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2017

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.

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.

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.

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:Epub ahead of print.

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:Epub ahead of print.

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.

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.

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.

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.

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):1.

Caviglia, Sara; Flores-Benitez, David; Lattner, Johanna; Luschnig, Stefan; Brankatschk, Marko (2017). Rabs on the fly: functions of Rab GTPases during development. Small GTPases:Epub ahead of print.

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:e1.

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.

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.

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

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.

2016

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.

de Ramon Francàs, Gemma; Zuñiga, Nikole R; Stoeckli, Esther T (2016). The spinal cord shows the way - How axons navigate intermediate targets. Developmental Biology:Epub ahead of print.

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.

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.

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; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Jensen, Lars Juhl; Martin, Maria J; Muffato, Matthieu; Quest for Orthologs consortium; Gabaldón, Toni; Lewis, Suzanna E; Thomas, Paul D; Sonnhammer, Erik; Dessimoz, Christophe (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.

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.

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.

2015

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.

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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.

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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/ß-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.

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

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.

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.

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.

2014

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.

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.

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.

2013

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.

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.

Raychaudhuri, Nitika Taneja. Epigenetic Control of Centromeric Cid/Cenp-A Levels During Spermatogenesis and Development. 2013, University of Zurich, Faculty of Science.

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.

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.

2012

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; Abrams, J M; Alnemri, E S; Baehrecke, E H; Blagosklonny, M V; Dawson, T M; Dawson, V L; El-Deiry, W S; Fulda, S; Gottlieb, E; Green, D R; Hengartner, M O; Kepp, O; Knight, R A; Kumar, S; Lipton, S A; Lu, X; Madeo, F; Malorni, W; Mehlen, P; Nuñez, G; Peter, M E; Piacentini, M; Rubinsztein, D C; Shi, Y; Simon, H U; Vandenabeele, P; White, E; Yuan, J; Zhivotovsky, B; Melino, G; Kroemer, G (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.

2011

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.

Atanesyan, L. Polyglutamine-mediated and heavy metal-induced transcription from Yeast to Humans. 2011, University of Zurich, Faculty of Science.

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, C M; Huang, Y Y; Neuhauss, S 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.

Althoff, Friederike Erika Andrea. Characterization of Drosophila Cyclin J and Mps1. 2011, University of Zurich, Faculty of Science.

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.

Stark, M. MLTreeMap - Maximum likelihood placement of environmental DNA sequence reads into curated reference phylogenies. 2011, University of Zurich, Faculty of Science.

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.

2010

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.

Püntener, Daniel. A live cell reporter of human adenovirus chromatin. 2010, University of Zurich, Faculty of Science.

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.

Günther, V. Molecular mechanisms of heavy metal homeostasis in flies and humans. 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.

Weiss, M. Evolution of protein abundances in eukaryotes. 2010, University of Zurich, Faculty of Science.

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.

Chaffron, S. Tracing microbes and their genes through the environment: diversity, ecology and evolution. 2010, University of Zurich, Faculty of Science.

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.

2009

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.

Dittrich, C. Identification of novel components in the DNA damage response pathways of Caenorhabditis elegans. 2009, University of Zurich, Faculty of Science.

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.

Kalvakuri, S. Transcriptional regulation and functions of the Drosophila paired gene. 2009, University of Zurich, Faculty of Science.

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.

Jiang, Y. Novel cell lineages controlled by Pox neuro of larval poly-innervated external sensory organs in Drosophila. 2009, University of Zurich, Faculty of Science.

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.

2008

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.

Barth, S. Functional Characterization of the Interaction of PHD2 with FKBP38. 2008, University of Zurich, Faculty of Science.

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.

2007

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, M (2007). Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer, 7 : 22:1-15.

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(1):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.

Affolter, M; Basler, K (2007). The Decapentaplegic morphogen gradient: from pattern formation to growth regulation. Nature Reviews. Genetics, 8(9):663-674.

2006

Bahadori, R; Rinner, O; Schonthaler, H B; Biehlmaier, O; Makhankov, Y V; Rao, P; Jagadeeswaran, P; Neuhauss, S C F (2006). The Zebrafish fade out mutant: a novel genetic model for Hermansky-Pudlak syndrome. Investigative Ophthalmology and Visual Science, 47(10):4523-4531.

Huang, Y Y; Rinner, O; Hedinger, P; Liu, S C; Neuhauss, S C F (2006). Oculomotor instabilities in zebrafish mutant belladonna: a behavioral model for congenital nystagmus caused by axonal misrouting. Journal of Neuroscience, 26(39):9873-9870.

Han, S M; Lee, T H; Mun, J Y; Kim, M J; Kritikou, E A; Lee, S J; Han, S S; Hengartner, M O; Koo, H S (2006). Deleted in cancer 1 (DICE1) is an essential protein controlling the topology of the inner mitochondrial membrane in C. elegans. Development, 133(18):3597-3606.

Rhiner, C; Hengartner, M O (2006). Sugar antennae for guidance signals: syndecans and glypicans integrate directional cues for navigating neurons. Scientific World Journal, 6:1024-1036.

