

Gay, Max Hans-Peter; Valenta, Tomas; Herr, Patrick; Paratore-Hari, Lisette; Basler, Konrad; Sommer, Lukas (2015). Distinct adhesion-independent functions of β-catenin control stage-specific sensory neurogenesis and proliferation. BMC Biology, 13(24):online.

Seebauer, Britta. Functional characterization of sequence variants in SRF, MKL1 and MKL2, presumably associated with exudative vitreoretinopathy (EVR). 2015, University of Zurich, Faculty of Science.

Musso, G; Mosimann, C; Panáková, D; Burger, A; Zhou, Y; Zon, L I; MacRae, C A (2015). Generating and evaluating a ranked candidate gene list for potential vertebrate heart field regulators. Genomics Data, 6:199-201.

Muff, Roman; Rath, Prisni; Ram Kumar, Ram Mohan; Husmann, Knut; Born, Walter; Baudis, Michael; Fuchs, Bruno (2015). Genomic instability of osteosarcoma cell lines in culture: impact on the prediction of metastasis relevant genes. PLoS ONE, 10(5):e0125611.

Drägert, Katja. Impact of Rictor Deletion in Adipocytes and Brain on Gene Expression in Perivascular Adipose Tissue and Blood Pressure Regulation. 2015, University of Zurich, Faculty of Medicine.

Stichling, Nicole. Innate Immune Mechanisms to Adenovirus in an Alveolar Macrophage-like. 2015, University of Zurich, Faculty of Science.

Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2015). Limits to robustness and reproducibility in the demarcation of operational taxonomic units. Environmental Microbiology, 17(5):1689-1706.

Zemke, Martina; Draganova, Kalina; Klug, Annika; Schöler, Anne; Zurkirchen, Luis; Gay, Max Hans-Peter; Cheng, Phil; Koseki, Haruhiko; Valenta, Tomas; Schübeler, Dirk; Basler, Konrad; Sommer, Lukas (2015). Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation. BMC Biology, 13:103.

Zahnleiter, Diana; Hauer, Nadine N; Kessler, Kristin; Uebe, Steffen; Sugano, Yuya; Neuhauss, Stephan C F; Giessl, Andreas; Ekici, Arif B; Blessing, Holger; Sticht, Heinrich; Dörr, Helmuth-Günther; Reis, André; Thiel, Christian T (2015). MAP4-dependent regulation of microtubule formation affects centrosome, cilia, and golgi architecture as a central mechanism in growth regulation. Human Mutation, 36(1):87-97.

Skaria, Tom. Mechanisms of Inflammation in Response to Wnt5A and IL-4 in Human vascular Endothelial Cells. 2015, University of Zurich, Faculty of Science.

Stirzaker, Clare; Zotenko, Elena; Song, Jenny Z; Qu, Wenjia; Nair, Shalima S; Locke, Warwick J; Stone, Andrew; Armstong, Nicola J; Robinson, Mark D; Dobrovic, Alexander; Avery-Kiejda, Kelly A; Peters, Kate M; French, Juliet D; Stein, Sandra; Korbie, Darren J; Trau, Matt; Forbes, John F; Scott, Rodney J; Brown, Melissa A; Francis, Glenn D; Clark, Susan J (2015). Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nature Communications, 6:5899.

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(05864):online.

Heazlewood, Joshua L; Schrimpf, Sabine P; Becher, Dörte; Riedel, Katrin; Tholey, Andreas; Bendixen, Emøke (2015). Multi-Organism Proteomes (iMOP): Advancing our Understanding of Human Biology. Proteomics, 15(17):2885-2894.

Yakimovich, Artur; Andriasyan, Vardan; Witte, Robert; Wang, I-Hsuan; Prasad, Vibhu; Suomalainen, Maarit; Greber, Urs F (2015). Plaque2.0-A high-throughput analysis framework to score virus-cell transmission and clonal cell expansion. PLoS ONE, 10(9):e0138760.

de la Mata, M; Gaidatzis, D; Vitanescu, M; Stadler, M B; Wentzel, C; Scheiffele, P; Filipowicz, W; Grosshans, H (2015). Potent degradation of neuronal miRNAs induced by highly complementary targets. EMBO Reports, 16(4):500-511.

Eltsov, Mikhail; Dubé, Nadia; Yu, Zhou; Pasakarnis, Laurynas; Haselmann-Weiss, Uta; Brunner, Damian; Frangakis, Achilleas S (2015). Quantitative analysis of cytoskeletal reorganization during epithelial tissue sealing by large-volume electron tomography. Nature Cell Biology, 17(5):605-614.

Vallelian, Florence; Garcia-Rubio, Ines; Puglia, Michele; Kahraman, Abdullah; Deuel, Jeremy W; Engelsberger, Wolfgang R; Mason, Ronald P; Buehler, Paul W; Schaer, Dominik J (2015). Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin : haptoglobin complex. Free Radical Biology & Medicine, 85:259-268.

Schmich, Fabian; Szczurek, Ewa; Kreibich, Saskia; Dilling, Sabrina; Andritschke, Daniel; Casanova, Alain; Low, Shyan Huey; Eicher, Simone; Muntwiler, Simone; Emmenlauer, Mario; Rämö, Pauli; Conde-Alvarez, Raquel; von Mering, Christian; Hardt, Wolf-Dietrich; Dehio, Christoph; Beerenwinkel, Niko (2015). gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens. Genome Biology, 16:220.

Rämö, Pauli; Drewek, Anna; Arrieumerlou, Cécile; Beerenwinkel, Niko; Ben-Tekaya, Houchaima; Cardel, Bettina; Casanova, Alain; Conde-Alvarez, Raquel; Cossart, Pascale; Csúcs, Gábor; Eicher, Simone; Emmenlauer, Mario; Greber, Urs; Hardt, Wolf-Dietrich; Helenius, Ari; Kasper, Christoph; Kaufmann, Andreas; Kreibich, Saskia; Kühbacher, Andreas; Kunszt, Peter; Low, Shyan Huey; Mercer, Jason; Mudrak, Daria; Muntwiler, Simone; Pelkmans, Lucas; Pizarro-Cerdá, Javier; Podvinec, Michael; Pujadas, Eva; Rinn, Bernd; Rouilly, Vincent; Schmich, Fabian; Siebourg-Polster, Juliane; Snijder, Berend; Stebler, Michael; Studer, Gabriel; Szczurek, Ewa; Truttmann, Matthias; von Mering, Christian; Vonderheit, Andreas; Yakimovich, Artur; Bühlmann, Peter; Dehio, Christoph (2014). Simultaneous analysis of large-scale RNAi screens for pathogen entry. BMC Genomics, 15:1162.

Roulin, Pascal S. Host membrane compartments supporting human rhinovirus. 2014, University of Zurich, Faculty of Science.

Frei, Jeannine A; Andermatt, Irwin; Gesemann, Matthias; Stoeckli, Esther T (2014). The SynCAM synaptic cell adhesion molecules are involved in sensory axon pathfinding by regulating axon-axon contacts. Journal of Cell Science, 127(24):5288-5302.

Meyer, S N; Amoyel, M; Bergantiños, C; de la Cova, C; Schertel, C; Basler, K; Johnston, L A (2014). An ancient defense system eliminates unfit cells from developing tissues during cell competition. Science, 346(6214):1258236.

Glasauer, Stella M K; Neuhauss, Stephan C F (2014). Whole-genome duplication in teleost fishes and its evolutionary consequences. Molecular Genetics and Genomics, 289(6):1045-1060.

Schulz, Juliane Caroline; Zampieri, Mattia; Wanka, Stefanie; von Mering, Christian; Sauer, Uwe (2014). Large-scale functional analysis of the roles of phosphorylation in yeast metabolic pathways. Science Signaling, 7(353):rs6.

Stoeckli, Esther T (2014). Wiring mechanisms for olfaction and vision--not completely different after all. Neuron, 84(4):655-657.

Roulin, Pascal S; Lötzerich, Mark; Torta, Federico; Tanner, Lukas B; van Kuppeveld, Frank J M; Wenk, Markus R; Greber, Urs F (2014). Rhinovirus uses a phosphatidylinositol 4-phosphate/cholesterol counter-current for the formation of replication compartments at the ER-Golgi interface. Cell Host & Microbe, 16(5):677-690.

Reim, Gerlinde; Hruzova, Martina; Goetze, Sandra; Basler, Konrad (2014). Protection of Armadillo/β-Catenin by Armless, a Novel Positive Regulator of Wingless Signaling. PLoS Biology, 12(11):e1001988.

Escobar-Restrepo, Juan M; Hajnal, Alex (2014). An intimate look at LET-23 EGFR trafficking in the vulval cells of live C. elegans larvae. Worm, 3(3):e965605.

Sirisi, Sònia; Folgueira, Mónica; López-Hernández, Tania; Minieri, Laura; Pérez-Rius, Carla; Gaitán-Peñas, Héctor; Zang, Jingjing; Martínez, Albert; Capdevila-Nortes, Xavier; De La Villa, Pedro; Roy, Upasana; Alia, A; Neuhauss, Stephan; Ferroni, Stefano; Nunes, Virginia; Estévez, Raúl; Barrallo-Gimeno, Alejandro (2014). Megalencephalic leukoencephalopathy with subcortical cysts protein 1 regulates glial surface localization of GLIALCAM from fish to humans. Human Molecular Genetics, 23(19):5069-5086.

Soste, Martin; Hrabakova, Rita; Wanka, Stefanie; Melnik, Andre; Boersema, Paul; Maiolica, Alessio; Wernas, Timon; Tognetti, Marco; von Mering, Christian; Picotti, Paola (2014). A sentinel protein assay for simultaneously quantifying cellular processes. Nature Methods, 11(10):1045-1048.

Skorobogata, Olga; Escobar-Restrepo, Juan M; Rocheleau, Christian E (2014). An AGEF-1/Arf GTPase/AP-1 ensemble antagonizes LET-23 EGFR basolateral localization and signaling during C. elegans vulva induction. PLoS Genetics, 10(10):e1004728.

Hall, Benjamin A; Jackson, Ethan; Hajnal, Alex; Fisher, Jasmin (2014). Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis. Journal of the Royal Society. Interface, 11(98):20140245.

Prasad, Vibhu; Suomalainen, Maarit; Pennauer, Mirjam; Yakimovich, Artur; Andriasyan, Vardan; Hemmi, Silvio; Greber, Urs F (2014). Chemical induction of unfolded protein response enhances cancer cell killing through lytic virus infection. Journal of Virology, 88(22):13086-13098.

Cantù, Claudio; Zimmerli, Dario; Hausmann, George; Valenta, Tomas; Moor, Andreas; Aguet, Michel; Basler, Konrad (2014). Pax6-dependent, but β-catenin-independent, function of Bcl9 proteins in mouse lens development. Genes and Development, 28(17):1879-1884.

Qeli, Ermir; Omasits, Ulrich; Goetze, Sandra; Stekhoven, Daniel J; Frey, Juerg E; Basler, Konrad; Wollscheid, Bernd; Brunner, Erich; Ahrens, Christian H (2014). Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. Journal of Proteomics, 108:269-283.

Caviglia, Sara. Genetic and Cellular Mechanisms of Epithelial Tube Fusion in Drosophila melanogaster. 2014, University of Zurich, Faculty of Science.

Sendoel, A; Maida, S; Zheng, X; Teo, Y; Stergiou, L; Rossi, C A; Subasic, D; Pinto, S M; Kinchen, J M; Shi, M; Boettcher, S; Meyer, J N; Manz, M G; Bano, D; Hengartner, M O (2014). DEPDC1/LET-99 participates in an evolutionarily conserved pathway for anti-tubulin drug-induced apoptosis. Nature Cell Biology, 16(8):812-820.

Bischof, Johannes; Sheils, Emma M; Björklund, Mikael; Basler, Konrad (2014). Generation of a transgenic ORFeome library in Drosophila. Nature Protocols, 9(7):1607-1620.

Wohlschlager, Therese; Butschi, Alex; Grassi, Paola; Sutov, Grigorij; Gauss, Robert; Hauck, Dirk; Schmieder, Stefanie S; Knobel, Martin; Titz, Alexander; Dell, Anne; Haslam, Stuart M; Hengartner, Michael O; Aebi, Markus; Künzler, Markus (2014). Methylated glycans as conserved targets of animal and fungal innate defense. Proceedings of the National Academy of Sciences of the United States of America, 111(27):E2787-E2796.

Misra, Tvisha. Metabolic control of tracheal branching in Drosophila. 2014, University of Zurich, Faculty of Science.

Schilling, Sabine; Steiner, Sarah; Zimmerli, Dario; Basler, Konrad (2014). A regulatory receptor network directs the range and output of the Wingless signal. Development, 141(12):2483-2493.

Haag, Andrea; Gutierrez, Peter; Bühler, Alessandra; Walser, Michael; Yang, Qiutan; Langouët, Maeva; Kradolfer, David; Fröhli, Erika; Herrmann, Christina J; Hajnal, Alex; Escobar-Restrepo, Juan M (2014). An in vivo EGF receptor localization screen in C. elegans Identifies the Ezrin homolog ERM-1 as a temporal regulator of signaling. PLoS Genetics, 10(5):e1004341.

Sendoel, Ataman; Hengartner, Michael O (2014). Apoptotic cell death under hypoxia. Physiology, 29(3):168-176.

Wang, I-Hsuan. Quantitative analyses of virus trafficking and viral genome. 2014, University of Zurich, Faculty of Science.

Zhou, Xiaobei; Lindsay, Helen; Robinson, Mark D (2014). Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Research, 42(11):e91.

Radermacher, Pablo T; Myachina, Faina; Bosshardt, Fritz; Pandey, Rahul; Mariappa, Daniel; Müller, H-Arno J; Lehner, Christian F (2014). O-GlcNAc reports ambient temperature and confers heat resistance on ectotherm development. Proceedings of the National Academy of Sciences of the United States of America, 111(15):5592-5597.

Handke, Björn. Organogenesis in Culture: Conditions for Growth and Development of Isolated Drosophila melanogaster Wing Imaginal Discs. 2014, University of Zurich, Faculty of Science.

Restrepo, Simon; Zartman, Jeremiah J; Basler, Konrad (2014). Coordination of patterning and growth by the Morphogen DPP. Current Biology, 24(6):R245-R255.

Frei, Jeannine A; Stoeckli, Esther T (2014). SynCAMs extend their functions beyond the synapse. European Journal of Neuroscience, 39(11):1752-1760.

Batz, T; Forster, D; Luschnig, S (2014). The transmembrane protein Macroglobulin complement-related is essential for septate junction formation and epithelial barrier function in Drosophila. Development, 141(4):899-908.

Hendrickx, Rodinde; Stichling, Nicole; Koelen, Jorien; Kuryk, Lukasz; Lipiec, Agnieszka; Greber, Urs F (2014). Innate Immunity to Adenovirus. Human Gene Therapy, 25(4):265-284.

Tuz, Karina; Bachmann-Gagescu, Ruxandra; O'Day, Diana R; Hua, Kiet; Isabella, Christine R; Phelps, Ian G; Stolarski, Allan E; O'Roak, Brian J; Dempsey, Jennifer C; Lourenco, Charles; Alswaid, Abdulrahman; Bönnemann, Carsten G; Medne, Livija; Nampoothiri, Sheela; Stark, Zornitza; Leventer, Richard J; Topçu, Meral; Cansu, Ali; Jagadeesh, Sujatha; Done, Stephen; Ishak, Gisele E; Glass, Ian A; Shendure, Jay; Neuhauss, Stephan C F; Haldeman-Englert, Chad R; Doherty, Dan; Ferland, Russell J (2014). Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without Jeune asphyxiating thoracic dystrophy. American Journal of Human Genetics, 94(1):62-72.

Cai, Haoyang; Kumar, Nitin; Ai, Ni; Gupta, Saumya; Rath, Prisni; Baudis, Michael (2014). Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Research, 42(D1):D1055-D1062.

Trachana, Kalliopi; Forslund, Kristoffer; Larsson, Tomas; Powell, Sean; Doerks, Tobias; von Mering, Christian; Bork, Peer (2014). A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS ONE, 9(11):e111122.

Riebler, Andrea; Menigatti, Mirco; Song, Jenny Z; Statham, Aaron L; Stirzaker, Clare; Mahmud, Nadiya; Mein, Charles A; Clark, Susan J; Robinson, Mark D (2014). BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach. Genome Biology, 15(2):R35.

Baderca, Flavia; Chiticariu, Elena; Baudis, Michael; Solovan, Caius (2014). Biopsying parapsoriasis: quo vadis? Are morphological stains enough or are ancillary tests needed? Romanian Journal of Morphology and Embryology = Revue Roumaine de Morphologie et Embryologie, 55(3 Suppl):1085-92.

Cai, Haoyang; Kumar, Nitin; Bagheri, Homayoun C; von Mering, Christian; Robinson, Mark D; Baudis, Michael (2014). Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics, 15:82.

Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2014). Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Computational Biology, 10(4):e1003594.

Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D (2014). Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Research, 42(Web Server):W436-W441.

Scott, Jeffrey G; Warren, Wesley C; Beukeboom, Leo W; Bopp, Daniel; Clark, Andrew G; Giers, Sarah D; Hediger, Monika; Jones, Andrew K; Kasai, Shinji; Leichter, Cheryl A; Li, Ming; Meisel, Richard P; Minx, Patrick; Murphy, Terence D; Nelson, David R; Reid, William R; Rinkevich, Frank D; Robertson, Hugh M; Sackton, Timothy B; Sattelle, David B; Thibaud-Nissen, Francoise; Tomlinson, Chad; van de Zande, Louis; Walden, Kimberly KO; Wilson, Richard K; Liu, Nannan (2014). Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment. Genome Biology, 15(10):466.

Meier, Roger; Franceschini, Andrea; Horvath, Peter; Tetard, Marilou; Mancini, Roberta; von Mering, Christian; Helenius, Ari; Lozach, Pierre-Yves (2014). Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration. Journal of Virology, 88(15):8565-8578.

Hickey, Peter F; Robinson, Mark D (2014). Genomics by the beach. Genome Biology, 15:304.

Matias Rodrigues, João F; von Mering, Christian (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30(2):287-288.

Greber, Urs F (2014). How cells tune viral mechanics-insights from biophysical measurements of influenza virus. Biophysical Journal, 106(11):2317-2321.

Rac, Jürgen. Impact of telomerase activity and toll-like receptor 9 activation on Epstein-Barr virus infection in epithelial cells. 2014, University of Zurich, Faculty of Science.

Andermatt, Irwin; Wilson, Nicole; Stoeckli, Esther T (2014). In ovo electroporation of miRNA-based-plasmids to investigate gene function in the developing neural tube. Methods in Molecular Biology, 1101:353-368.

Huber-Reggi, Sabina P; Mueller, Kaspar P; Straumann, Dominik; Huang, Melody Ying-Yu; Neuhauss, Stephan C F (2014). Individual larvae of the zebrafish mutant belladonna display multiple infantile nystagmus-like waveforms that are influenced by viewing conditions. Investigative Ophthalmology & Visual Science [IOVS], 55(6):3971-3978.

Marty, Florian; Rockel-Bauer, Claudia; Simigdala, Nikiana; Brunner, Erich; Basler, Konrad (2014). Large-scale imaginal disc sorting: A protocol for "omics"-approaches. Methods, 68(1):260-264.

van der Bent, M Leontien; Sterken, Mark G; Volkers, Rita J M; Riksen, Joost A G; Schmid, Tobias; Hajnal, Alex; Kammenga, Jan E; Snoek, L Basten (2014). Loss-of-function of β-catenin bar-1 slows development and activates the Wnt pathway in Caenorhabditis elegans. Scientific Reports, 4(4926):online.

Luschnig, Stefan; Uv, Anne (2014). Luminal matrices: An inside view on organ morphogenesis. Experimental Cell Research, 321(1):64-70.

Hodel, Corinne; Niklaus, Stephanie; Heidemann, Martina; Klooster, Jan; Kamermans, Maarten; Biehlmaier, Oliver; Gesemann, Matthias; Neuhauss, Stephan C F (2014). Myosin VIIA is a marker for the cone accessory outer segment in zebrafish. Anatomical Record, 297(9):1777-1784.

Stoeckli, Esther T (2014). Protocadherins: not just neuron glue, more too! Developmental Cell, 30(6):643-644.

Andermatt, Irwin; Stoeckli, Esther T (2014). RNAi-based gene silencing in chicken brain development. Methods in Molecular Biology, 1082:253-266.

Baillon, Ludovic; Basler, Konrad (2014). Reflections on cell competition: Growth, proliferation, morphogens and apoptosis. Seminars in Cell & Developmental Biology, 32:137-144.

Almouzni, G; et al; Widschwendter, Martin (2014). Relationship between genome and epigenome - challenges and requirements for future research. BMC Genomics, 15:487.

Andermatt, Irwin; Wilson, Nicole H; Bergmann, Timothy; Mauti, Olivier; Gesemann, Matthias; Sockanathan, Shanthini; Stoeckli, Esther T (2014). Semaphorin 6B acts as a receptor in post-crossing commissural axon guidance. Development, 141(19):3709-3720.

Bopp, D; Saccone, G; Beye, M (2014). Sex determination in insects: variations on a common theme. Sexual Development, 8(1-3):20-28.

Neukomm, Lukas J; Zeng, Sheng; Frei, Andreas P; Huegli, Philip A; Hengartner, Michael O (2014). Small GTPase CDC-42 promotes apoptotic cell corpse clearance in response to PAT-2 and CED-1 in C. elegans. Cell Death and Differentiation, 21(6):845-853.

Franceschini, Andrea; Meier, Roger; Casanova, Alain; Kreibich, Saskia; Daga, Neha; Andritschke, Daniel; Dilling, Sabrina; Rämö, Pauli; Emmenlauer, Mario; Kaufmann, Andreas; Conde-Álvarez, Raquel; Low, Shyan Huey; Pelkmans, Lucas; Helenius, Ari; Hardt, Wolf-Dietrich; Dehio, Christoph; von Mering, Christian (2014). Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proceedings of the National Academy of Sciences of the United States of America, 111(12):4548-4553.

Robinson, Mark D; Kahraman, Abdullah; Law, Charity W; Lindsay, Helen; Nowicka, Malgorzata; Weber, Lukas M; Zhou, Xiaobei (2014). Statistical methods for detecting differentially methylated loci and regions. Frontiers in Genetics:5:324.

Mueller, Kaspar P; Neuhauss, Stephan C F (2014). Sunscreen for fish: co-option of UV light protection for camouflage. PLoS ONE, 9(1):e87372.

Bartnicka, Kamila Joanna. The Interplay Between Hypoxia (HIF) and Inflammation (NF-B) in Colon Cancer. 2014, University of Zurich, Faculty of Science.

Urban, Evelin; Nagarkar-Jaiswal, Sonal; Lehner, Christian F; Heidmann, Stefan K (2014). The cohesin subunit Rad21 is required for synaptonemal complex maintenance, but not sister chromatid cohesion, during Drosophila female meiosis. PLoS Genetics, 10(8):e1004540.

Handke, Björn; Szabad, János; Lidsky, Peter V; Hafen, Ernst; Lehner, Christian F (2014). Towards long term cultivation of Drosophila wing imaginal discs in vitro. PLoS ONE, 9(9):e107333.

Caviglia, Sara; Luschnig, Stefan (2014). Tube fusion: Making connections in branched tubular networks. Seminars in Cell & Developmental Biology, 31:82-90.

Chen, C C; Bockisch, C J; Bertolini, G; Olasagasti, I; Neuhauss, S C F; Weber, K P; Straumann, D; Huang, M Y (2014). Velocity storage mechanism in zebrafish larvae. Journal of Physiology, 592(1):203-214.

Nikolayeva, Olga; Robinson, Mark D (2014). edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods in Molecular Biology, 1150:45-79.

Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J; von Mering, Christian; Bork, Peer (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(1):D231-D239.

Stoeckli, Esther T; Kilinc, Devrim; Kunz, Beat; Kunz, Stefan; Lee, Gil U; Martines, Elena; Rader, Christoph; Suter, Daniel (2013). Analysis of cell-cell contact mediated by Ig superfamily cell adhesion molecules. Current Protocols in Cell Biology, 61:9.5.1-9.5.85.

Krieger, Michael; Roos, Andreas; Stendel, Claudia; Claeys, Kristl G; Sonmez, Fatma Mujgan; Baudis, Michael; Bauer, Peter; Bornemann, Antje; de Goede, Christian; Dufke, Andreas; Finkel, Richard S; Goebel, Hans H; Häussler, Martin; Kingston, Helen; Kirschner, Janbernd; Medne, Livija; Muschke, Petra; Rivier, François; Rudnik-Schöneborn, Sabine; Spengler, Sabrina; Inzana, Francesca; Stanzial, Franco; Benedicenti, Francesco; Synofzik, Matthis; Lia Taratuto, Ana; Pirra, Laura; Tay, Stacey Kiat-Hong; Topaloglu, Haluk; Uyanik, Gökhan; Wand, Dorothea; Williams, Denise; Zerres, Klaus; Weis, Joachim; Senderek, Jan (2013). SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome. Brain, 136(12):3634-3644.

Yakimovich, A. Measuring and predicting transmission of viruses between cells. 2013, University of Zurich, Faculty of Science.

Eberhard, Ralf; Stergiou, Lilli; Hofmann, E Randal; Hofmann, Jen; Haenni, Simon; Teo, Youjin; Furger, André; Hengartner, Michael O (2013). Ribosome synthesis and MAPK activity modulate ionizing radiation-induced germ cell apoptosis in Caenorhabditis elegans. PLoS Genetics, 9(11):e1003943.

Wang, I-Hsuan; Suomalainen, Maarit; Andriasyan, Vardan; Kilcher, Samuel; Mercer, Jason; Neef, Anne; Luedtke, Nathan W; Greber, Urs F (2013). Tracking viral genomes in host cells at single-molecule resolution. Cell Host & Microbe, 14(4):468-480.

Lidsky, Peter V; Sprenger, Frank; Lehner, Christian F (2013). Distinct modes of centromere protein dynamics during cell cycle progression in Drosophila S2R+ cells. Journal of Cell Science, 126(Pt 20):4782-4793.

Gerber, Florian; Marty, Florian; Eijkel, Gert B; Basler, Konrad; Brunner, Erich; Furrer, Reinhard; Heeren, Ron M A (2013). Multi order correction algorithms to remove image distortions from mass spectrometry imaging datasets. Analytical Chemistry, 85(21):10249-10254.

Suomalainen, Maarit; Luisoni, Stefania; Boucke, Karin; Bianchi, Sarah; Engel, Daniel A; Greber, Urs F (2013). A direct and versatile assay measuring membrane penetration of adenovirus in single cells. Journal of Virology, (01833):13.

Tholey, Andreas; Treitz, Christian; Kussmann, Martin; Bendixen, Emöke; Schrimpf, Sabine P; Hengartner, Michael O (2013). Model organisms proteomics--from holobionts to human nutrition. Proteomics, 13(17):2537-2541.

Wilson, Nicole H; Stoeckli, Esther T (2013). Sonic hedgehog regulates its own receptor on postcrossing commissural axons in a glypican1-dependent manner. Neuron, 79(3):478-491.

Meyer, Joel N; Leung, Maxwell C K; Rooney, John P; Sendoel, Ataman; Hengartner, Michael O; Kisby, Glen E; Bess, Amanda S (2013). Mitochondria as a target of environmental toxicants. Toxicological Sciences, 134(1):1-17.

Avilés, Evelyn C; Wilson, Nicole H; Stoeckli, Esther T (2013). Sonic hedgehog and Wnt: antagonists in morphogenesis but collaborators in axon guidance. Frontiers in Cellular Neuroscience:7:86.

Verhulst, Eveline C; Lynch, Jeremy A; Bopp, Daniel; Beukeboom, Leo W; van de Zande, Louis (2013). A new component of the nasonia sex determining cascade is maternally silenced and regulates transformer expression. PLoS ONE, 8(5):e63618.

Pepperl, Julia; Reim, Gerlinde; Lüthi, Ursula; Kaech, Andres; Hausmann, George; Basler, Konrad (2013). Sphingolipid depletion impairs endocytic traffic and inhibits Wingless signaling. Mechanisms of development, 130(9-10):493-505.

Bischof, Johannes; Björklund, Mikael; Furger, Edy; Schertel, Claus; Taipale, Jussi; Basler, Konrad (2013). A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila. Development, 140(11):2434-2442.

Cantù, Claudio; Valenta, Tomas; Hausmann, George; Vilain, Nathalie; Aguet, Michel; Basler, Konrad (2013). The Pygo2-H3K4me2/3 interaction is dispensable for mouse development and Wnt signaling-dependent transcription. Development, 140(11):2377-2386.

Anders, Simon; McCarthy, Davis J; Chen, Yunshun; Okoniewski, Michal; Smyth, Gordon K; Huber, Wolfgang; Robinson, Mark D (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols, 8(9):1765-1786.

Schertel, Claus; Huang, Dashun; Björklund, Mikael; Bischof, Johannes; Yin, Dingzi; Li, Rongxia; Wu, Yi; Zeng, Rong; Wu, Jiarui; Taipale, Jussi; Song, Haiyun; Basler, Konrad (2013). Systematic screening of a Drosophila ORF library in vivo uncovers Wnt/Wg pathway components. Developmental Cell, 25(2):207-219.

Cantù, Claudio; Valenta, Tomas; Basler, Konrad (2013). A RING finger to wed TCF and β-catenin. EMBO Reports, 14(4):295-296.

Caviglia, S; Luschnig, S (2013). The ETS domain transcriptional repressor Anterior open inhibits MAP kinase and Wingless signaling to couple tracheal cell fate with branch identity. Development, 140(6):1240-1249.

Trinh, Hung V; Grossmann, Jonas; Gehrig, Peter; Roschitzki, Bernd; Schlapbach, Ralph; Greber, Urs F; Hemmi, Silvio (2013). iTRAQ-based and label-free proteomics approaches for studies of human adenovirus infections. International Journal of Proteomics, 2013:581862.

Kalueff, Allan V; Gebhardt, Michael; Stewart, Adam Michael (2013). Towards a comprehensive catalog of Zebrafish behavior 1.0 and beyond. Zebrafish, 10(1):70-86.

Sugano, Yuya; Neuhauss, Stephan C F (2013). Reverse genetics tools in zebrafish: a forward dive into endocrinology. General and Comparative Endocrinology, 188:303-308.

Wippich, Frank; Bodenmiller, Bernd; Trajkovska, Maria Gustafsson; Wanka, Stefanie; Aebersold, Ruedi; Pelkmans, Lucas (2013). Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell, 152(4):791-805.

Zartman, Jeremiah; Restrepo, Simon; Basler, Konrad (2013). A high-throughput template for optimizing Drosophila organ culture with response-surface methods. Development, 140(3):667-674.

Morf, Matthias K; Rimann, Ivo; Alexander, Mariam; Roy, Peter; Hajnal, Alex (2013). The Caenorhabditis elegans homolog of the Opitz syndrome gene, madd-2/Mid1, regulates anchor cell invasion during vulval development. Developmental Biology, 374(1):108-114.

Bontron, Séverine; Jaquenoud, Malika; Vaga, Stefania; Talarek, Nicolas; Bodenmiller, Bernd; Aebersold, Ruedi; De Virgilio, Claudio (2013). Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. Cell Reports, 3(1):16-22.

Suomalainen, Maarit; Greber, Urs F (2013). Uncoating of non-enveloped viruses. Current Opinion in Virology, (12):192-197.

Picotti, Paola; Bodenmiller, Bernd; Aebersold, Ruedi (2013). Proteomics meets the scientific method. Nature Methods, 10(1):24-27.

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A (2013). WormQTL-public archive and analysis web portal for natural variation data in Caenorhabditis spp. Nucleic Acids Research, 41(D1):D738-D743.

Simigdala, Nikiana. A high-throughput strategy for the discovery of novel compartment-specific genes in the drosophila wing imaginal disc. 2013, University of Zurich, Faculty of Science.

Gysi, Stephan; Rhiner, Christa; Flibotte, Stephane; Moerman, Donald G; Hengartner, Michael O (2013). A network of HSPG core proteins and HS modifying enzymes regulates netrin-dependent guidance of D-type motor neurons in Caenorhabditis elegans. PLoS ONE, 8(9):e74908.

Wolfrum, Nina; Greber, Urs F (2013). Adenovirus Signalling in Entry. Cellular Microbiology, 15(1):53-62.

Huber-Reggi, Sabina P; Mueller, Kaspar P; Neuhauss, Stephan C F (2013). Analysis of optokinetic response in zebrafish by computer-based eye tracking. In: Weber, Bernhard H F; Langmann, Thomas. Retinal Degeneration. Methods and Protocols. Totowa: Humana Press, 139-160.