Kritikou, E A; Milstein, S; Vidalain, P O; Lettre, G; Bogan, E; Doukoumetzidis, K; Gray, P; Chappell, T G; Vidal, M; Hengartner, M O (2006). C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival. Genes and Development, 20(16):2279-2292.

Schmitz, M; Graf, C; Gut, T; Sirena, D; Peter, I; Dummer, R; Greber, U F; Hemmi, S (2006). Melanoma cultures show different susceptibility towards E1A-, E1B-19 kDa- and fiber-modified replication-competent adenoviruses. Gene Therapy, 13(11):893-905.

Hodel, C; Neuhauss, S C F; Biehlmaier, O (2006). Time course and development of light adaptation processes in the outer zebrafish retina. Anatomical Record, 288(6):653-662.

Bänziger, C; Soldini, D; Schütt, C; Zipperlen, P; Hausmann, G; Basler, K (2006). Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells. Cell, 125(3):509-522.

Mosimann, C; Hausmann, G; Basler, K (2006). Parafibromin/Hyrax activates Wnt/Wg target gene transcription by direct association with beta-catenin/Armadillo. Cell, 125(2):327-341.

Ninkovic, J; Folchert, A; Makhankov, Y V; Neuhauss, S C F; Sillaber, I; Straehle, U; Bally-Cuif, L (2006). Genetic identification of AChE as a positive modulator of addiction to the psychostimulant D-amphetamine in zebrafish. Developmental Neurobiology, 66(5):463-475.

Greber, U F; Way, M (2006). A superhighway to virus infection. Cell, 124(4):741-754.

Stoeckli, E T (2006). Longitudinal axon guidance. Current Opinion in Neurobiology, 16(1):35-39.

Parusel, C T; Kritikou, E A; Hengartner, M O; Krek, W; Gotta, M (2006). URI-1 is required for DNA stability in C. elegans. Development, 113(4):621-629.

Seth, A; Culverwell, J; Walkowicz, M; Toro, S; Rick, J M; Neuhauss, S C F; Varga, Z M; Karlstrom, R O (2006). belladonna/(Ihx2) is required for neural patterning and midline axon guidance in the zebrafish forebrain. Development, 133(4):725-735.

Kallivretaki, E; Eggen, R; Neuhauss, S C F; Alberti, M; Kausch, U; Segner, H (2006). Aromatase in zebrafish: A potential target for endocrine disrupting chemicals. Marine Environmental Research, 62(S1):S187-S190.

Stetak, A; Hoier, E; Croce, A; Cassata, G; Di Fiore, P P; Hajnal, A (2006). Cell fate-specific regulation of EGF receptor trafficking during Caenorhabditis elegans vulval development. EMBO Journal, 25(11):2347-2357.

Liu, J; Mohammed, J; Carter, J; Ranka, S; Kahveci, T; Baudis, M (2006). Distance-based clustering of CGH data. Bioinformatics, 22(16):1971-1978.

Walser, C B; Battu, G; Hoier, E; Hajnal, A (2006). Distinct roles of the Pumilio and FBF translational repressors during C. elegans vulval development. Development, 133(17):3461-3471.

Baudis, Michael (2006). Online database and bioinformatics toolbox to support data mining in cancer cytogenetics. BioTechniques, 40(3):269-272.

Su, C W; Tharin, S; Jin, Y; Wightman, B; Spector, M; Meili, D; Tsung, N; Rhiner, C; Bourikas, D; Stoeckli, E T; Garriga, G; Horvitz, H R; Hengartner, M O (2006). The short coiled-coil domain-containing protein UNC-69 cooperates with UNC-76 to regulate axonal outgrowth and normal presynaptic organization in Caenorhabditis elegans. Journal of Biology, 5(4):9.

Fleisch, V; Neuhauss, S C F (2006). Visual Behavior in Zebrafish. Zebrafish, 3(2):191-201.

Jovanovic, M; Hengartner, M O (2006). miRNAs and apoptosis: RNAs to die for. Oncogene, 25(46):6176-6187.

2005

Sirena, D; Ruzsics, Z; Schaffner, Walter; Greber, U F; Hemmi, S (2005). The nucleotide sequence and a first generation gene transfer vector of species B human adenovirus serotype 3. Virology, 343(2):283-298.

Geuking, Peter; Narasimamurthy, Rajesh; Basler, Konrad (2005). A genetic screen targeting the tumor necrosis factor/Eiger signaling pathway: identification of Drosophila TAB2 as a functionally conserved component. Genetics, 171(4):1683-1694.

Städeli, R; Basler, K (2005). Dissecting nuclear Wingless signalling: recruitment of the transcriptional co-activator Pygopus by a chain of adaptor proteins. Mechanisms of Development, 122(11):1171-1182.

Rhiner, C; Gysi, S; Fröhli, E; Hengartner, M O; Hajnal, A (2005). Syndecan regulates cell migration and axon guidance in C. elegans. Development, 132(20):4621-4633.

Schonthaler, H B; Lampert, J M; von Lintig, J; Schwarz, H; Geisler, R; Neuhauss, S C F (2005). A mutation in the silver gene leads to defects in melanosome biogenesis and alterations in the visual system in the zebrafish mutant fading vision. Developmental Biology, 284(2):421-436.