Radermacher, Pablo Till. Coping with temperature change during drosophila melanogaster development: The role of O-GlcNAc modification. 2013, University of Zurich, Faculty of Science.

Omasits, Ulrich; Quebatte, Maxime; Stekhoven, Daniel J; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D; Dehio, Christoph; Ahrens, Christian H (2013). Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Research, 23(11):1916-1927.

Menigatti, M; Staiano, T; Manser, C N; Bauerfeind, P; Komljenovic, A; Robinson, M; Jiricny, J; Buffoli, F; Marra, G (2013). Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis, 2:e56.

Meier, Nicole; Käppeli, Simone Catherine; Hediger Niessen, Monika; Billeter, Jean-Christophe; Goodwin, Stephen F; Bopp, Daniel (2013). Genetic control of courtship behavior in the housefly: evidence for a conserved bifurcation of the sex-determining pathway. PLoS ONE, 8(4):e62476.

Salaverria, Itziar; Martin-Guerrero, Idoia; Burkhardt, Birgit; Kreuz, Markus; Zenz, Thorsten; Oschlies, Ilske; Arnold, Norbert; Baudis, Michael; Bens, Susanne; García-Orad, Africa; Lisfeld, Jasmin; Schwaenen, Carsten; Szczepanowski, Monika; Wessendorf, Swen; Pfreundschuh, Michael; Trümper, Lorenz; Klapper, Wolfram; Siebert, Reiner (2013). High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas. Genes, Chromosomes and Cancer, 52(2):150-155.

Geiger, Roger; Luisoni, Stefania; Johnsson, Kai; Greber, Urs F; Helenius, Ari (2013). Investigating endocytic pathways to the endoplasmic reticulum and to the cytosol using SNAP-trap. Traffic, 14(1):36-46.

Gafner, Lucia; Dalessi, Sascha; Escher, Eliane; Pyrowolakis, George; Bergmann, Sven; Basler, Konrad (2013). Manipulating the sensitivity of signal-induced repression: quantification and consequences of altered brinker gradients. PLoS ONE, 8(8):e71224.

Greber, Urs F; Arnberg, Niklas; Wadell, Göran; Benkő, Mária; Kremer, Eric J (2013). Meeting Report: Adenoviruses - from pathogens to therapeutics. Cellular Microbiology, 15(1):16-23.

Maier, Lisa; Vyas, Rounak; Cordova, Carmen Dolores; Lindsay, Helen; Schmidt, Thomas Sebastian Benedikt; Brugiroux, Sandrine; Periaswamy, Balamurugan; Bauer, Rebekka; Sturm, Alexander; Schreiber, Frank; von Mering, Christian; Robinson, Mark D; Stecher, Bärbel; Hardt, Wolf-Dietrich (2013). Microbiota-derived hydrogen fuels salmonella typhimurium invasion of the gut ecosystem. Cell Host & Microbe, 14(6):641-651.

Bluwstein, A; Kumar, N; Léger, K; Traenkle, J; van Oostrum, J; Rehrauer, H; Baudis, M; Hottiger, M O (2013). PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts. Cell Death and Disease, 4:e498.

Kastenhuber, Edda; Gesemann, Matthias; Mickoleit, Michaela; Neuhauss, Stephan C F (2013). Phylogenetic analysis and expression of zebrafish transient receptor potential melastatin family genes. Developmental Dynamics, 242(11):1236-1249.

Haug, Marion F; Gesemann, Matthias; Mueller, Thomas; Neuhauss, Stephan C F (2013). Phylogeny and expression divergence of metabotropic glutamate receptor genes in the brain of zebrafish (Danio rerio). Journal of Comparative Neurology, 521(7):1533-1560.

Von Niederhäusern, Valentin; Kastenhuber, Edda; Stäuble, Andreas; Gesemann, Matthias; Neuhauss, Stephan C F (2013). Phylogeny and expression of canonical transient receptor potential (TRPC) genes in developing zebrafish. Developmental Dynamics, 242(12):1427-1441.

Martin-Guerrero, Idoia; Salaverria, Itziar; Burkhardt, Birgit; Szczepanowski, Monika; Baudis, Michael; Bens, Susanne; de Leval, Laurence; Garcia-Orad, Africa; Horn, Heike; Lisfeld, Jasmin; Pellissery, Shoji; Klapper, Wolfram; Oschlies, Ilske; Siebert, Reiner (2013). Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas. Haematologica, 98(8):1237-1241.

Bert, Saul A; Robinson, Mark D; Strbenac, Dario; Statham, Aaron L; Song, Jenny Z; Hulf, Toby; Sutherland, Robert L; Coolen, Marcel W; Stirzaker, Clare; Clark, Susan J (2013). Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell, 23(1):9-22.

Graziano, Vito; McGrath, William J; Suomalainen, Maarit; Greber, Urs F; Freimuth, Paul; Blainey, Paul C; Luo, Guobin; Xie, X Sunney; Mangel, Walter F (2013). Regulation of a viral proteinase by a peptide and DNA in one-dimensional space. I. binding to DNA and to hexon of the precursor to protein VI, pVI, of human adenovirus. Journal of Biological Chemistry, 288(3):2059-2067.

Franceschini, Andrea; Szklarczyk, Damian; Frankild, Sune; Kuhn, Michael; Simonovic, Milan; Roth, Alexander; Lin, Jianyi; Minguez, Pablo; Bork, Peer; von Mering, Christian; Jensen, Lars J (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research, 41(D 1):D808-D815.

Dooley, Christopher M; Schwarz, Heinz; Mueller, Kaspar P; Mongera, Alessandro; Konantz, Martina; Neuhauss, Stephan C F; Nüsslein-Volhard, Christiane; Geisler, Robert (2013). Slc45a2 and V-ATPase are regulators of melanosomal pH homeostasis in zebrafish, providing a mechanism for human pigment evolution and disease. Pigment Cell & Melanoma Research, 26(2):205-217.

Handke, Björn; Poernbacher, Ingrid; Goetze, Sandra; Ahrens, Christian H; Omasits, Ulrich; Marty, Florian; Simigdala, Nikiana; Meyer, Imke; Wollscheid, Bernd; Brunner, Erich; Hafen, Ernst; Lehner, Christian F (2013). The hemolymph proteome of fed and starved Drosophila larvae. PLoS ONE, 8(6):e67208.

Mercer, Jason; Greber, Urs F (2013). Virus interactions with endocytic pathways in macrophages and dendritic cells. Trends in Microbiology, 21(8):380-388.

Zhou, Xiaobei; Oshlack, Alicia; Robinson, Mark D (2013). miRNA-Seq normalization comparisons need improvement. RNA, 19(6):733-734.

Raychaudhuri, Nitika; Dubruille, Raphaelle; Orsi, Guillermo A; Bagheri, Homayoun C; Loppin, Benjamin; Lehner, Christian F (2012). Transgenerational propagation and quantitative maintenance of paternal centromeres depends on Cid/Cenp-A presence in Drosophila sperm. PLoS Biology, 10(12):e1001434.

Hödl, Martina; Basler, Konrad (2012). Transcription in the absence of Histone H3.2 and H3K4 Methylation. Current Biology, 22(23):2253-2257.

Pinto, Sérgio Morgado; Hengartner, Michael Otmar (2012). Cleaning up the mess: cell corpse clearance in Caenorhabditis elegans. Current Opinion in Cell Biology, 24(6):881-888.

Schertel, Claus; Rutishauser, Tobias; Förstemann, Klaus; Basler, Konrad (2012). Functional characterization of Drosophila microRNAs by a novel in vivo library. Genetics, 192(4):1543-52.

Philipp, Melanie; Niederkofler, Vera; Debrunner, Marc; Alther, Tobias; Kunz, Beat; Stoeckli, Esther T (2012). RabGDI controls axonal midline crossing by regulating Robo1 surface expression. Neural Development, 7:36.

Mueller, Kaspar P; Neuhauss, Stephan C F (2012). Light perception: more than meets the eyes. Current Biology, 22(21):R912-R914.

Jurgeit, Andreas; McDowell, Robert; Moese, Stefan; Meldrum, Eric; Schwendener, Reto; Greber, Urs F (2012). Niclosamide is a proton carrier and targets acidic endosomes with broad antiviral effects. PLoS Pathogens, 8(10):e1002976.

Wilson, Nicole H; Stoeckli, Esther T (2012). In ovo electroporation of miRNA-based plasmids in the developing neural tube and assessment of phenotypes by DiI injection in open-book preparations. Journal of Visualized Experiments, (68):e4384.

Nusser-Stein, Stefanie; Beyer, Antje; Rimann, Ivo; Adamczyk, Magdalene; Piterman, Nir; Hajnal, Alex; Fisher, Jasmin (2012). Cell-cycle regulation of NOTCH signaling during C. elegans vulval development. Molecular Systems Biology, 8:618.

Engelke, Martin Felix Bernhard. Quantitative analysis of the role of motor proteins in adenovirus infection. 2012, University of Zurich, Faculty of Science.

Farooqui, Sarfarazhussain; Pellegrino, Mark W; Rimann, Ivo; Morf, Matthias K; Müller, Louisa; Fröhli, Erika; Hajnal, Alex (2012). Coordinated Lumen Contraction and Expansion during Vulval Tube Morphogenesis in Caenorhabditis elegans. Developmental Cell, 23(3):494-506.

Glover, Greta; Mueller, Kaspar P; Söllner, Christian; Neuhauss, Stephan C F; Nicolson, Teresa (2012). The Usher gene cadherin 23 is expressed in the zebrafish brain and a subset of retinal amacrine cells. Molecular Vision, 18:2309-2322.

Neuromedia. Art and Neuroscience Research. Edited by: Scott, Jill; Stoeckli, Esther (2012). Heidelberg [etc.]: Springer.

Kumar, Nitin; Cai, Haoyang; von Mering, Christian; Baudis, Michael (2012). Specific Genomic Regions Are Differentially Affected by Copy Number Alterations across Distinct Cancer Types, in Aggregated Cytogenetic Data. PLoS ONE, 7(8):e43689.

Valdés-Mora, Fátima; Song, Jenny Z; Statham, Aaron L; Strbenac, Dario; Robinson, Mark D; Nair, Shalima S; Patterson, Kate I; Tremethick, David J; Stirzaker, Clare; Clark, Susan J (2012). Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Research, 22(2):307-321.

Bodenmiller, Bernd; Zunder, Eli R; Finck, Rachel; Chen, Tiffany J; Savig, Erica S; Bruggner, Robert V; Simonds, Erin F; Bendall, Sean C; Sachs, Karen; Krutzik, Peter O; Nolan, Garry P (2012). Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators. Nature Biotechnology, 30(9):858-867.

Robinson, Mark D; Strbenac, Dario; Stirzaker, Clare; Statham, Aaron L; Song, Jenny Z; Speed, Terence P; Clark, Susan J (2012). Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Research, 22(12):2489-2496.

Eggermann, Thomas; Spengler, Sabrina; Venghaus, Andreas; Denecke, Bernd; Zerres, Klaus; Baudis, Michael; Ensenauer, Regina (2012). 2p21 Deletions in hypotonia-cystinuria syndrome. European Journal of Medical Genetics, 55(10):561-563.

Herr, Patrick; Hausmann, George; Basler, Konrad (2012). WNT secretion and signalling in human disease. Trends in Molecular Medicine, 18(8):483-493.

Yakimovich, A; Gumpert, H; Burckhardt, C J; Lutschg, V A; Jurgeit, A; Sbalzarini, I F; Greber, U F (2012). Cell-free transmission of human adenovirus by passive mass transfer in cell culture simulated in a computer model. Journal of Virology, 86(18):10123-10137.

Kumar, Nitin. Oncogenomic pattern detection in cancer copy number alteration data for pathway description and dieases classification. 2012, University of Zurich, Faculty of Science.

von Bueren, André O; Gerss, Joachim; Hagel, Christian; Cai, Haoyang; Remke, Marc; Hasselblatt, Martin; Feuerstein, Burt G; Pernet, Sarah; Delattre, Olivier; Korshunov, Andrey; Rutkowski, Stefan; Pfister, Stefan M; Baudis, Michael (2012). DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis. Journal of Neuro-Oncology, 109(2):415-423.

Althoff, F; Karess, R E; Lehner, C F (2012). Spindle checkpoint-independent inhibition of mitotic chromosome segregation by Drosophila Mps1. Molecular Biology of the Cell, 23(12):2275-2291.

Statham, Aaron L; Robinson, Mark D; Song, Jenny Z; Coolen, Marcel W; Stirzaker, Clare; Clark, Susan J (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Research, 22(6):1120-1127.

Vermezovic, J; Stergiou, L; Hengartner, M O; d'Adda di Fagagna, F (2012). Differential regulation of DNA damage response activation between somatic and germline cells in Caenorhabditis elegans. Cell Death and Differentiation, 19(11):1847-1855.

Fienberg, Harris G; Simonds, Erin F; Fantl, Wendy J; Nolan, Garry P; Bodenmiller, Bernd (2012). A platinum-based covalent viability reagent for single-cell mass cytometry. Cytometry. Part A, 81A(6):467-475.

Baudis, M; Giefing, M; Cai, Haoyang; Kumar, Nitin; Vater, I; Ricter, J; Siebert, R (2012). Array-basierter Nachweis chromosomaler Aberrationen bei malignen Neoplasien. Medizinische Genetik, 24(2):114-122.

Valenta, Tomas; Hausmann, George; Basler, Konrad (2012). The many faces and functions of β-catenin. EMBO Journal, 31(12):2714-2736.

Cai, Haoyang; Kumar, Nitin; Baudis, Michael (2012). arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies. PLoS ONE, 7(5):e36944.

Schubert, Mario; Bleuler-Martinez, Silvia; Butschi, Alex; Wälti, Martin A; Egloff, Pascal; Stutz, Katrin; Yan, Shi; Wilson, Iain B H; Hengartner, Michael O; Aebi, Markus; Allain, Frédéric H-T; Künzler, Markus (2012). Plasticity of the β-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System. PLoS Pathogens, 8(5):e1002706.

Wernstedt, Annekatrin; Valtorta, Emanuele; Armelao, Franco; Togni, Roberto; Girlando, Salvatore; Baudis, Michael; Heinimann, Karl; Messiaen, Ludwine; Staehli, Noemie; Zschocke, Johannes; Marra, Giancarlo; Wimmer, Katharina (2012). Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL. Genes, Chromosomes & Cancer, 51(9):819-831.

Pelkmans, Lucas (2012). Cell Biology. Using cell-to-cell variability--a new era in molecular biology. Science, 336(6080):425-426.

Wang, Mingcong; Weiss, Manuel; Simonovic, Milan; Haertinger, Gabriele; Schrimpf, Sabine P; Hengartner, Michael O; von Mering, Christian (2012). PaxDb, a database of protein abundance averages across all three domains of life. Molecular & Cellular Proteomics, 11(8):492-500.

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. Molecular Systems Biology, 8(579):1-18.

Haenni, Simon; Ji, Zhe; Hoque, Mainul; Rust, Nigel; Sharpe, Helen; Eberhard, Ralf; Browne, Cathy; Hengartner, Michael O; Mellor, Jane; Tian, Bin; Furger, André (2012). Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. Nucleic Acids Research, 40(13):6304-6318.

Förster, Dominique; Luschnig, Stefan (2012). Src42A-dependent polarized cell shape changes mediate epithelial tube elongation in Drosophila. Nature Cell Biology, 14(5):526-534.

Mueller, Kaspar P; Neuhauss, Stephan C F (2012). Automated visual choice discrimination learning in zebrafish (Danio rerio). Journal of Integrative Neuroscience, 11(1):73-85.

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael (2012). Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Research, 40(W1):W615-W621.

Dittrich, Christina M; Kratz, Katja; Sendoel, Ataman; Gruenbaum, Yosef; Jiricny, Josef; Hengartner, Michael O (2012). LEM-3 - A LEM domain containing nuclease involved in the DNA damage response in C. elegans. PLoS ONE, 7(2):e24555.

Armbruster, Kristina; Luschnig, Stefan (2012). The Drosophila Sec7 domain guanine nucleotide exchange factor protein Gartenzwerg localizes at the cis-Golgi and is essential for epithelial tube expansion. Journal of Cell Science, 125(5):1318-1328.

Schwank, G; Yang, S F; Restrepo, S; Basler, K (2012). Comment on "Dynamics of dpp signaling and proliferation control". Science, 335(6067):401.

Pelkmans, Lindsey G; Aarnoudse, Albert-Jan L H; Hendriksz, Tadek R; van Bommel, Eric F H (2012). Value of acute-phase reactants in monitoring disease activity and treatment response in idiopathic retroperitoneal fibrosis. Nephrology, Dialysis, Transplantation, 27(7):2819-2825.

Luebke, A M; Baudis, M; Matthaei, H; Vashist, Y K; Verde, P E; Hosch, S B; Erbersdobler, A; Klein, C A; Izbicki, J R; Knoefel, W T; Stoecklein, N H (2012). Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma. Pancreatology, 12(1):16-22.

Günther, V; Lindert, U; Schaffner, W (2012). The taste of heavy metals: Gene regulation by MTF-1. Biochimica et Biophysica Acta, 1823(9):1416-1425.

Günther, V; Strassen, T; Lindert, U; Dagani, P; Waldvogel, D; Georgiev, O; Schaffner, W; Bethge, T (2012). Simian virus 40 (SV40) strains with novel properties generated by replacing the viral enhancer with synthetic oligonucleotides. Journal of Virology, 86(6):3135-3142.

Günther, V; Davis, A M; Georgiev, O; Schaffner, W (2012). A conserved cysteine cluster, essential for transcriptional activity, mediates homodimerization of human metal-responsive transcription factor-1 (MTF-1). Biochimica et Biophysica Acta, 1823(2):476-483.

Beyer, A; Eberhard, R; Piterman, N; Hengartner, M O; Hajnal, A; Fisher, J (2012). A dynamic physical model of cell migration, differentiation and apoptosis in Caenorhabditis elegans. In: Goryanin, I I; Goryachev, A B. Advances in systems biology. New York, NY, US: Springer New York, 211-233.

Traber, G L; Chen, C C; Huang, Y Y; Spoor, M; Roos, J; Frens, M A; Straumann, D; Grimm, C (2012). Albino mice as an animal model for infantile nystagmus syndrome. Investigative Ophthalmology and Visual Science, 53(9):5737-5747.

Pelkmans, L; de Laat, B (2012). Antibodies against domain I of β2-glycoprotein I: the one and only? Lupus, 21(7):769-772.

Prasad, V R; Isler, K (2012). Assessment of phylogenetic structure in genome size - gene content correlations. Genome (Génome), 55(5):391-395.

Trinh, H V; Lesage, G; Chennamparampil, V; Vollenweider, B; Burckhardt, C J; Schauer, S; Havenga, M; Greber, U F; Hemmi, S (2012). Avidity binding of human adenovirus serotypes 3 and 7 to the membrane cofactor CD46 triggers infection. Journal of Virology, 86(3):1623-1637.

Atamna-Ismaeel, Nof; Finkel, Omri; Glaser, Fabian; von Mering, Christian; Vorholt, Julia A; Koblížek, Michal; Belkin, Shimshon; Béjà, Oded (2012). Bacterial anoxygenic photosynthesis on plant leaf surfaces. Environmental Microbiology Reports, 4(2):209-216.

Herr, Parick. Dissecting the Mechanism of Wntless-dependent Wnt Secretion in Drosophila and the Mouse. 2012, University of Zurich, Faculty of Science.

Günther, V; Waldvogel, D; Nosswitz, M; Georgiev, O; Schaffner, W (2012). Dissection of Drosophila MTF-1 reveals a domain for differential target gene activation upon copper overload vs. copper starvation. International Journal of Biochemistry & Cell Biology, 44(2):404-411.

Gafner, Lucia. Functional analysis of brinker silencer elements in vivo. 2012, University of Zurich, Faculty of Science.

Claassen, M; Reiter, L; Hengartner, M O; Buhmann, J M; Aebersold, R (2012). Generic comparison of protein inference engines. Molecular & Cellular Proteomics, 11(4):O110.007088.

Juhas, Mario; Stark, Manuel; von Mering, Christian; Lumjiaktase, Puthapoom; Crook, Derrick W; Valvano, Miguel A; Eberl, Leo (2012). High confidence prediction of essential genes in burkholderia cenocepacia. PLoS ONE, 7(6):e40064.

Aegerter-Wilmsen, Tinri; Heimlicher, Maria B; Smith, Alister C; de Reuille, Pierre Barbier; Smith, Richard S; Aegerter, Christof M; Basler, Konrad (2012). Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc size. Development, 139(17):3221-3231.

Beleut, Manfred; Zimmermann, Philip; Baudis, Michael; Bruni, Nicole; Bühlmann, Peter; Laule, Oliver; Luu, Van-Duc; Gruissem, Wilhelm; Schraml, Peter; Moch, Holger (2012). Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome. BMC Cancer, 12:310.

Knief, C; Delmotte, N; Chaffron, S; Stark, M; Innerebner, G; Wassmann, R; von Mering, C; Vorholt, J A (2012). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME Journal, 6(7):1378-1390.

Spengler, Sabrina; Begemann, Matthias; Ortiz Brüchle, Nadina; Baudis, Michael; Denecke, Bernd; Kroisel, Peter Michael; Oehl-Jaschkowitz, Barbara; Schulze, Bernd; Raabe-Meyer, Gisela; Spaich, Christiane; Blümel, Peter; Jauch, Anna; Moog, Ute; Zerres, Klaus; Eggermann, Thomas (2012). Molecular Karyotyping as a relevant diagnostic tool in children with growth retardation with Silver-Russell features. Journal of Pediatrics, 161(5):933-942.e1.

Galluzzi, L; Vitale, I; et al (2012). Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012. Cell Death and Differentiation, 19(1):107-120.

Huang, Y Y; Haug, M F; Gesemann, M; Neuhauss, S C F (2012). Novel expression patterns of metabotropic glutamate receptor 6 in the zebrafish nervous system. PLoS ONE, 7(4):e35256.

Nakdimon, Itay; Walser, Michael; Fröhli, Erika; Hajnal, Alex (2012). PTEN negatively regulates MAPK signaling during Caenorhabditis elegans vulval development. PLoS Genetics, 8(8):e1002881.

Atanesyan, L; Güther, V; Dichtl, B; Georgiev, O; Schaffner, W (2012). Polyglutamine tracts as modulators of transcriptional activation from yeast to mammals. Biological Chemistry, 393(1-2):63-70.

Herr, P; Basler, K (2012). Porcupine-mediated lipidation is required for Wnt recognition by Wls. Developmental Biology, 361(2):392-402.

Jovanovic, Marko; Reiter, Lukas; Clark, Alejandra; Weiss, Manuel; Picotti, Paola; Rehrauer, Hubert; Frei, Andreas; Neukomm, Lukas; Kaufman, Ethan; Wollscheid, Bernd; Simard, Martin J; Miska, Eric; Aebersold, Ruedi; Gerber, Andre P; Hengartner, Michael O (2012). RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans. Genome Research, 22(7):1360-1371.

Huber-Reggi, Sabina P; Chen, Chien-Cheng; Grimm, Lea; Straumann, Dominik; Neuhauss, Stephan C F; Huang, Melody Ying-Yu (2012). Severity of infantile nystagmus syndrome-like ocular motor phenotype is linked to the extent of the underlying optic nerve projection defect in zebrafish belladonna mutant. Journal of Neuroscience, 32(50):18079-18086.

Wilson, Nicole H; Stoeckli, Esther T (2012). Sonic Hedgehog regulates Wnt activity during neural circuit formation. Vitamins and Hormones, 88:173-209.

Förster, Dominique. Systematic analysis of cell behaviour in epithelial tube expansion. 2012, University of Zurich, Faculty of Science.

Jones, A M E; Aebersold, R; Ahrens, C H; Apweiler, R; Baerenfaller, K; Baker, M; Bendixen, E; Briggs, S; Brownridge, P; Brunner, E; Daube, M; Deutsch, E W; Grossniklaus, U; Heazlewood, J L; Hengartner, M O; Hermjakob, H; Jovanovic, M; Lawless, C; Lochnit, G; Martens, L; Ravnsborg, C; Schrimpf, S P; Shim, Y H; Subasic, D; Tholey, A; van Wijk, K; von Mering, C; Weiss, M; Zheng, X (2012). The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics, 12(3):340-345.

Wippich, Frank. The dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. 2012, University of Zurich, Faculty of Science.

Schrimpf, S P; von Mering, C; Bendixen, E; Heazlewood, J L; Bumann, D; Omenn, G; Hengartner, M O (2012). The initiative on Model Organism Proteomes (iMOP) Session September 6, 2011, Geneva, Switzerland. Proteomics, 12(3):346-350.

Gestri, G; Link, B A; Neuhauss, S C F (2012). The visual system of zebrafish and its use to model human ocular diseases. Developmental Neurobiology, 72(3):302-327.

Kalueff, A V; Stewart, A M; Kyzar, E J; Cachat, J; Gebhardt, M; Landsman, S; Robinson, K; Maximino, C; Herculano, A M; Jesuthasan, S; Wisenden, B; Bally-Cuif, L; Lange, M; Vernier, P; Norton, W; Tierney, K; Tropepe, V; Neuhauss, S C F (2012). Time to recognize zebrafish ‘affective’ behavior. Behaviour, 149(10-12):1019-1036.

Steiner, Sarah. Transcriptional Outputs and Gradient Formation of Wg. 2012, University of Zurich, Faculty of Science.

Stoeckli, Esther T (2012). What does the developing brain tell us about neural diseases? European Journal of Neuroscience, 35(12):1811-1817.

Powell, S; Szklarczyk, D; Trachana, K; Roth, A; Kuhn, M; Muller, J; Arnold, R; Rattei, T; Letunic, I; Doerks, T; Jensen, L J; von Mering, C; Bork, P (2012). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Research, 40(D1):D284-D289.

Kastenhuber, E; Neuhauss, S C F (2011). Acoustic communication: sound advice from piranhas. Current Biology, 21(24):R986-R988.

Zielke, N; Kim, K J; Tran, V; Shibutani, S T; Bravo, M J; Nagarajan, S; van Straaten, M; Woods, B; von Dassow, G; Rottig, C; Lehner, C F; Grewal, S S; Duronio, R J; Edgar, B A (2011). Control of Drosophila endocycles by E2F and CRL4(CDT2). Nature, 480(7375):123-144.

Fejer, G; Freudenberg, M; Greber, U F; Gyory, I (2011). Adenovirus-triggered innate signalling pathways. European Journal of Microbiology and Immunology, 1(4):279-288.

Wilson, N H; Stoeckli, E T (2011). Cell type specific, traceable gene silencing for functional gene analysis during vertebrate neural development. Nucleic Acids Research, 39(20):e133.

Pellegrino, M W; Farooqui, S; Fröhli, E; Rehrauer, H; Kaeser-Pebernard, S; Müller, F; Gasser, R B; Hajnal, A (2011). LIN-39 and the EGFR/RAS/MAPK pathway regulate C. elegans vulval morphogenesis via the VAB-23 zinc finger protein. Development, 138(21):4649-4660.

Mueller, K P; Schnaedelbach, O D R; Russig, H D; Neuhauss, S C F (2011). VisioTracker, an innovative automated approach to oculomotor analysis. Journal of Visualized Experiments, (56):e3556.

Strunze, S; Engelke, M F; Wang, I-H; Puntener, D; Boucke, K; Schleich, S; Way, M; Schoenenberger, P; Burckhardt, C J; Greber, U F (2011). Kinesin-1-mediated capsid disassembly and disruption of the nuclear pore complex promote virus infection. Cell Host & Microbe, 10(3):210-223.

Hua, H; Münter, L; Harmeier, A; Georgiev, O; Multhaup, G; Schaffner, W (2011). Toxicity of Alzheimer's disease-associated Aβ peptide is ameliorated in a Drosophila model by tight control of zinc and copper availability. Biological Chemistry, 392(10):919-926.

Schwank, G; Dalessi, S; Yang, S-F; Yagi, R; de Lachapelle, A M; Affolter, M; Bergmann, S; Basler, K (2011). Formation of the long range dpp morphogen gradient. PLoS Biology, 9(7):e1001111.

Huisman, S M; Brunner, D (2011). Cell polarity in fission yeast: A matter of confining, positioning, and switching growth zones. Seminars in Cell and Developmental Biology, 22(8):799-805.

Wohlschlager, T; Butschi, A; Zurfluh, K; Vonesch, S C; Auf dem Keller, U; Gehrig, P; Bleuler-Martinez, S; Hengartner, M O; Aebi, M; Künzler, M (2011). Nematotoxicity of Marasmius oreades Agglutinin (MOA) Depends on Glycolipid Binding and Cysteine Protease Activity. Journal of Biological Chemistry, 286(35):30337-30343.

Imelli, Nicola. Endocytosis of Species C Adenovirus : much more complex than just clathrin mediated endocytosis. 2011, University of Zurich, Faculty of Science.

Engelke, M F; Burckhardt, C J; Morf, M K; Greber, U F (2011). The dynactin complex enhances the speed of microtubule-dependent motions of adenovirus both towards and away from the nucleus. Viruses, 3(3):233-253.

Kumar, N; Rehrauer, H; Cai, H; Baudis, M (2011). CDCOCA: A statistical method to define complexity dependence of co-occuring chromosomal aberrations. BMC Medical Genomics, 4:21.

Höög, J L; Huisman, S M; Sebö-Lemke, Z; Sandblad, L; McIntosh, J R; Antony, C; Brunner, D (2011). Electron tomography reveals a flared morphology on growing microtubule ends. Journal of Cell Science, 124(Pt 5):693-698.

Grillo, M; Furriols, M; Casanova, J; Luschnig, S (2011). Control of germline torso expression by the BTB/POZ domain protein pipsqueak is required for embryonic terminal patterning in drosophila. Genetics, 187(2):513-521.

Neukomm, L J; Frei, A P; Cabello, J; Kinchen, J M; Zaidel-Bar, R; Ma, Z; Haney, L B; Hardin, J; Ravichandran, K S; Moreno, S; Hengartner, M O (2011). Loss of the RhoGAP SRGP-1 promotes the clearance of dead and injured cells in Caenorhabditis elegans. Nature Cell Biology, 13(2):182.

Snijder, B; Pelkmans, L (2011). Origins of regulated cell-to-cell variability. Nature Reviews. Molecular Cell Biology, 12(2):119-125.

Renninger, S L; Schonthaler, H B; Neuhauss, S C F; Dahm, R (2011). Investigating the genetics of visual processing, function and behaviour in zebrafish. Neurogenetics, 12(2):97-116.

Schwank, G; Tauriello, G; Yagi, R; Kranz, E; Koumoutsakos, P; Basler, K (2011). Antagonistic growth regulation by dpp and fat drives uniform cell proliferation. Developmental Cell, 20(1):123-130.

Harterink, M; Port, F; Lorenowicz, M J; McGough, I J; Silhankova, M; Betist, M C; van Weering, J R T; van Heesbeen, R G H P; Middelkoop, T C; Basler, K; Cullen, P J; Korswagen, H C (2011). A SNX3-dependent retromer pathway mediates retrograde transport of the Wnt sorting receptor Wntless and is required for Wnt secretion. Nature Cell Biology, 13(8):914-923.

Almendinger, J; Doukoumetzidis, K; Kinchen, J M; Kaech, A; Ravichandran, K S; Hengartner, M O (2011). A conserved role for SNX9-family members in the regulation of phagosome maturation during engulfment of apoptotic cells. PLoS ONE, 6(4):e18325.

Port, F; Hausmann, G; Basler, K (2011). A genome-wide RNA interference screen uncovers two p24 proteins as regulators of Wingless secretion. EMBO Reports, 12(11):1144-1152.

Bleuler-Martinez, S; Butschi, A; Garbani, M; Wälti, M A; Wohlschlager, T; Potthoff, E; Sabotiĉ, J; Pohleven, J; Lüthy, P; Hengartner, M O; Aebi, M; Künzler, M (2011). A lectin-mediated resistance of higher fungi against predators and parasites. Molecular Ecology, 20(14):3056-3070.

Gysi, S. A screen for axon guidance genes in parallel to heparan sulfate proteoglycans in C. elegans. 2011, University of Zurich, Faculty of Science.

Cotrufo, T; Pérez-Brangulí, F; Muhaisen, A; Ros, O; Andrés, R; Baeriswyl, T; Fuschini, G; Tarrago, T; Pascual, M; Ureña, J; Blasi, J; Giralt, E; Stoeckli, E T; Soriano, E (2011). A signaling mechanism coupling netrin-1/deleted in colorectal cancer chemoattraction to SNARE-mediated exocytosis in axonal growth cones. Journal of Neuroscience, 31(41):14463-14480.