Fleischli, C; Verhaagh, S; Havenga, M; Sirena, D; Schaffner, Walter; Cattaneo, R; Greber, U F; Hemmi, S (2005). The distal short consensus repeats 1 and 2 of the membrane cofactor protein CD46 and their distance from the cell membrane determine productive entry of species B adenovirus serotype 35. Journal of Virology, 79(15):10013-10022.

Rinner, O; Makhankov, Y V; Biehlmaier, O; Neuhauss, S C F (2005). Knockdown of cone-specific kinase GRK7 in larval zebrafish leads to impaired cone response recovery and delayed dark adaptation. Neuron, 47(2):231-242.

Hoffmans, R; Städeli, R; Basler, K (2005). Pygopus and legless provide essential transcriptional coactivator functions to armadillo/beta-catenin. Current Biology, 15(13):1207-1211.

Stalleicken, J; Mukhida, M; Labhart, T; Wehner, R; Frost, B; Mouritsen, H (2005). Do monarch butterflies use polarized skylight for migratory orientation? Journal of Experimental Biology, 208(12):2399-2408.

Strunze, S; Trotman, L C; Boucke, K; Greber, U F (2005). Nuclear targeting of adenovirus type 2 requires CRM1-mediated nuclear export. Molecular Biology of the Cell, 16(6):2999-3009.

Greber, U F (2005). Viral trafficking violations in axons: the herpesvirus case. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 102(16):5639-5640.

Stepanek, L; Stoker, A W; Stoeckli, E T; Bixby, J L (2005). Receptor tyrosine phosphatases guide vertebrate motor axons during development. Journal of Neuroscience, 25(15):3813-3823.

Burghardt, G; Hediger, M; Siegenthaler, C; Moser, M; Dübendorfer, A; Bopp, D (2005). The transformer2 gene in Musca domestica is required for selecting and maintaining the female pathway of development. Development Genes and Evolution, 215(4):165-176.

Kinchen, J M; Cabello, J; Klingele, D; Wong, K; Feichtinger, R; Schnabel, H; Schnabel, R; Hengartner, M O (2005). Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. Nature, 434(7029):93-99.

Bourikas, Dimitris; Pekarik, Vladimir; Baeriswyl, T; Grunditz, A; Sadhu, R; Nardó, M; Stoeckli, E T (2005). Sonic hedgehog guides commissural axons along the longitudinal axis of the spinal cord. Nature Neuroscience, 8(3):297-304.

Lu, M; Kinchen, J M; Rossman, K L; Grimsley, C M; Hall, M; Sondek, J; Hengartner, M O; Yajnik, V; Ravichandran, K S (2005). A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs. Current Biology, 15(4):371-377.

Hengartner, M O (2005). Cell biology: divide and conquer. Nature, 433(7027):692-694.

Schumacher, B; Hanazawa, M; Lee, M H; Nayak, S; Volkmann, K; Hofmann, E R; Hofmann, R; Hengartner, M O; Schedl, T; Gartner, A (2005). Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis. Cell, 120(3):357-368.

Seiler, C; Finger-Baier, K C; Rinner, O; Makhankov, Y V; Schwarz, H; Neuhauss, S C F; Nicolson, T (2005). Duplicated genes with split functions: independent roles of protocadherin15 orthologues in zebrafish hearing and vision. Development, 132(3):615-623.

Meier, O; Gastaldelli, M; Boucke, K; Hemmi, S; Greber, U F (2005). Early steps of clathrin-mediated endocytosis involved in phagosomal escape of Fcgamma receptor-targeted adenovirus. Journal of Virology, 79(4):2604-2613.

Trueb, B; Neuhauss, S C F; Baertschi, S; Rieckmann, T; Schild, C; Taeschler, S (2005). Fish possess multiple copies of fgfrl1, the gene for a novel FGF receptor. Biochimica et Biophysica Acta, 1727(1):65-74.

Rinner, O; Rick, J M; Neuhauss, S C F (2005). Contrast sensitivity, spatial and temporal tuning of the larval zebrafish optokinetic response. Investigative Ophthalmology and Visual Science, 46(1):137-142.

Zipperlen, P; Nairz, K; Rimann, I; Basler, K; Hafen, E; Hengartner, M; Hajnal, A (2005). A universal method for automated gene mapping. Genome Biology, 6(2):R19.

Braissant, O; Henry, H; Villard, A M; Speer, O; Wallimann, T; Bachmann, C (2005). Creatine synthesis and transport during rat embryogenesis: spatiotemporal expression of AGAT, GAMT and CT1. BMC Developmental Biology, 5:9.

Mao, X; Hamoudi, R A; Zhao, P; Baudis, M (2005). Genetic losses in breast cancer: toward an integrated molecular cytogenetic map. Cancer Genetics and Cytogenetics, 160(2):141-151.

Hidalgo, A; Baudis, M; Petersen, I; Arreola, H; Piña, P; Vázquez-Ortiz, G; Hernandez, D; Gonzáles, J; Lazos, M; Lopez, R; Perez, C; Garcia, J; Vazquez, K; Alatorre, B; Salcedo, M (2005). Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma. BMC Cancer, 5:77.