Maurer, Colette M; Huang, Ying-Yu; Neuhauss, Stephan C F (2011). Application of zebrafish oculomotor behavior to model human disorders. Reviews in the Neurosciences, 22(1):5-16.

Sironi, L; Solon, J; Conrad, C; Mayer, T U; Brunner, D; Ellenberg, J (2011). Automatic quantification of microtubule dynamics enables RNAi-screening of new mitotic spindle regulators. Cytoskeleton, 68(5):266-278.

Affolter, M; Basler, K (2011). Cell biology. Cytonemes show their colors. Science, 332(6027):312-313.

Schilling, S; Willecke, M; Aegerter-Wilmsen, T; Cirpka, O A; Basler, K; von Mering, C (2011). Cell-sorting at the a/p boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of hh signaling. PLoS Computational Biology, 7(4):e1002025.

Atanesyan, L; Günther, V; Celniker, S E; Georgiev, O; Schaffner, W (2011). Characterization of MtnE, the fifth metallothionein member in Drosophila. Journal of Biological Inorganic Chemistry, 16(7):1047-1056.

Lütschg, V; Boucke, K; Hemmi, S; Greber, U F (2011). Chemotactic antiviral cytokines promote infectious apical entry of human adenovirus into polarized epithelial cells. Nature Communications, 2:391.

Huang, M Y; Chen, C C; Huber-Reggi, S P; Neuhauss, S C F; Straumann, D (2011). Comparison of infantile nystagmus syndrome in achiasmatic zebrafish and humans. Annals of the New York Academy of Sciences, 1233:285-91.

Renninger, S L; Gesemann, M; Neuhauss, S C F (2011). Cone arrestin confers cone vision of high temporal resolution in zebrafish larvae. European Journal of Neuroscience, 33(4):658-667.

Ratna, P; Becskei, A (2011). Construction of cis-regulatory input functions of yeast promoters. In: Becskei, A. Yeast Genetic Networks : Methods and Protocols. New York [etc.]: Springer, 45-61.

Hua, H; Günther, V; Georgiev, O; Schaffner, W (2011). Distorted copper homeostasis with decreased sensitivity to cisplatin upon chaperone Atox1 deletion in Drosophila. BioMetals, 24(3):445-453.

Burckhardt, C J; Suomalainen, M; Schoenenberger, P; Boucke, K; Hemmi, S; Greber, U F (2011). Drifting Motions of the Adenovirus Receptor CAR and Immobile Integrins Initiate Virus Uncoating and Membrane Lytic Protein Exposure. Cell Host & Microbe, 10(2):105-117.

Bacon, C; Endris, V; Andermatt, I; Niederkofler, V; Waltereit, R; Bartsch, D; Stoeckli, E T; Rappold, G (2011). Evidence for a role of srGAP3 in the positioning of commissural axons within the ventrolateral funiculus of the mouse spinal cord. PLoS ONE, 6(5):e19887.

Trinh, H V. Functional genomic approaches to study human adenoviruses and frontier research on miRNAs. 2011, University of Zurich, Faculty of Science.

Fellmann, C; Zuber, J; McJunkin, K; Chang, K; Malone, C D; Dickins, R A; Xu, Q; Hengartner, M O; Elledge, S J; Hannon, G J; Lowe, S W (2011). Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Molecular Cell, 41(6):733-746.

Armbruster, K. Genetic Control of Epithelial Tube Expansion in Drosophila melanogaster. 2011, University of Zurich, Faculty of Science.

Hemmi, S; Vidovszky, M Z; Ruminska, J; Ramelli, S; Decurtins, W; Greber, U F; Harrach, B (2011). Genomic and phylogenetic analyses of murine adenovirus 2. Virus Research, 160(1-2):128-135.

Gasnereau, I; Herr, P; Chia, P Z C; Basler, K; Gleeson, P A (2011). Identification of an endocytosis motif in an intracellular loop of Wntless, essential for its recycling and the control of Wnt signalling. Journal of Biological Chemistry, 286(50):43324-43333.

Takeuchi, Yayoi; Salcher, Michaela M; Ushio, Masayuki; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K (2011). In situ enzyme activity in the dissolved and particulate fraction of the fluid from four pitcher plant species of the genus nepenthes. PLoS ONE, 6(9):e25144.

Atamna-Ismaeel, N; Finkel, O M; Glaser, F; Sharon, I; Schneider, R; Post, A F; Spudich, J L; von Mering, C; Vorholt, J A; Iluz, D; Béjà, O; Belkin, S (2011). Microbial rhodopsins on leaf surfaces of terrestrial plants. Environmental Microbiology, 14(1):140-146.

Martinez, J; Almendinger, J; Oberst, A; Ness, R; Dillon, C P; Fitzgerald, P; Hengartner, M O; Green, D R (2011). Microtubule-associated protein 1 light chain 3 alpha (LC3)-associated phagocytosis is required for the efficient clearance of dead cells. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 108(42):17396-17401.

Becskei, A; Scherrer, S; Kelemen, J Z; Murray, A E (2011). Modeling of chromosomal epigenetic silencing processes. Transcription, 2(4):173-178.

Restrepo, S; Basler, K (2011). Morphogen gradients: expand and repress. Current Biology, 21(19):R815-7.

Stergiou, L; Eberhard, R; Doukoumetzidis, K; Hengartner, M O (2011). NER and HR pathways act sequentially to promote UV-C-induced germ cell apoptosis in caenorhabditis elegans. Cell Death and Differentiation, 18(5):897-906.

Saini, N; Georgiev, O; Schaffner, W (2011). Parkin mutant in the fly is largely rescued by metal-responsive transcription factor (MTF-1). Molecular and Cellular Biology, 31(10):2151-2161.

Bodenmiller, Bernd; Aebersold, Ruedi (2011). Phosphoproteome resource for systems biology research. Methods in Molecular Biology, 694:307-322.

Laurell, Eva; Beck, Katja; Krupina, Ksenia; Theerthagiri, Gandhi; Bodenmiller, Bernd; Horvath, Peter; Aebersold, Ruedi; Antonin, Wolfram; Kutay, Ulrike (2011). Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry. Cell, 144(4):539-550.

Misselwitz, B; Dilling, S; Vonaesch, P; Sacher, R; Snijder, B; Schlumberger, M; Rout, S; Stark, M; von Mering, C; Pelkmans, L; Hardt, W D (2011). RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Molecular Systems Biology, 7:474.

Joset, P; Wacker, A; Babey, R; Ingold, E A; Andermatt, I; Stoeckli, E T; Gesemann, M (2011). Rostral growth of commissural axons requires the cell adhesion molecule MDGA2. Neural Development, 6:22.

Kuhn, M; Szklarczyk, D; Franceschini, A; von Mering, C; Jensen, L J; Bork, P (2011). STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Research:Online.

Begemann, M; Spengler, S; Kanber, D; Haake, A; Baudis, M; Leisten, I; Binder, G; Markus, S; Rupprecht, T; Segerer, H; Fricke-Otto, S; Mühlenberg, R; Siebert, R; Buiting, K; Eggermann, T (2011). Silver-Russell patients showing a broad range of ICR1 and ICR2 hypomethylation in different tissues. Clinical Genetics, 80(1):83-88.

Püntener, D; Engelke, M F; Ruzsics, Z; Strunze, S; Wilhelm, C; Greber, U F (2011). Stepwise loss of fluorescent core protein V from human adenovirus during entry into cells. Journal of Virology, 85(1):481-496.

Stetak, A; Hajnal, A (2011). The C. elegans MAGI-1 protein is a novel component of cell junctions that is required for junctional compartmentalization. Developmental Biology, 350(1):24-31.

Szklarczyk, D; Franceschini, A; Kuhn, M; Simonovic, M; Roth, A; Minguez, P; Doerks, T; Stark, M; Muller, J; Bork, P; Jensen, L J; von Mering, C (2011). The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research, 39(Sup 1):D561-D568.

Aitman, T J; Boone, C; Churchill, G A; Hengartner, M O; Mackay, T F C; Stemple, D L (2011). The future of model organisms in human disease research. Nature Reviews. Genetics, 12(8):575-582.

Neukomm, L J; Nicot, A S; Kinchen, J M; Almendinger, J; Pinto, S M; Zeng, S; Doukoumetzidis, K; Tronchère, H; Payrastre, B; Laporte, J F; Hengartner, M O (2011). The phosphoinositide phosphatase MTM-1 regulates apoptotic cell corpse clearance through CED-5-CED-12 in C. elegans. Development, 138(10):2003-2014.

Greber, U F; Cosset, F L (2011). Too smart to fail—how viruses exploit the complexity of host cells during entry. Current Opinion in Virology, 1(1):3-5.

Seto, D; Chodosh, J; Brister, J R; Jones, M S (2011). Using the whole-genome sequence to characterize and name human adenoviruses. Journal of Virology, 85(11):5701-5702.

Dutt, S; Cassoly, E; Dours-Zimmermann, M T; Matasci, M; Stoeckli, E T; Zimmermann, D R (2011). Versican v0 and v1 direct the growth of peripheral axons in the developing chick hindlimb. Journal of Neuroscience, 31(14):5262-5270.

Reiter, L; Rinner, O; Picotti, P; Hüttenhain, R; Beck, M; Brusniak, M Y; Hengartner, M O; Aebersold, R (2011). mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature Methods, 8(5):430-435.

Hemminki, O; Bauerschmitz, G; Hemmi, S; Lavilla-Alonso, S; Diaconu, I; Guse, K; Koski, A; Desmond, R A; Lappalainen, M; Kanerva, A; Cerullo, V; Pesonen, S; Hemminki, A (2010). Oncolytic adenovirus based on serotype 3. Cancer Gene Therapy, 18:288-296.

Holz, Andreas; Kollmus, Heike; Ryge, Jesper; Niederkofler, Vera; Dias, Jose; Ericson, Johan; Stoeckli, Esther T; Kiehn, Ole; Arnold, Hans-Henning (2010). The transcription factors Nkx2.2 and Nkx2.9 play a novel role in floor plate development and commissural axon guidance. Development, 137(24):4249-4260.

Fleisch, V C; Neuhauss, S C F (2010). Parallel visual cycles in the zebrafish retina. Progress in Retinal and Eye Research, 29(6):476-486.

Silhankova, M; Port, F; Harterink, M; Basler, K; Korswagen, H C (2010). Wnt signalling requires MTM-6 and MTM-9 myotubularin lipid-phosphatase function in Wnt-producing cells. The EMBO Journal, 29(24):4094-4105.

Stein, D; Charatsi, I; Cho, Y S; Zhang, Z; Nguyen, J; Delotto, Ro; Luschnig, S; Moussian, B (2010). Localization and activation of the Drosophila protease Easter require the ER-resident Saposin-like rotein Seele. Current Biology, 20(21):1953-1958.

Tschopp, M; Takamiya, M; Cerveny, K L; Gestri, G; Biehlmaier, O; Wilson, S W; Strähle, U; Neuhauss, S C F (2010). Funduscopy in adult zebrafish and its application to isolate mutant strains with ocular defects. PLoS ONE, 5(11):e15427.

Mariconti, L; Loll, B; Schlinkmann, K; Wengi, A; Meinhart, A; Dichtl, B (2010). Coupled RNA polymerase II transcription and 3' end formation with yeast whole-cell extracts. RNA, 16(11):2205-2217.

Jurgeit, Andreas. Towards systems and cell biology of human rhinovirus infection. 2010, University of Zurich, Faculty of Science.

Alexander, R D; Barrass, J D; Dichtl, B; Kos, M; Obtulowicz, T; Robert, M C; Koper, M; Karkusiewicz, I; Mariconti, L; Tollervey, D; Dichtl, B; Kufel, J; Bertrand, E; Beggs, J D (2010). RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae. RNA, 16:2570-2580.

Stoeckli, E T (2010). Neural circuit formation in the cerebellum is controlled by cell adhesion molecules of the contactin family. Cell Adhesion and Migration, 4(4):523-526.

Ahrens, C H; Brunner, E; Qeli, E; Basler, K; Aebersold, R (2010). Generating and navigating proteome maps using mass spectrometry. Nature Reviews. Molecular Cell Biology, 11(11):789-801.

Jurgeit, A; Moese, S; Roulin, P; Dorsch, A; Lötzerich, M; Lee, W M; Greber, U F (2010). An RNA replication-center assay for high content image-based quantifications of human rhinovirus and coxsackievirus infections. Virology Journal, 7(1):264.

Schrimpf, S P; Hengartner, M O (2010). A worm rich in protein: quantitative, differential, and global proteomics in Caenorhabditis elegans. Journal of Proteomics, 73(11):2186-2197.

Maurer, C M; Schönthaler, H B; Mueller, K P; Neuhauss, S C F (2010). Distinct retinal deficits in a zebrafish pyruvate dehydrogenase-deficient mutant. Journal of Neuroscience, 30(36):11962-11972.

Hodel, C. Der kleine Zebrafisch hilft taubblinden Menschen. In: Gentage-Zeitung, 5, 1 September 2010, p.14.

Yagi, R; Mayer, F; Basler, K (2010). Refined LexA transactivators and their use in combination with the Drosophila Gal4 system. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(37):16166-16171.

Stark, M; Berger, S A; Stamatakis, A; von Mering, C (2010). MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics, 11:461.

Huang, Y Y; Tschopp, M; Straumann, D; Neuhauss, S C F (2010). Vestibular deficits do not underlie looping behavior in achiasmatic fish. Communicative & Integrative Biology, 3(4):379-381.

Lütschg, Verena Alice. Human adenovirus species C entry into polarized lung epithelial cells. 2010, University of Zurich, Faculty of Science.

Almendinger, J. Genetic regulation of apoptotic cell corpse clearance in caenorhabditis elegans. 2010, University of Zurich, Faculty of Science.

Petrinovic, M M; Duncan, C S; Bourikas, D; Weinman, O; Montani, L; Schroeter, A; Maerki, D; Sommer, L; Stoeckli, E T; Schwab, M E (2010). Neuronal Nogo-A regulates neurite fasciculation, branching and extension in the developing nervous system. Development, 137(15):2539-2550.

Eggermann, T; Spengler, S; Bachmann, N; Baudis, M; Mau-Holzmann, U A; Singer, S; Rossier, E (2010). Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15). American Journal of Medical Genetics. Part A, 152A(6):1484-1487.

Kälin, S; Amstutz, B; Gastaldelli, M; Wolfrum, N; Boucke, K; Havenga, M; Digennaro, F; Liska, N; Hemmi, S; Greber, U F (2010). Macropinocytotic uptake and infection of human epithelial cells with species B2 adenovirus type 35. Journal of Virology, 84(10):5336-5350.

Mueller, K P; Labhart, T (2010). Polarizing optics in a spider eye. Journal of Comparative Physiology A, 196(5):335-348.

Bogan, E. The stochastic process of life and death as ruled by APE-1. 2010, University of Zurich, Faculty of Science.

Penno, A; Reilly, M M; Houlden, H; Laurá, M; Rentsch, K; Niederkofler, V; Stoeckli, E T; Nicholson, G; Eichler, F; Brown, R H; von Eckardstein, Arnold; Hornemann, T (2010). Hereditary sensory neuropathy type 1 is caused by the accumulation of two neurotoxic sphingolipids. Journal of Biological Chemistry, 285(15):11178-11187.

Butschi, A. Lectin-warfare between nematode and fungi : a conserved defense strategy modelled in Caenorhabditis elegans. 2010, University of Zurich, Faculty of Science.

Vogirala, R P. Synergy of repression and silencing gradients along the chromosome in saccharomyces cerevisiae. 2010, University of Zurich, Faculty of Science.

Schonthaler, H B; Franz-Odendaal, T A; Hodel, C; Gehring, I; Geisler, R; Schwarz, H; Neuhauss, S C F; Dahm, R (2010). The zebrafish mutant bumper shows a hyperproliferation of lens epithelial cells and fibre cell degeneration leading to functional blindness. Mechanisms of Development, 127(3-4):203-219.

Haug, M F; Biehlmaier, O; Mueller, K P; Neuhauss, S C F (2010). Visual acuity in larval zebrafish: behavior and histology. Frontiers in Zoology, 7(3):8.

Shetty, C. Switches in cell-cycle: role of sic1 multisite phosphorylation and degradation in regulating genomic instability. 2010, University of Zurich, Faculty of Science.

Mueller, K P; Neuhauss, S C F (2010). Behavioral neurobiology: how larval fish orient towards the light. Current Biology, 20(4):R159-R161.