Tao, W Andy; Wollscheid, Bernd; O'Brien, Robert; Eng, Jimmy K; Li, Xiao-jun; Bodenmiller, Bernd; Watts, Julian D; Hood, Leroy; Aebersold, Ruedi (2005). Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nature Methods, 2(8):591-598.

Kinchen, J M; Hengartner, M O (2005). Tales of cannibalism, suicide, and murder: Programmed cell death in C. elegans. Current Topics in Developmental Biology, 65:1-145.

Berset, T A; Fröhli-Hoier, E; Hajnal, A (2005). The C. elegans homolog of the mammalian tumor suppressor Dep-1/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions. Genes and Development, 19(11):1328-1340.

Canevascini, S; Marti, M; Fröhli, E; Hajnal, A (2005). The Caenorhabditis elegans homologue of the proto-oncogene ect-2 positively regulates RAS signalling during vulval development. EMBO Reports, 6(12):1169-1175.

Vandesompele, J; Baudis, M; De Preter, K; Van Roy, N; Ambros, P; Bown, N; Brinkschmidt, C; Christiansen, H; Combaret, V; Lastowska, M; Nicholson, J; O'Meara, A; Plantaz, D; Stallings, R; Brichard, B; Van den Broecke, C; De Bie, S; De Paepe, A; Laureys, G; Speleman, F (2005). Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. Journal of Clinical Oncology, 23(10):2280-2299.

2004

deBakker, C D; Haney, L B; Kinchen, J M; Grimsley, C M; Lu, M; Klingele, D; Hsu, P K; Chou, B K; Cheng, L C; Blangy, A; Sondek, J; Hengartner, M O; Wu, Y C; Ravichandran, K S (2004). Phagocytosis of apoptotic cells is regulated by a UNC-73/TRIO-MIG-2/RhoG signaling module and armadillo repeats of CED-12/ELMO. Current Biology, 14(24):2208-2216.

Dutt, A; Canevascini, S; Fröhli-Hoier, E; Hajnal, A (2004). EGF signal propagation during C. elegans vulval development mediated by ROM-1 rhomboid. PLoS Biology, 2(11):e344.

Lettre, G; Kritikou, E A; Jaeggi, M; Calixto, A; Fraser, A G; Kamath, R S; Ahringer, J; Hengartner, M O (2004). Genome-wide RNAi identifies p53-dependent and -independent regulators of germ cell apoptosis in C. elegans. Cell Death and Differentiation, 11(11):1198-1203.

Pearman, P B; Garner, T W J; Straub, M; Greber, U F (2004). Response of the Italian agile frog (Rana latastei) to a Ranavirus, frog virus 3: a model for viral emergence in naïve populations. Journal of Wildlife Diseases, 40(4):660-669.

Hoeppner, D J; Spector, M S; Ratliff, T M; Kinchen, J M; Granat, S; Lin, S C; Bhusri, S S; Conradt, B; Herman, M A; Hengartner, M O (2004). eor-1 and eor-2 are required for cell-specific apoptotic death in C. elegans. Developmental Biology, 274(1):125-138.

Hoffmans, R; Basler, K (2004). Identification and in vivo role of the Armadillo-Legless interaction. Development, 131(17):4393-4400.

Deng, X; Hofmann, E R; Villanueva, A; Hobert, O; Capodieci, P; Veach, D R; Yin, Xianglei; Campodonico, L; Glekas, A; Cordon-Cardo, C; Clarkson, B; Bornmann, W G; Fuks, Z; Hengartner, M O; Kolesnick, R N (2004). Caenorhabditis elegans ABL-1 antagonizes p53-mediated germline apoptosis after ionizing irradiation. Nature Genetics, 36(8):906-912.

Lu, M; Kinchen, J M; Rossman, K L; Grimsley, C M; deBakker, C D; Brugnera, E; Tosello-Trampont, A C; Haney, L B; Klingele, D; Sondek, J; Hengartner, M O; Ravichandran, K S (2004). PH domain of ELMO functions in trans to regulate Rac activation via Dock180. Nature Structural and Molecular Biology, 11(8):756-762.

Pyrowolakis, G; Hartmann, B; Müller, B; Basler, K; Affolter, M (2004). A simple molecular complex mediates widespread BMP-induced repression during Drosophila development. Developmental Cell, 7(2):229-240.

Scholz, N; Basler, K; Saur, P; Burchardi, H; Felder, S (2004). Outcome prediction in critical care: physicians' prognoses vs. scoring systems. European Journal of Anaesthesiology : EJA, 21(8):606-611.

Makhankov, Y V; Rinner, O; Neuhauss, S C F (2004). An inexpensive device for non-invasive electroretinography in small aquatic vertebrates. Journal of Neuroscience Methods, 135(1-2):205-210.

Züllig, S; Hengartner, M O (2004). Cell biology. Tickling macrophages, a serious business. Science, 304(5674):1123-1124.

Sirena, D; Lilienfeld, B; Eisenhut, M; Kälin, S; Boucke, K; Beerli, R R; Vogt, Lorenz; Ruedl, C; Bachmann, M F; Greber, U F; Hemmi, S (2004). The human membrane cofactor CD46 is a receptor for species B adenovirus serotype 3. Journal of Virology, 78(9):4454-4462.

Moreno, E; Basler, K (2004). dMyc transforms cells into super-competitors. Cell, 117(1):117-129.

Imelli, N; Meier, O; Boucke, K; Hemmi, S; Greber, U F (2004). Cholesterol is required for endocytosis and endosomal escape of adenovirus type 2. Journal of Virology, 78(6):3089-3098.

Grimsley, C M; Kinchen, J M; Tosello-Trampont, A C; Brugnera, E; Haney, L B; Lu, M; Chen, Q; Klingele, D; Hengartner, M O; Ravichandran, K S (2004). Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration. Journal of Biological Chemistry, 279(7):6087-6097.

Meier, O; Greber, U F (2004). Adenovirus endocytosis. Journal of Gene Medicine, 6(S1):S152-S163.

Stergiou, L; Hengartner, M O (2004). Death and more: DNA damage response pathways in the nematode C. elegans. Cell Death and Differentiation, 11(1):21-28.

Hediger, M; Burghardt, G; Siegenthaler, C; Buser, N; Hilfiker-Kleiner, D; Dübendorfer, A; Bopp, D (2004). Sex determination in Drosophila melanogaster and Musca domestica converges at the level of the terminal regulator doublesex. Development Genes and Evolution, 214(1):29-42.

Nairz, K; Zipperlen, P; Dearolf, C; Basler, K; Hafen, E (2004). A reverse genetic screen in Drosophila using a deletion-inducing mutagen. Genome Biology, 5(10):R83.

Veljkovic, E; Bacconi, A; Stetak, A; Hajnal, A; Stasiuk, S; Skelly, P J; Forster, I; Shoemaker, C B; Verrey, F (2004). Aromatic amino acid transporter AAT-9 of Caenorhabditis elegans localizes to neurons and muscle cells. Journal of Biological Chemistry, 279(47):49268-49273.

Greber, U F; Fornerod, M (2004). Nuclear import in viral infections. In: Mash, M. Membrane Trafficking in Viral Replication. Berlin: Springer, 109-138.

2003

Galli Marxer, C; Collaud Coen, M; Greber, T; Greber, U F; Schlapbach, L (2003). Cell spreading on quartz crystal microbalance elicits positive frequency shifts indicative of viscosity changes. Analytical and Bioanalytical Chemistry, 377(3):578-586.

Galli Marxer, C; Collaud Coen, M; Bissig, H; Greber, U F; Schlapbach, L (2003). Simultaneous measurement of the maximum oscillation amplitude and the transient decay time constant of the QCM reveals stiffness changes of the adlayer. Analytical and Bioanalytical Chemistry, 377(3):570-577.

Biehlmaier, O; Neuhauss, S C F; Kohler, Konrad (2003). Synaptic plasticity and functionality at the cone terminal of the developing zebrafish retina. Developmental Neurobiology, 56(3):222-236.

Bahadori, R; Huber, M; Rinner, O; Seeliger, M W; Geiger-Rudolph, S; Geisler, R; Neuhauss, S C F (2003). Retinal function and morphology in two zebrafish models of oculo-renal syndromes. European Journal of Neuroscience, 18(6):1377-1386.

Nagel, H; Maag, S; Tassis, A; Nestlé, F O; Greber, U F; Hemmi, S (2003). The alphavbeta5 integrin of hematopoietic and nonhematopoietic cells is a transduction receptor of RGD-4C fiber-modified adenoviruses. Gene Therapy, 10(19):1643-1653.

Neuhauss, S C F; Seeliger, M W; Schepp, C P; Biehlmaier, O (2003). Retinal defects in the zebrafish bleached mutant. Documenta Ophthalmologica, 107(1):71-78.

Trotman, L C; Achermann, D P; Keller, S; Straub, M; Greber, U F (2003). Non-classical export of an adenovirus structural protein. Traffic, 4(6):390-402.

Battu, G; Froehli Hoier, E; Hajnal, A (2003). The C. elegans G-protein-coupled receptor SRA-13 inhibits RAS/MAPK signalling during olfaction and vulval development. Development, 130(12):2567-2577.

Senti, K A; Usui, T; Boucke, K; Greber, U F; Uemura, T; Dickson, B J (2003). Flamingo regulates R8 axon-axon and axon-target interactions in the Drosophila visual system. Current Biology, 13(10):828-832.

Schweizer, L; Nellen, D; Basler, K (2003). Requirement for Pangolin/dTCF in Drosophila Wingless signaling. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 100(10):5846-5851.

Müller, B; Hartmann, B; Pyrowolakis, G; Affolter, M; Basler, K (2003). Conversion of an extracellular Dpp/BMP morphogen gradient into an inverse transcriptional gradient. Cell, 113(2):221-233.

Peter, I; Graf, C; Dummer, R; Schaffner, W; Greber, U F; Hemmi, S (2003). A novel attenuated replication-competent adenovirus for melanoma therapy. Gene Therapy, 10(7):530-9.