Ahrens, C H; Brunner, E; Basler, K (2010). Quantitative proteomics: a central technology for systems biology. Journal of Proteomics, 73(4):820-827.

Eggermann, T; Schönherr, N; Spengler, S; Jäger, S; Denecke, B; Binder, G; Baudis, M (2010). Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region. American Journal of Medical Genetics. Part A, 152A(2):356-359.

Förster, D; Armbruster, K; Luschnig, S (2010). Sec24-Dependent Secretion Drives Cell-Autonomous Expansion of Tracheal Tubes in Drosophila. Current Biology, 20(1):62-68.

Niederkofler, V; Baeriswyl, T; Ott, R; Stoeckli, E T (2010). Nectin-like molecules/SynCAMs are required for post-crossing commissural axon guidance. Development, 137(3):427-435.

Minocha, S. A role of Pox neuro in the developing Drosophila brain : determination of large-field neurons essential for ellipsoid body formation and of ventral projection neurons. 2010, University of Zurich, Faculty of Science.

Zanotelli, V R; Neuhauss, S C F; Ehrengruber, M U (2010). Long-term exposure to bis(2-ethylhexyl)phthalate (DEHP) inhibits growth of guppy fish (Poecilia reticulata). Journal of Applied Toxicology, 30(1):29-33.

Hediger, M; Henggeler, C; Meier, N; Perez, R; Saccone, G; Bopp, D (2010). Molecular characterization of the key switch F provides a basis for understanding the rapid divergence of the sex-determining pathway in the housefly. Genetics, 184:155-170.

Mueller, K P; Neuhauss, S C F (2010). Quantitative measurements of the optokinetic response in adult fish. Journal of Neuroscience Methods, 186(1):29-34.

Schwank, G; Basler, K (2010). Regulation of organ growth by morphogen gradients. Cold Spring Harbor Perspectives in Biology, 2(1):a001669.

Saini, N. Relationship between parkin function, heavy metal homeostasis. 2010, University of Zurich, Faculty of Science.

Chaffron, S; Rehrauer, H; Pernthaler, J; von Mering, C (2010). A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Research, 20(7):947-959.

Jovanovic, M; Reiter, L; Picotti, P; Lange, V; Bogan, E; Hurschler, B A; Blenkiron, C; Lehrbach, N J; Ding, X C; Weiss, M; Schrimpf, S P; Miska, E A; Grosshans, H; Aebersold, R; Hengartner, M O (2010). A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nature Methods, 7(10):837-842.

Bopp, D (2010). About females and males: continuity and discontinuity in flies. Journal of Genetics, 89(3):315-323.

Fontecedro, A C; Lutschg, V; Eichhoff, O; Dummer, R; Greber, U F; Hemmi, S (2010). Analysis of adenovirus trans-complementation-mediated gene expression controlled by melanoma-specific TETP promoter in vitro. Virology Journal, 7(1):175.

Samardzija, M; Neuhauss, S C F; Joly, S; Kurz-Levin, M; Grimm, C (2010). Animal models for retinal degeneration. In: Pang, I-H; Clark, A F. Animal Models of Retinal Disease. New York: The Humana Press Inc, 51-79.

Wuest, S E; Vijverberg, K; Schmidt, A; Weiss, M; Gheyselinck, J; Lohr, M; Wellmer, F; Rahnenführer, J; von Mering, C; Grossniklaus, U (2010). Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Current Biology, 20(6):506-512.

Deka, J; Wiedemann, N; Anderle, P; Murphy-Seiler, F; Bultinck, J; Eyckerman, S; Stehle, J C; André, S; Vilain, N; Zilian, O; Robine, S; Delorenzi, M; Basler, K; Aguet, M (2010). Bcl9/Bcl9l are critical for Wnt-mediated regulation of stem cell traits in colon epithelium and adenocarcinomas. Cancer Research, 70(16):6619-6628.

Künzler, M; Bleuler-Martinez, S; Butschi, A; Garbani, M; Lüthy, P; Hengartner, M O; Aebi, M (2010). Biotoxicity assays for fruiting body lectins and other cytoplasmic proteins. Methods in Enzymology, 480:141-50.

Butschi, A; Titz, A; Wälti, M A; Olieric, V; Paschinger, K; Nöbauer, K; Guo, X; Seeberger, P H; Wilson, I B H; Aebi, M; Hengartner, M O; Künzler, M (2010). Caenorhabditis elegans N-glycan core beta-galactoside confers sensitivity towards nematotoxic fungal galectin CGL2. PLoS Pathogens, 6(1):e1000717.

Schaufelberger, S. Contribution of estrogen and its metabolites in the pathophysiology and biology of neurodegenerative disorders: role of estradiol-receptors and -metabolism. 2010, ETH Zuerich, Faculty of Science.

Song, H; Goetze, S; Bischof, J; Spichiger-Haeusermann, C; Kuster, M; Brunner, E; Basler, K (2010). Coop functions as a corepressor of Pangolin and antagonizes Wingless signaling. Genes and Development, 24(9):881-886.

Kratz, K; Schöpf, B; Kaden, S; Sendoel, A; Eberhard, R; Lademann, C; Cannavó, E; Sartori, A A; Hengartner, M O; Jiricny, J (2010). Deficiency of FANCD2-associated nuclease KIAA1018/FAN1 sensitizes cells to interstrand crosslinking agents. Cell, 142(1):77-88.

Schittenhelm, R B; Althoff, F; Heidmann, S; Lehner, C F (2010). Detrimental incorporation of excess Cenp-A/Cid and Cenp-C into Drosophila centromeres is prevented by limiting amounts of the bridging factor Cal1. Journal of Cell Science, 123(21):3768-3779.

Gesemann, M; Maurer, C M; Neuhauss, S C F (2010). Excitatory amino acid transporters in the zebrafish: Letter to "Expression and functional analysis of Na(+)-dependent glutamate transporters from zebrafish brain" from Rico et al. Brain Research Bulletin, 83(5):202-206.

Aegerter-Wilmsen, T; Smith, A C; Christen, A J; Aegerter, C M; Hafen, E; Basler, K (2010). Exploring the effects of mechanical feedback on epithelial topology. Development, 137(3):499-506.

Saini, N; Oelhafen, S; Hua, H; Georgiev, O; Schaffner, W; Büeler, H (2010). Extended lifespan of Drosophila parkin mutants through sequestration of redox-active metals and enhancement of anti-oxidative pathways. Neurobiology of Disease, 40(1):82-92.

Hödl, M. Genetic analysis of histone 3 and its posttranslational modifications in D. melanogaster. 2010, University of Zurich, Faculty of Science.

Sendoel, A; Kohler, I; Fellmann, C; Lowe, S W; Hengartner, M O (2010). HIF-1 antagonizes p53-mediated apoptosis through a secreted neuronal tyrosinase. Nature, 465(7298):577-583.

Hua, H; Georgiev, O; Schaffner, W; Steiger, D (2010). Human copper transporter Ctr1 is functional in Drosophila, revealing a high degree of conservation between mammals and insects. Journal of Biological Inorganic Chemistry, 15(1):107-113.

Peralta, R; Baudis, M; Vazquez, G; Juárez, S; Ortiz, R; Decanini, H; Hernandez, D; Gallegos, F; Valdivia, A; Piña, P; Salcedo, M (2010). Increased expression of cellular retinol-binding protein 1 in laryngeal squamous cell carcinoma. Journal of Cancer Research and Clinical Oncology, 136(6):931-938.

Stecher, B; Chaffron, S; Käppeli, R; Hapfelmeier, S; Freedrich, S; Weber, T C; Kirundi, J; Suar, M; McCoy, K D; von Mering, C; Macpherson, A J; Hardt, W D (2010). Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathogens, 6(1):e1000711.

Lacunza, E; Baudis, M; Colussi, A G; Segal-Eiras, A; Croce, M V; Abba, M C (2010). MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells. Cancer Genetics and Cytogenetics, 201(2):102-110.

Gerrits, Bertran; Bodenmiller, Bernd (2010). Mapping of phosphorylation sites by LC-MS/MS. Methods in Molecular Biology, 658:127-136.

Schaufelberger, S. Neuroprotective actions of estradiol: Potential role of estradiol receptors and metablism. 2010, University of Zurich, Faculty of Science.

Neuhauss, S C F; Rico, E P; Gesemann, M (2010). Nomenclature of glutamate transporters in zebrafish and other vertebrates. Brain Research Bulletin, 83(6):297.

Hill, A; Boll, W; Ries, C; Warner, L; Osswalt, M; Hill, M; Noll, M (2010). Origin of Pax and Six gene families in sponges: Single PaxB and Six1/2 orthologs in Chalinula loosanoffi. Developmental Biology, 343(1-2):106-123.

Breslow, David K; Collins, Sean R; Bodenmiller, Bernd; Aebersold, Ruedi; Simons, Kai; Shevchenko, Andrej; Ejsing, Christer S; Weissman, Jonathan S (2010). Orm family proteins mediate sphingolipid homeostasis. Nature, 463(7284):1048-1053.

Bodenmiller, B; Wanka, S; Kraft, C; Urban, J; Campbell, D; Pedrioli, P G; Gerrits, B; Picotti, P; Lam, H; Vitek, O; Brusniak, M Y; Roschitzki, B; Zhang, C; Shokat, K M; Schlapbach, R; Colman-Lerner, A; Nolan, G P; Nesvizhskii, A I; Peter, M; Loewith, R; von Mering, C; Aebersold, R (2010). Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Science Signaling, 3(153):rs4.

Gesemann, M; Lesslauer, A; Maurer, C M; Schönthaler, H B; Neuhauss, S C F (2010). Phylogenetic analysis of the vertebrate excitatory/neutral amino acid transporter (SLC1/EAAT) family reveals lineage specific subfamilies. BMC Evolutionary Biology, 10:117.

Bodenmiller, Bernd; Aebersold, Ruedi (2010). Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Methods in enzymology, 470:317-334.

Port, F. Regulation of wingless secretion in drosophila melanogaster. 2010, University of Zurich, Faculty of Science.

Bandyopadhyay, Sourav; Mehta, Monika; Kuo, Dwight; Sung, Min-Kyung; Chuang, Ryan; Jaehnig, Eric J; Bodenmiller, Bernd; Licon, Katherine; Copeland, Wilbert; Shales, Michael; Fiedler, Dorothea; Dutkowski, Janusz; Guénolé, Aude; van Attikum, Haico; Shokat, Kevan M; Kolodner, Richard D; Huh, Won-Ki; Aebersold, Ruedi; Keogh, Michael-Christopher; Krogan, Nevan J; Ideker, Trey (2010). Rewiring of genetic networks in response to DNA damage. Science, 330(6009):1385-1389.

Bätz, Tilmann. Role of the Apical Extracellular Matrix in Epithelial Morphogenesis and Size Control in Drosophila. 2010, University of Zurich, Faculty of Science.

Kuhn, M; Szklarczyk, D; Franceschini, A; Campillos, M; von Mering, C; Jensen, L J; Beyer, A; Bork, P (2010). STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research, 38 (Da:D552-D556.

Weiss, M; Schrimpf, S; Hengartner, M O; Lercher, M J; von Mering, C (2010). Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Proteomics, 10(6):1297-1306.

Domanitskaya, E; Wacker, Z; Mauti, O; Baeriswyl, T; Esteve, P; Bovolenta, Z; Stoeckli, E T (2010). Sonic hedgehog guides post-crossing commissural axons both directly and indirectly by regulating Wnt activity. Journal of Neuroscience, 30(33):11167-11176.

Kelemen, J Z; Ratna, P; Scherrer, S; Becskei, A (2010). Spatial epigenetic control of mono- and bistable gene expression. PLoS Biology, 8(3):e1000332.

Spengler, S; Schönherr, N; Binder, G; Wollmann, H; Fricke-Otto, S; Mühlenberg, R; Denecke, B; Baudis, M; Eggermann, T (2010). Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome. Journal of Medical Genetics, 47(5):356-360.

Sun, L; Becskei, A (2010). Systems biology: The cost of feedback control. Nature, 467(7312):163-164.

Steiger, D; Fetchko, M; Vardanyan, A; Atanesyan, L; Steiner, K; Turski, M L; Thiele, D J; Georgiev, O; Schaffner, W (2010). The Drosophila copper transporter Ctr1C functions in male fertility. The Journal of Biological Chemistry, 285(22):17089-17097.

Cabello, J; Neukomm, L J; Günesdogan, U; Burkart, K; Charette, S J; Lochnit, G; Hengartner, M O; Schnabel, R (2010). The Wnt pathway controls cell death engulfment, spindle orientation, and migration through CED-10/Rac. PLoS Biology, 8(2):e1000297.

Endt, K; Stecher, B; Chaffron, S; Slack, E; Tchitchek, N; Benecke, A; Van Maele, L; Sirard, J-C; Mueller, A J; Heikenwalder, M; Macpherson, A J; Strugnell, R; von Mering, C; Hardt, W-D (2010). The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathogens, 6(9):e1001097.

Hodel, C. Visual behaviour and ocular morphology of larval and adult zebrafish with an eye towrads art. 2010, University of Zurich, Faculty of Science.

Port, F; Basler, K (2010). Wnt trafficking: new insights into Wnt naturation, secretion and spreading. Traffic, 11(10):1265-1271.

Saini, N; Schaffner, W (2010). Zinc supplement greatly improves the condition of parkin mutant Drosophila. Biological Chemistry, 391(5):513-518.

Nieto, C; Almendinger, J; Gysi, S; Gómez-Orte, E; Kaech, A; Hengartner, M O; Schnabel, R; Moreno, S; Cabello, J (2010). ccz-1 mediates the digestion of apoptotic corpses in C. elegans. Journal of Cell Science, 123(12):2001-2007.

Muller, J; Szklarczyk, D; Julien, P; Letunic, I; Roth, A; Kuhn, M; Powell, S; von Mering, C; Doerks, T; Jensen, L J; Bork, P (2010). eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Research, 38 (Da:D190-D195.

Gazzola, M; Burckhardt, C J; Bayati, B; Engelke, M; Greber, U F; Koumoutsakos, P (2009). A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus. PLoS Computational Biology, 5(12):e1000623.

Froehlicher, M; Liedtke, A; Groh, K J; Neuhauss, S C F; Segner, H; Eggen, R I (2009). Zebrafish (Danio rerio) neuromast: Promising biological endpoint linking developmental and toxicological studies. Aquatic Toxicology, 95(4):307-319.

Gallant, P; Steiger, D (2009). Myc's secret life without Max. Cell Cycle, 8(23):3848-3853.

Lindert, U; Cramer, M; Meuli, M; Georgiev, O; Schaffner, W (2009). Metal-responsive transcription factor 1 (MTF-1) activity is regulated by a nonconventional nuclear localization signal and a metal-responsive transactivation domain. Molecular and Cellular Biology, 29(23):6283-6293.

Titz, A; Butschi, A; Henrissat, B; Fan, Y Y; Hennet, T; Razzazi-Fazeli, E; Hengartner, M O; Wilson, I B H; Kuenzler, M; Aebi, M (2009). Molecular basis for galactosylation of core fucose residues in invertebrates: Identification of Caenorhabditis elegans N-glycan core {alpha}1,6-fucoside {beta}1,4-galactosyltransferase GALT-1 as a member of a novel glycosyltransferase family. Journal of Biological Chemistry, 284(52):36223-36233.

Byun, R; Becskei, A (2009). Biology inspires engineering. Genome Biology, 10(11):317.

Geuking, P; Narasimamurthy, R; Lemaitre, B; Basler, K; Leulier, F (2009). A non-redundant role for Drosophila Mkk4 and hemipterous/Mkk7 in TAK1-mediated activation of JNK. PLoS ONE, 4(11):e7709.

Reiter, L; Claassen, M; Schrimpf, S P; Jovanovic, M; Schmidt, A; Buhmann, J M; Hengartner, M O; Aebersold, R (2009). Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular & Cellular Proteomics, 8(11):2405-2417.

Burckhardt, C J; Greber, U F (2009). Virus movements on the plasma membrane support infection and transmission between cells. PLoS Pathogens, 5(11):e1000621.

Hamaratoglu, F; Basler, K; Affolter, M (2009). Confronting morphogen gradients: how important are they for growth? Science Signaling, 2(94):pe67.

Imelli, N; Ruzsics, Z; Puntener, D; Gastaldelli, M; Greber, U F (2009). Genetic reconstitution of the human adenovirus type 2 temperature-sensitive 1 mutant defective in endosomal escape. Virology Journal, 6:174.