Greber, U F; Fassati, A (2003). Nuclear import of viral DNA genomes. Traffic, 4(3):136-143.

Neuhauss, S C F (2003). Behavioral genetic approaches to visual system development and function in zebrafish. Developmental Neurobiology, 54(1):148-160.

Pekarik, Vladimir; Bourikas, Dimitris; Miglino, N; Joset, P; Preiswerk, S; Stoeckli, E T (2003). Screening for gene function in chicken embryo using RNAi and electroporation. Nature Biotechnology, 21(1):93-96.

Végh, M; Basler, K (2003). A genetic screen for hedgehog targets involved in the maintenance of the Drosophila anteroposterior compartment boundary. Genetics, 163(4):1427-1438.

Biehlmaier, O; Neuhauss, S C F; Kohler, K (2003). Double cone dystrophy and RPE degeneration in the retina of the zebrafish gnn mutant. Investigative Ophthalmology and Visual Science, 44(3):1287-1298.

Bourikas, Dimitris; Stoeckli, E T (2003). New tools for gene manipulation in chicken embryos. Oligonucleotides, 13(5):411-419.

2002

Hofmann, E R; Milstein, S; Boulton, S J; Ye, M; Hofmann, J J; Stergiou, L; Gartner, A; Vidal, M; Hengartner, M O (2002). Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis. Current Biology, 12(22):1908-1918.

Gagnon, S N; Hengartner, M O; Desnoyers, S (2002). The genes pme-1 and pme-2 encode two poly(ADP-ribose) polymerases in Caenorhabditis elegans. Biochemical Journal, 368(1):263-271.

Horváth, G; Gál, J; Labhart, T; Wehner, R (2002). Does reflection polarization by plants influence colour perception in insects? Polarimetric measurements applied to a polarization-sensitive model retina of Papilio butterflies. Journal of Experimental Biology, 205(21):3281-3298.

Mabit, H; Nakano, M Y; Prank, U; Saam, B; Döhner, K; Sodeik, B; Greber, U F (2002). Intact microtubules support adenovirus and herpes simplex virus infections. Journal of Virology, 76(19):9962-9971.

Meier, O; Boucke, K; Hammer, S V; Keller, S; Stidwill, R P; Hemmi, S; Greber, U F (2002). Adenovirus triggers macropinocytosis and endosomal leakage together with its clathrin-mediated uptake. Journal of Cell Biology, 158(6):1119-1131.

Künzi, V; Glatzel, M; Nakano, M Y; Greber, U F; Van Leuven, F; Aguzzi, A (2002). Unhampered prion neuroinvasion despite impaired fast axonal transport in transgenic mice overexpressing four-repeat tau. Journal of Neuroscience, 22(17):7471-7477.

Hajnal, A; Berset, T (2002). The C.elegans MAPK phosphatase LIP-1 is required for the G(2)/M meiotic arrest of developing oocytes. The EMBO Journal, 21(16):4317-4326.

Giannakakou, P; Nakano, M Y; Nicolaou, K C; O'Brate, A; Yu, J; Blagosklonny, M V; Greber, U F; Fojo, T (2002). Enhanced microtubule-dependent trafficking and p53 nuclear accumulation by suppression of microtubule dynamics. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 99(16):10855-10860.

Hajnal, A (2002). Fine-tuning the RAS signaling pathway: Zn(2+) makes the difference. Molecular Cell, 9(5):927-928.

Greber, U F; Carafoli, E (2002). Signalling takes control of nucleo-cytoplasmic trafficking. Workshop on signal-regulated nuclear transport. EMBO Reports, 3(5):410-414.

Harrington, R J; Gutch, M J; Hengartner, M O; Tonks, N K; Chisholm, A D (2002). The C. elegans LAR-like receptor tyrosine phosphatase PTP-3 and the VAB-1 Eph receptor tyrosine kinase have partly redundant functions in morphogenesis. Development, 129(9):2141-2153.

Moreno, E; Basler, K; Morata, G (2002). Cells compete for decapentaplegic survival factor to prevent apoptosis in Drosophila wing development. Nature, 416(6882):755-759.

Greber, U F (2002). Signalling in viral entry. Cellular and Molecular Life Sciences, 59(4):608-626.

Degtyareva, N P; Greenwell, P; Hofmann, E R; Hengartner, M O; Zhang, L; Culotti, J G; Petes, T D (2002). Caenorhabditis elegans DNA mismatch repair gene msh-2 is required for microsatellite stability and maintenance of genome integrity. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 99(4):2158-2163.

Seeliger, M W; Rilk, A; Neuhauss, S C F (2002). Ganzfeld ERG in zebrafish larvae. Documenta Ophthalmologica, 104(1):57-68.

Dübendorfer, A; Hediger, M; Burghardt, G; Bopp, D (2002). Musca domestica, a window on the evolution of sex-determining mechanisms in insects. International Journal of Developmental Biology, 46(1):75-79.

Streit, A; Bernasconi, L; Sergeev, P; Cruz, A; Steinmann-Zwicky, M (2002). mgm 1, the earliest sex-specific germline marker in Drosophila, reflects expression of the gene esg in male stem cells. International Journal of Developmental Biology, 46(1):159-166.