Clements, J; Hens, K; Merugu, S; Dichtl, B; de Couet, H G; Callaerts, P (2009). Mutational analysis of the eyeless gene and phenotypic rescue reveal that an intact Eyeless protein is necessary for normal eye and brain development in Drosophila. Developmental Biology, 334(2):503-512.

Song, H; Spichiger-Haeusermann, C; Basler, K (2009). The ISWI-containing NURF complex regulates the output of the canonical Wingless pathway. EMBO Reports, 10(10):1140-1146.

Halbach, A; Zhang, H; Wengi, A; Jablonska, Z; Gruber, I M L; Halbeisen, R E; Dehé, P M; Kemmeren, P; Holstege, F; Géli, V; Gerber, A P; Dichtl, B (2009). Cotranslational assembly of the yeast SET1C histone methyltransferase complex. The EMBO Journal, 28(19):2959-2970.

Köhler, K; Brunner, E; Guan, X L; Boucke, K; Greber, U F; Mohanty, S; Barth, J M; Wenk, M R; Hafen, E (2009). A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy, 5(7):980-990.

Pellegrino, M W; Gasser, R B; Sprenger, F; Stetak, A; Hajnal, A (2009). The conserved zinc finger protein VAB-23 is an essential regulator of epidermal morphogenesis in Caenorhabditis elegans. Developmental Biology, 336(1):84-93.

Kim, S; Gailite, I; Moussian, B; Luschnig, S; Goette, M; Fricke, K; Honemann-Capito, M; Grubmüller, H; Wodarz, A (2009). Kinase-activity-independent functions of atypical protein kinase C in Drosophila. Journal of Cell Science, 122(PT 20):3759-3771.

Delmotte, N; Knief, C; Chaffron, S; Innerebner, G; Roschitzki, B; Schlapbach, R; von Mering, C; Vorholt, J A (2009). Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 106(38):16428-16433.

Althoff, F; Viktorinová, I; Kastl, J; Lehner, C F (2009). Drosophila Cyclin J is a mitotically stable Cdk1 partner without essential functions. Developmental Biology, 333(2):263-272.

Liu, J; Bandyopadhyay, N; Ranka, S; Baudis, M; Kahveci, T (2009). Inferring progression models for CGH data. Bioinformatics, 25(17):2208-2215.

Gruber, I. Functional analysis of the H3K4 histone methyltransferase SET1C in saccharomyces cerevisiae. 2009, University of Zurich, Faculty of Science.

Huang, Y Y; Tschopp, M; Neuhauss, S C F (2009). Illusionary self-motion perception in zebrafish. PLoS ONE, 4(8):e6550.

Lindert, U. Comparison and functional characterization of the metal-responsive transcription factor 1 (MTF-1) from rodents and human. 2009, University of Zurich, Faculty of Science.

Reiter, L. Development of algorithms for mass spectrometry based proteomics. 2009, University of Zurich, Faculty of Science.

Galluzzi, L; et al (2009). Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes. Cell Death and Differentiation, 16(8):1093-1107.

Schlegel, N C; Eichhoff, O M; Hemmi, S; Werner, S; Dummer, R; Hoek, K S (2009). Id2 suppression of p15 counters TGF-beta-mediated growth inhibition of melanoma cells.counters TGF-beta-mediated growth inhibition of melanoma cells. Pigment Cell & Melanoma Research, 22(4):445-453.

Tan, C S H; Bodenmiller, B; Pasculescu, A; Jovanovic, M; Hengartner, M O; Jørgensen, C; Bader, G D; Aebersold, R; Pawson, T; Linding, R (2009). Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling, 2(81):ra39.

Schittenhelm, R B; Chaleckis, R; Lehner, C F (2009). Intrakinetochore localization and essential functional domains of Drosophila Spc105. EMBO Journal, 28(16):2374-2386.

Helmuth, J A; Burckhardt, C J; Greber, U F; Sbalzarini, I F (2009). Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. Journal of Structural Biology, 167(1):1-10.

Shi, Y; Noll, M (2009). Determination of cell fates in the R7 equivalence group of the Drosophila eye by the concerted regulation of D-Pax2 and TTK88. Developmental Biology, 331(1):68-77.

Greber, U F; Puntener, D (2009). DNA-tumor virus entry-From plasma membrane to the nucleus. Seminars in Cell and Developmental Biology, 20(5):631-642.

Stetak, A; Hörndli, F; Maricq, A V; van den Heuvel, S; Hajnal, A (2009). Neuron-specific regulation of associative learning and memory by MAGI-1 in C. elegans. PLoS ONE, 4(6):e6019-e6019.

Hausmann, G; von Mering, C; Basler, K (2009). The hedgehog signaling pathway: where did it come from? PLoS Biology, 7(6):e1000146.

Holbein, S; Wengi, A; Decourty, L; Freimoser, F M; Jacquier, A; Dichtl, B (2009). Cordycepin interferes with 3' end formation in yeast independently of its potential to terminate RNA chain elongation. RNA, 15(5):837-849.

Jovanovich, M. Development of experimental large-scale approaches to identify microRNA target genes in Caenorhabditis elegans. 2009, University of Zurich, Faculty of Science.

Menuz, V; Howell, K S; Gentina, S; Epstein, S; Riezman, I; Fornallaz-Mulhauser, M; Hengartner, M O; Gomez, M; Riezman, H; Martinou, J C (2009). Protection of C. elegans from anoxia by HYL-2 ceramide synthase. Science, 324(5925):381-384.

Mosimann, C; Hausmann, G; Basler, K (2009). Beta-catenin hits chromatin: regulation of Wnt target gene activation. Nature Reviews. Molecular Cell Biology, 10(4):276-286.

Ratna, P; Scherrer, S; Fleischli, C; Becskei, A (2009). Synergy of repression and silencing gradients along the chromosome. Journal of Molecular Biology, 387(4):826-839.

Krstic, D. Influence of Pox neuro on courtship behavior of the Drosophila male: Dissection of sensory cues and neuronal network underlying olfactory pheromone processing in the adult brain. 2009, University of Zurich, Faculty of Science.

Stoeckli, E; Zou, Y (2009). How are neurons wired to form functional and plastic circuits? Meeting on Axon Guidance, Synaptogenesis & Neural Plasticity. EMBO Reports, 10(4):326-330.

Narasimamurthy, R; Geuking, P; Ingold, K; Willen, L; Schneider, P; Basler, K (2009). Structure-function analysis of Eiger, the Drosophila TNF homolog. Cell Research, 19(3):392-394.

Becskei, A (2009). Linearization through distortion: a new facet of negative feedback in signalling. Molecular Systems Biology, 5:255.

Hoerndli, F J; Walser, M; Fröhli Hoier, E; de Quervain, D; Papassotiropoulos, A; Hajnal, A (2009). A conserved function of c. elegans CASY-1 calsyntenin in associative learning. PLoS ONE, 4(3):e4880.

Froehlicher, M; Liedtke, A; Groh, K; López-Schier, H; Neuhauss, S C F; Segner, H; Eggen, R I L (2009). Estrogen receptor subtype beta2 is involved in neuromast development in zebrafish (Danio rerio) larvae. Developmental Biology, 330(1):32-43.

Boerma, E G; Siebert, R; Kluin, P M; Baudis, M (2009). Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge. Leukemia, 23(2):225-234.

Spirov, A; Fahmy, K; Schneider, M; Frei, E; Noll, M; Baumgartner, S (2009). Formation of the bicoid morphogen gradient: an mRNA gradient dictates the protein gradient. Development, 136(4):605-614.

Balamurugan, K; Hua, H; Georgiev, O; Schaffner, W (2009). Mercury and cadmium trigger expression of the copper importer Ctr1B, which enables Drosophila to thrive on heavy metal-loaded food. Biological Chemistry, 390(2):109-113.

Jensen, L J; Kuhn, M; Stark, M; Chaffron, S; Creevey, C; Muller, J; Doerks, T; Julien, P; Roth, A; Simonovic, M; Bork, P; von Mering, C (2009). STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Research, 37(Databa):D412-D416.

Riemer, Jan; Appenzeller-Herzog, Christian; Johansson, Linda; Bodenmiller, Bernd; Hartmann-Petersen, Rasmus; Ellgaard, Lars (2009). A luminal flavoprotein in endoplasmic reticulum-associated degradation. Proceedings of the National Academy of Sciences of the United States of America, 106(35):14831-14836.

Huber, Alexandre; Bodenmiller, Bernd; Uotila, Aino; Stahl, Michael; Wanka, Stefanie; Gerrits, Bertran; Aebersold, Ruedi; Loewith, Robbie (2009). Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes and Development, 23(16):1929-1943.

Schrimpf, S P; Weiss, M; Reiter, L; Ahrens, C H; Jovanovic, M; Malmström, J; Brunner, E; Mohanty, S; Lercher, M J; Hunziker, P E; Aebersold, R; von Mering, C; Hengartner, M O (2009). Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biology, 7(3):e48.

Ulintz, Peter J; Yocum, Anastasia K; Bodenmiller, Bernd; Aebersold, Ruedi; Andrews, Philip C; Nesvizhskii, Alexey I (2009). Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. Journal of Proteome Research, 8(2):887-899.

Buetti-Dinh, A; Ungricht, R; Kelemen, J Z; Shetty, C; Ratna, P; Becskei, A (2009). Control and signal processing by transcriptional interference. Molecular Systems Biology, 5:300.

Grobei, M A; Qeli, E; Brunner, E; Rehrauer, H; Zhang, R; Roschitzki, B; Basler, K; Ahrens, C H; Grossniklaus, U (2009). Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Research, 19(10):1786-1800.

Domon, Bruno; Bodenmiller, Bernd; Carapito, Christine; Hao, Zhiqi; Huehmer, Andreas; Aebersold, Ruedi (2009). Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. Journal of Proteome Research, 8(6):2633-2639.

Smith, A. Four ways to leave the epithelium: clonal elimination in the drosophila wing disc. 2009, University of Zurich, Faculty of Science.

Picotti, Paola; Bodenmiller, Bernd; Mueller, Lukas N; Domon, Bruno; Aebersold, Ruedi (2009). Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell, 138(4):795-806.

Schwank, G. Growth regulation in the drosophila wing imaginal disc. 2009, University of Zurich, Faculty of Science.

Siegenthaler, C; Maroy, P; Hediger, M; Dübendorfer, A; Bopp, D (2009). Hormones and sex-specific transcription factors jointly control yolk protein synthesis in Musca domestica. International Journal of Evolutionary Biology, 2009:291236.

Schittenhelm, R B. Identification and Characterization of Kinetochore Components in Drosophila melanogaster. 2009, University of Zurich, Faculty of Science.

Goetze, S; Qeli, E; Mosimann, C; Staes, A; Gerrits, B; Roschitzki, B; Mohanty, S; Niederer, E M; Laczko, E; Timmerman, E; Lange, V; Hafen, E; Aebersold, R; Vandekerckhove, J; Basler, K; Ahrens, C H; Gevaert, K; Brunner, E (2009). Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biology, 7(11):e1000236.

Gerstung, M; Baudis, M; Moch, H; Beerenwinkel, N (2009). Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 25(21):2809-2815.

Bug, S; Dürig, J; Oyen, F; Klein-Hitpass, L; Martin-Subero, J I; Harder, L; Baudis, M; Arnold, N; Kordes, U; Dührsen, U; Schneppenheim, R; Siebert, R (2009). Recurrent loss, but lack of mutations, of the SMARCB1 tumor suppressor gene in T-cell prolymphocytic leukemia with TCL1A-TCRAD juxtaposition. Cancer Genetics and Cytogenetics, 192(1):44-47.

Sumara, Grzegorz; Formentini, Ivan; Collins, Stephan; Sumara, Izabela; Windak, Renata; Bodenmiller, Bernd; Ramracheya, Reshma; Caille, Dorothée; Jiang, Huiping; Platt, Kenneth A; Meda, Paolo; Aebersold, Rudolf; Rorsman, Patrik; Ricci, Romeo (2009). Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis. Cell, 136(2):235-248.

Krstic, D; Boll, W; Noll, M (2009). Sensory integration regulating male courtship behavior in Drosophila. PLoS ONE, 4(2):e4457.

Kessler, R; Hausmann, G; Basler, K (2009). The PHD domain is required to link Drosophila Pygopus to Legless/beta-catenin and not to histone H3. Mechanisms of Development, 126(8-9):752-759.

Mosimann, C; Hausmann, G; Basler, K (2009). The role of Parafibromin/Hyrax as a nuclear Gli/Ci-interacting protein in Hedgehog target gene control. Mechanisms of Development, 126(5-6):394-405.

Hödl, M; Basler, K (2009). Transcription in the absence of histone H3.3. Current Biology, 19(14):1221-1226.

Kuster, M. WNT/Wg signaling - ligand secretion and target gene activation. 2009, University of Zurich, Faculty of Science.

Kappeler, M; Kranz, E; Woolcock, K; Georgiev, O; Schaffner, W (2008). Drosophila bloom helicase maintains genome integrity by inhibiting recombination between divergent DNA sequences. Nucleic Acids Research, 36(21):6907-6917.

Schwank, G; Restrepo, S; Basler, K (2008). Growth regulation by Dpp: an essential role for Brinker and a non-essential role for graded signaling levels. Development, 135(24):4003-4013.

Garas, M; Dichtl, B; Keller, W (2008). The role of the putative 3' end processing endonuclease Ysh1p in mRNA and snoRNA synthesis. RNA, 14(12):2671-2684.

Mauti, O; Baeriswyl, T; Stoeckli, E T (2008). Gene Silencing by Injection and Electroporation of dsRNA in Avian Embryos. Cold Spring Harbor Protocols:5094.

Stetak, A; Gutierrez, P; Hajnal, A (2008). Tissue-specific functions of the Caenorhabditis elegans p120 Ras GTPase activating protein GAP-3. Developmental Biology, 323(2):166-176.

Fejer, G; Drechsel, L; Liese, J; Schleicher, U; Ruzsics, Z; Imelli, N; Greber, U F; Keck, S; Hildenbrand, B; Krug, A; Bogdan, C; Freudenberg, M A (2008). Key role of splenic myeloid DCs in the IFN-alphabeta response to adenoviruses in vivo. PLoS Pathogens, 4(11):e1000208.

Gastaldelli, M; Imelli, N; Boucke, K; Amstutz, B; Meier, O; Greber, U F (2008). Infectious Adenovirus Type 2 Transport Through Early but not Late Endosomes. Traffic, 9(12):2265-2278.

Grieder, N C; Caussinus, E; Parker, D S; Cadigan, K; Affolter, M; Luschnig, S (2008). γCOP is required for apical protein secretion and epithelial morphogenesis in Drosophila Melanogaster. PLoS ONE, 3(9):e3241.

Roos, A; Elbracht, M; Baudis, M; Senderek, J; Schönherr, N; Eggermann, T; Schüler, H M (2008). A 10.7 Mb interstitial deletion of 13q21 without phenotypic effect defines a further non-pathogenic euchromatic variant. American Journal of Medical Genetics. Part A, 146A(18):2417-2420.

Dichtl, B (2008). Transcriptional ShortCUTs. Molecular Cell, 31(5):617-618.

Fleisch, V C; Schonthaler, H B; von Lintig, J; Neuhauss, S C F (2008). Subfunctionalization of a retinoid-binding protein provides evidence for two parallel visual cycles in the cone-dominant zebrafish retina. Journal of Neuroscience, 28(33):8208-8216.

Lindert, U; Leuzinger, L; Steiner, K; Georgiev, O; Schaffner, W (2008). Characterization of metal-responsive transcription factor (MTF-1) from the giant rodent capybara reveals features in common with human as well as with small rodents (mouse, rat). Short communication. Chemistry & Biodiversity, 5(8):1485-1494.

Hoischen, A; Ehrler, M; Fassunke, J; Simon, M; Baudis, M; Landwehr, C; Radlwimmer, B; Lichter, P; Schramm, J; Becker, A J; Weber, R G (2008). Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathology, 18(3):326-337.

Galluzzi, L; Joza, N; Tasdemir, E; Maiuri, M C; Hengartner, M; Abrams, J M; Tavernarakis, N; Penninger, J; Madeo, F; Kroemer, G (2008). No death without life: vital functions of apoptotic effectors. Cell Death and Differentiation, 15(7):1113-1123.

Affolter, M; Pyrowolakis, G; Weiss, A; Basler, K (2008). Signal-induced repression: the exception or the rule in developmental signaling? Developmental Cell, 15(1):11-22.