Gerlitz, O; Nellen, D; Ottiger, M; Basler, K (2002). A screen for genes expressed in Drosophila imaginal discs. International Journal of Developmental Biology, 46(1):173-176.

Moreno, E; Yan, M; Basler, K (2002). Evolution of TNF signaling mechanisms: JNK-dependent apoptosis triggered by Eiger, the Drosophila homolog of the TNF superfamily. Current Biology, 12(14):1263-1268.

Ma, Y; Erkner, A; Gong, R; Yao, S; Taipale, J; Basler, K; Beachy, P A (2002). Hedgehog-mediated patterning of the mammalian embryo requires transporter-like function of dispatched. Cell, 111(1):63-75.

Bellotto, M; Bopp, D; Senti, K A; Burke, R; Deak, P; Maroy, P; Dickson, B J; Basler, K; Hafen, E (2002). Maternal-effect loci involved in Drosophila oogenesis and embryogenesis: P element-induced mutations on the third chromosome. International Journal of Developmental Biology, 41(1):149-157.

Kaiser, U; Uebelacker, I; Abel, U; Birkmann, J; Trümper, L; Schmalenberg, H; Karakas, T; Metzner, B; Hossfeld, D K; Bischoff, H G; Franke, A; Reiser, M; Müller, P; Mantovani, L; Grundeis, M; Rothmann, F; von Seydewitz, C U; Mesters, R M; Steinhauer, E U; Krahl, D; Schumacher, K; Kneba, M; Baudis, M; Schmitz, N; Pfab, R; Köppler, H; Parwaresch, R; Pfreundschuh, M; Havemann, K (2002). Randomized study to evaluate the use of high-dose therapy as part of primary treatment for "aggressive" lymphoma. Journal of Clinical Oncology, 20(22):4413-4419.

Gerlitz, O; Basler, K (2002). Wingful, an extracellular feedback inhibitor of wingless. Genes and Development, 16(9):1055-1059.

Kramps, T; Peter, O; Brunner, E; Nellen, D; Froesch, B; Chatterjee, S; Murone, M; Züllig, S; Basler, K (2002). Wnt/wingless signaling requires BCL9/legless-mediated recruitment of pygopus to the nuclear beta-catenin-TCF complex. Cell, 109(1):47-60.

2001

Ahmed, S; Alpi, A; Hengartner, M O; Gartner, A (2001). C. elegans RAD-5/CLK-2 defines a new DNA damage checkpoint protein. Current Biology, 11(24):1934-1944.

Trotman, L C; Mosberger, N; Fornerod, M; Stidwill, R P; Greber, U F (2001). Import of adenovirus DNA involves the nuclear pore complex receptor CAN/Nup214 and histone H1. Nature Cell Biology, 3(12):1092-1100.

Kaufmann, S H; Hengartner, M O (2001). Programmed cell death: alive and well in the new millennium. Trends in Cell Biology, 11(12):526-534.

Biehlmaier, O; Neuhauss, S C F; Kohler, K (2001). Onset and time course of apoptosis in the developing zebrafish retina. Cell and Tissue Research, 306(2):199-207.

McGregor, A P; Shaw, P J; Hancock, J M; Bopp, D; Hediger, M; Wratten, N S; Dover, G A (2001). Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution. Evolution and Development, 3(6):397-407.

Hasson, P; Müller, B; Basler, K; Paroush, Z (2001). Brinker requires two corepressors for maximal and versatile repression in Dpp signalling. The EMBO Journal, 20(20):5725-5736.

Gumienny, T L; Brugnera, E; Tosello-Trampont, A C; Kinchen, J M; Haney, L B; Nishiwaki, K; Walk, S F; Nemergut, M E; Macara, I G; Francis, R; Schedl, T; Qin, Y; Van Aelst, L; Hengartner, M O; Ravichandran, K S (2001). CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration. Cell, 107(1):27-41.

Villanueva, A; Lozano, J; Morales, A; Lin, X; Deng, X; Hengartner, M O; Kolesnick, R N (2001). jkk-1 and mek-1 regulate body movement coordination and response to heavy metals through jnk-1 in Caenorhabditis elegans. The EMBO Journal, 20(18):5114-5128.

Chamoun, Z; Mann, R K; Nellen, D; von Kessler, D P; Bellotto, M; Beachy, P A; Basler, K (2001). Skinny hedgehog, an acyltransferase required for palmitoylation and activity of the hedgehog signal. Science, 393(5537):2080-2084.

Hoeppner, D J; Hengartner, M O; Schnabel, R (2001). Engulfment genes cooperate with ced-3 to promote cell death in Caenorhabditis elegans. Nature, 412(6843):202-206.

Saydam, N; Georgiev, O; Nakano, M Y; Greber, U F; Schaffner, W (2001). Nucleo-cytoplasmic trafficking of metal-regulatory transcription factor 1 is regulated by diverse stress signals. Journal of Biological Chemistry, 276(27):25487-25495.

Hengartner, M O (2001). Apoptosis. DNA destroyers. Nature, 412(6842):27-29.