Vardanyan, A; Atanesyan, L; Egli, D; Raja, S J; Steinmann-Zwicky, M; Renkawitz-Pohl, R; Georgiev, O; Schaffner, W (2008). Dumpy-30 family members as determinants of male fertility and interaction partners of metal-responsive transcription factor 1 (MTF-1) in Drosophila. BMC Developmental Biology, 8:68.

Zielke, N; Querings, S; Rottig, C; Lehner, C F; Sprenger, F (2008). The anaphase-promoting complex/cyclosome (APC/C) is required for rereplication control in endoreplication cycles. Genes and Development, 22(12):1690-1703.

Chen, X; Hua, H; Balamurugan, K; Kong, X; Zhang, L; George, G N; Georgiev, O; Schaffner, W; Giedroc, D P (2008). Copper sensing function of Drosophila metal-responsive transcription factor-1 is mediated by a tetranuclear Cu(I) cluster. Nucleic Acids Research, 36(9):3128-3138.

Haecker, A; Bergman, M; Neupert, C; Moussian, B; Luschnig, S; Aebi, M; Mannervik, M (2008). Wollknäuel is required for embryo patterning and encodes the Drosophila ALG5 UDP-glucose:dolichyl-phosphate glucosyltransferase. Development, 135(10):1745-1749.

Baeriswyl, T; Mauti, O; Stoeckli, E T (2008). Temporal control of gene silencing by in ovo electroporation. In: Barik, S. RNAi: Design and Application. Totowa, NJ: Springer, 231-244.

Richards, S; Bopp, D; et al (2008). The genome of the model beetle and pest Tribolium castaneum. Nature, 452(7190):949-955.

Baeriswyl, T; Stoeckli, E T (2008). Axonin-1/TAG-1 is required for pathfinding of granule cell axons in the developing cerebellum. Neural Development, 3:7.

Neuhauss, S C F (2008). Biochemie der Zapfen: Mit Zebrafischen dem Sehen bei Tageslicht auf der Spur. BIOforum, 02:38-40.

Amstutz, B; Gastaldelli, M; Kälin, S; Imelli, N; Boucke, K; Wandeler, E; Mercer, J; Hemmi, S; Greber, U F (2008). Subversion of CtBP1-controlled macropinocytosis by human adenovirus serotype 3. EMBO Journal, 27(7):956-969.

Muraro, N I; Weston, A J; Gerber, A P; Luschnig, S; Moffat, K G; Baines, R A (2008). Pumilio binds para mRNA and requires Nanos and Brat to regulate sodium current in Drosophila motoneurons. Journal of Neuroscience, 28(9):2099-2109.

Pauli, A; Althoff, F; Oliveira, R A; Heidmann, S; Schuldiner, O; Lehner, C F; Dickson, B J; Nasmyth, K (2008). Cell-type-specific TEV protease cleavage reveals Cohesin functions in Drosophila neurons. Developmental Cell, 14(2):239-251.

Holbein, S; Freimoser, F M; Werner, T P; Wengi, A; Dichtl, B (2008). Cordycepin-hypersensitive growth links elevated polyphosphate levels to inhibition of poly(A) polymerase in Saccharomyces cerevisiae. Nucleic Acids Research, 36(2):353-363.

Hoek, K S; Eichhoff, O M; Schlegel, N C; Döbbeling, U; Kobert, N; Schaerer, L; Hemmi, S; Dummer, R (2008). In vivo switching of human melanoma cells between proliferative and invasive states. Cancer Research, 68(3):650-656.

Katanaev, V L; Solis, G P; Hausmann, G; Buestorf, S; Katanayeva, N; Schrock, Y; Stuermer, C A O; Basler, K (2008). Reggie-1/flotillin-2 promotes secretion of the long-range signalling forms of Wingless and Hedgehog in Drosophila. The EMBO Journal, 27(3):509-521.

Doukoumetzidis, K; Hengartner, M O (2008). Cell biology: dying to hold you. Nature, 451(7178):530-531.

Burckhardt, C J; Greber, U F (2008). Redox rescues virus from ER trap. Nature Cell Biology, 10(1):9-11.

Schonthaler, H B; Fleisch, V C; Biehlmaier, O; Makhankov, Y; Rinner, O; Bahadori, R; Geisler, R; Schwarz, H; Neuhauss, S C F; Dahm, R (2008). The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles. Development, 135(2):387-399.

Jensen, L J; Julien, P; Kuhn, M; von Mering, C; Muller, J; Doerks, T; Bork, P (2008). eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Research, 36(Databa):D250-D254.

Kinchen, J M; Doukoumetzidis, K; Almendinger, J; Stergiou, L; Tosello-Trampont, A C; Sifri, C D; Hengartner, M O; Ravichandran, K S (2008). A pathway for phagosome maturation during engulfment of apoptotic cells. Nature Cell Biology, 10(5):556-566.

Röthlisberger, M. A protease that regulates Drosophila BMP signaling and a microarray based screen for Targets of Drosophila BMP signaling. 2008, University of Zurich, Faculty of Science.

Schmidt, Alexander; Gehlenborg, Nils; Bodenmiller, Bernd; Mueller, Lukas N; Campbell, Dave; Mueller, Markus; Aebersold, Ruedi; Domon, Bruno (2008). An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Molecular & Cellular Proteomics, 7(11):2138-2150.

Bauer, V L; Braselmann, H; Henke, M; Mattern, D; Walch, A; Unger, K; Baudis, M; Lassmann, S; Huber, R; Wienberg, J; Werner, M; Zitzelsberger, H F (2008). Chromosomal changes characterize head and neck cancer with poor prognosis. Journal of Molecular Medicine, 86(12):1353-1365.

Hodel, C; Neuhauss, S C F (2008). Computer-based analysis of the optokinetic response in zebrafish larvae. Cold Spring Harbor Protocols:4961.

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D (2008). Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics, 9:542.

Hua, H. Drosophila melanogaster as a model to study metal homeostasis and amyyloid-b toxicity. 2008, University of Zurich, Faculty of Science.

Fleisch, V C; Jametti, T; Neuhauss, S C F (2008). Electroretinogram (ERG) measurements in larval zebrafish. Cold Spring Harbor Protocols:4973.

Dorner, M. Impact of innate and adative immunity on Epstein-Barr virus infection and persistence. 2008, University of Zurich, Faculty of Science.

Ulintz, Peter J; Bodenmiller, Bernd; Andrews, Philip C; Aebersold, Ruedi; Nesvizhskii, Alexey I (2008). Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Molecular & Cellular Proteomics, 7(1):71-87.

Kunin, V; Raes, J; Harris, J K; Spear, J R; Walker, J J; Ivanova, N; von Mering, C; Bebout, B M; Pace, N R; Bork, P; Hugenholtz, P (2008). Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Molecular Systems Biology, 4:198.

Zhang, C. Pax genes in Drosophila myogenesis: their functions and regulation. 2008, University of Zurich, Faculty of Science.

Bodenmiller, B; Campbell, D; Gerrits, B; Lam, H; Jovanovic, M; Picotti, P; Schlapbach, R; Aebersold, R (2008). PhosphoPep--a database of protein phosphorylation sites in model organisms. Nature Biotechnology, 26(12):1339-1340.

Tress, Michael L; Bodenmiller, Bernd; Aebersold, Ruedi; Valencia, Alfonso (2008). Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome biology, 9(11):R162.

Bischof, J; Basler, K (2008). Recombinases and their use in gene activation, gene inactivation, and transgenesis. In: Dahmann, C. Drosophila : methods and protocols. Totowa, N.J., US: Springer, 175-195.

Nieländer, I; Martín-Subero, J I; Wagner, F; Baudis, M; Gesk, S; Harder, L; Hasenclever, D; Klapper, W; Kreuzer, M; Pott, C; Martinez-Climent, J A; Dreyling, M; Arnold, N; Siebert, R (2008). Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma. Haematologica, 93(6):949-950.

Kappeler, M. Repair of double strand breaks in Drosophila melanogaster. 2008, University of Zurich, Faculty of Science.

Kuhn, M; von Mering, C; Campillos, M; Jensen, L J; Bork, P (2008). STITCH: interaction networks of chemicals and proteins. Nucleic Acids Research, 36(Databa):D684-D688.

Holbein, S. The molecular effects of the antitumor antibiotic cordycepin in sacharomyces cerevisiae. 2008, University of Zurich, Faculty of Science.

Huang, Y Y; Neuhauss, S C F (2008). The optokinetic response in zebrafish and its applications. Frontiers in Bioscience, 13:1899-1916.

Chilaka, S. Transvection and enhancer-promoter specificity at the D-Pax2 locus during Drosophila development. 2008, University of Zurich, Faculty of Science.

Port, F; Kuster, M; Herr, P; Furger, E; Bänziger, C; Hausmann, G; Basler, K (2008). Wingless secretion promotes and requires retromer-dependent cycling of Wntless. Nature Cell Biology, 10(2):178-185.

Mauti, O; Domanitskaya, E; Andermatt, I; Sadhu, R; Stoeckli, E T (2007). Semaphorin6A acts as a gate keeper between the central and the peripheral nervous system. Neural Development, 2:28.

Baudis, Michael (2007). Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer, 7:226.

Fleischli, C; Sirena, D; Lesage, G; Havenga, M J E; Cattaneo, R; Greber, U F; Hemmi, S (2007). Species B adenovirus serotypes 3, 7, 11 and 35 share similar binding sites on the membrane cofactor protein CD46 receptor. Journal of General Virology, 88(11):2925-2934.

Schonthaler, H B; Lampert, J M; Isken, A; Rinner, O; Mader, A; Gesemann, M; Oberhauser, V; Golczak, M; Biehlmaier, O; Palczewski, K; Neuhauss, S C F; von Lintig, J (2007). Evidence for RPE65-independent vision in the cone-dominated zebrafish retina. European Journal of Neuroscience, 26(7):1940-1949.

Kallivretaki, E; Eggen, R I L; Neuhauss, S C F; Kah, O; Segner, H (2007). The zebrafish, brain-specific, aromatase cyp19a2 is neither expressed nor distributed in a sexually dimorphic manner during sexual differentiation. Developmental Dynamics, 236(11):3155-3166.

Dürig, J; Bug, S; Klein-Hitpass, L; Boes, T; Jöns, T; Martin-Subero, J I; Harder, L; Baudis, M; Dührsen, U; Siebert, R (2007). Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia, 21(10):2153-2163.

Greber, U F; Gastaldelli, M (2007). Junctional gating: the achilles' heel of epithelial cells in pathogen infection. Cell Host & Microbe, 2(3):143-146.

Pandey, R; Heeger, S; Lehner, C F (2007). Rapid effects of acute anoxia on spindle kinetochore interactions activate the mitotic spindle checkpoint. Journal of Cell Science, 120(16):2807-2818.

Rimann, I; Hajnal, A (2007). Regulation of anchor cell invasion and uterine cell fates by the egl-43 Evi-1 proto-oncogene in Caenorhabditis elegans. Developmental Biology, 308(1):187-195.

Deng, S; Hirschberg, A; Worzfeld, T; Penachioni, J Y; Korostylev, A; Swiercz, J M; Vodrazka, P; Mauti, O; Stoeckli, E T; Tamagnone, L; Offermanns, S; Kuner, R (2007). Plexin-B2, but not Plexin-B1, critically modulates neuronal migration and patterning of the developing nervous system in vivo. Journal of Neuroscience, 27(23):6333-6347.

Biehlmaier, O; Makhankov, Y; Neuhauss, S C F (2007). Impaired retinal differentiation and maintenance in zebrafish laminin mutants. Investigative Ophthalmology and Visual Science, 48(6):2887-2894.

Haecker, A; Qi, D; Lilja, T; Moussian, B; Andrioli, L P; Luschnig, S; Mannervik, M (2007). Drosophila brakeless interacts with atrophin and is required for tailless-mediated transcriptional repression in early embryos. PLoS Biology, 5(6):e145.

Fisher, J; Piterman, N; Hajnal, A; Henzinger, T A (2007). Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology, 3(5):e92.

Helmuth, J A; Burckhardt, C J; Koumoutsakos, P; Greber, U F; Sbalzarini, I F (2007). A novel supervised trajectory segmentation algorithm identifies distinct types of human adenovirus motion in host cells. Journal of Structural Biology, 159(3):347-358.

Schittenhelm, R B; Heeger, S; Althoff, F; Walter, A; Heidmann, S; Mechtler, K; Lehner, C F (2007). Spatial organization of a ubiquitous eukaryotic kinetochore protein network in Drosophila chromosomes. Chromosoma, 116(4):385-402.

Schuh, M; Lehner, C F; Heidmann, S (2007). Incorporation of Drosophila CID/CENP-A and CENP-C into centromeres during early embryonic anaphase. Current Biology, 17(3):237-243.

Bodenmiller, Bernd; Mueller, Lukas N; Pedrioli, Patrick G A; Pflieger, Delphine; Jünger, Martin A; Eng, Jimmy K; Aebersold, Ruedi; Tao, W Andy (2007). An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. Molecular Biosystems, 3(4):275-286.

Taylor, R C; Brumatti, G; Ito, S; Hengartner, M O; Derry, W B; Martin, S J (2007). Establishing a blueprint for CED-3-dependent killing through identification of multiple substrates for this protease. Journal of Biological Chemistry, 282(20):15011-15021.

Hausmann, G; Bänziger, C; Basler, K (2007). Helping Wingless take flight: how WNT proteins are secreted. Nature Reviews. Molecular Cell Biology, 8(4):331-336.

Tosello-Trampont, A C; Kinchen, J M; Brugnera, E; Haney, L B; Hengartner, M O; Ravichandran, K S (2007). Identification of two signaling submodules within the CrkII/ELMO/Dock180 pathway regulating engulfment of apoptotic cells. Cell Death and Differentiation, 14(5):963-972.

Geisler, R; Rauch, G J; Geiger-Rudolph, S; Albrecht, A J; van Bebber, F; Berger, A; Busch-Nentwich, E; Dahm, R; Dekens, M P S; Dooley, C; Elli, A F; Gehring, I; Geiger, H; Geisler, M; Glaser, S; Holley, S; Huber, M; Kerr, A; Kirn, A; Knirsch, M; Konantz, M; Küchler, A M; Maderspacher, F; Neuhauss, S C F; Nicolson, T; Ober, E A; Praeg, E; Ray, R; Rentzsch, B; Rick, J M; Rief, E; Schauerte, H E; Schepp, C P; Schönberger, U; Schonthaler, H B; Seiler, C; Sidi, S; Söllner, C; Wehner, A; Weiler, C; Nüsslein-Volhard, C (2007). Large-scale mapping of mutations affecting zebrafish development. BMC Genomics, 8:11.

Bodenmiller, B; Malmstrom, J; Gerrits, B; Campbell, D; Lam, H; Schmidt, A; Rinner, O; Mueller, L N; Shannon, P T; Pedrioli, P G; Panse, C; Lee, H K; Schlapbach, R; Aebersold, R (2007). PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology, 3:139.

Raes, J; Korbel, J O; Lercher, M J; von Mering, C; Bork, P (2007). Prediction of effective genome size in metagenomic samples. Genome Biology, 8:R10.

Harrington, E D; Singh, A H; Doerks, T; Letunic, I; von Mering, C; Jensen, L J; Raes, J; Bork, P (2007). Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 104(35):13913-13918.

von Mering, C; Hugenholtz, P; Raes, J; Tringe, S G; Doerks, T; Jensen, L J; Ward, N; Bork, P (2007). Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315(5815):1126-1130.

Bodenmiller, Bernd; Mueller, Lukas N; Mueller, Markus; Domon, Bruno; Aebersold, Ruedi (2007). Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nature Methods, 4(3):231-237.

von Mering, C; Jensen, L J; Kuhn, M; Chaffron, S; Doerks, T; Krüger, B; Snel, B; Bork, P (2007). STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Research, 35(Databa):D358-D362.

Stecher, B; Robbiani, R; Walker, A W; Westendorf, A M; Barthel, M; Kremer, M; Chaffron, S; Macpherson, A J; Buer, J; Parkhill, J; Dougan, G; von Mering, C; Hardt, W-D (2007). Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biology, 5(10):2177-2189.

Mueller, Lukas N; Rinner, Oliver; Schmidt, Alexander; Letarte, Simon; Bodenmiller, Bernd; Brusniak, Mi-Youn; Vitek, Olga; Aebersold, Ruedi; Müller, Markus (2007). SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics, 7(19):3470-3480.

Chaffron, S; von Mering, C (2007). Termites in the woodwork. Genome Biology, 8:229.