Perrin, F E; Rathjen, F G; Stoeckli, E T (2001). Distinct subpopulations of sensory afferents require F11 or axonin-1 for growth to their target layers within the spinal cord of the chick. Neuron, 30(3):707-723.

Gumienny, T L; Hengartner, M O (2001). How the worm removes corpses: the nematode C. elegans as a model system to study engulfment. Cell Death and Differentiation, 8(6):564-568.

Gnuegge, L; Schmid, S; Neuhauss, S C F (2001). Analysis of the activity-deprived zebrafish mutant macho reveals an essential requirement of neuronal activity for the development of a fine-grained visuotopic map. Journal of Neuroscience, 21(10):3542-3548.

Hediger, M; Niessen, M; Wimmer, E A; Dübendorfer, A; Bopp, D (2001). Genetic transformation of the housefly Musca domestica with the lepidopteran derived transposon piggyBac. Insect Molecular Biology, 10(2):113-119.

Bopp, D (2001). Merging sex and position. BioEssays, 23(4):304-306.

Suomalainen, M; Nakano, M Y; Boucke, K; Keller, S; Greber, U F (2001). Adenovirus-activated PKA and p38/MAPK pathways boost microtubule-mediated nuclear targeting of virus. The EMBO Journal, 20(6):1310-1319.

Méthot, N; Basler, K (2001). An absolute requirement for Cubitus interruptus in Hedgehog signaling. Development, 128(5):733-742.

Hengartner, M O (2001). Apoptosis: corralling the corpses. Cell, 104(3):325-328.

Berset, T; Froehli Hoier, E; Battu, G; Canevascini, S; Hajnal, A (2001). Notch inhibition of RAS signaling through MAP kinase phosphatase LIP-1 during C. elegans vulval development. Science, 291(5506):1055-1058.

Sergeev, P; Streit, A; Heller, A; Steinmann-Zwicky, M (2001). The Drosophila dorsoventral determinant PIPE contains ten copies of a variable domain homologous to mammalian heparan sulfate 2-sulfotransferase. Developmental Dynamics, 220(2):122-132.

Janzer, B; Steinmann-Zwicky, M (2001). Cell-autonomous and somatic signals control sex-specific gene expression in XY germ cells of Drosophila. Mechanisms of Development, 100(1):3-13.

Ebbinghaus, C; Al-Jaibaji, A; Operschall, E; Schöffel, A; Peter, I; Greber, U F; Hemmi, S (2001). Functional and selective targeting of adenovirus to high-affinity Fcgamma receptor I-positive cells by using a bispecific hybrid adapter. Journal of Virology, 75(1):480-489.

Samuel, A D; Murthy, V N; Hengartner, M O (2001). Calcium dynamics during fertilization in C. elegans. BMC Developmental Biology, 1:8.

Bentz, M; Barth, T F; Brüderlein, S; Bock, D; Schwerer, M J; Baudis, M; Joos, S; Viardot, A; Feller, A C; Müller-Hermelink, H K; Lichter, P; Döhner, H; Möller, P (2001). Gain of chromosome arm 9p is characteristic of primary mediastinal B-cell lymphoma (MBL): comprehensive molecular cytogenetic analysis and presentation of a novel MBL cell line. Genes, Chromosomes & Cancer, 30(4):393-401.

Wessendorf, S; Lichter, P; Schwänen, C; Fritz, B; Baudis, M; Walenta, K; Kloess, M; Döhner, H; Bentz, M (2001). Potential of chromosomal and matrix-based comparative genomic hybridization for molecular diagnostics in lymphomas. Annals of Hematology, 80 (S 3):B35-B37.

2000

Chung, S; Gumienny, T L; Hengartner, M O; Driscoll, M (2000). A common set of engulfment genes mediates removal of both apoptotic and necrotic cell corpses in C. elegans. Nature Cell Biology, 2(12):931-937.

Sivasankaran, R; Vigano, M A; Müller, B; Affolter, M; Basler, K (2000). Direct transcriptional control of the Dpp target omb by the DNA binding protein Brinker. The EMBO Journal, 19(22):6162-6172.

Hengartner, M O (2000). The biochemistry of apoptosis. Nature, 407(6805):770-776.

Marty, T; Müller, B; Basler, K; Affolter, M (2000). Schnurri mediates Dpp-dependent repression of brinker transcription. Nature Cell Biology, 2(10):745-749.

Méthot, N; Basler, K (2000). Suppressor of fused opposes hedgehog signal transduction by impeding nuclear accumulation of the activator form of Cubitus interruptus. Development, 127(18):4001-4010.

Zou, Y; Stoeckli, E T; Chen, H; Tessier-Lavigne, M (2000). Squeezing axons out of the gray matter: a role for slit and semaphorin proteins from midline and ventral spinal cord. Cell, 102(3):363-375.

Waterbury, J A; Horabin, J I; Bopp, D; Schedl, P (2000). Sex determination in the Drosophila germline is dictated by the sexual identity of the surrounding soma. Genetics, 155(4):1741-1756.

Nakano, M Y; Boucke, K; Suomalainen, M; Stidwill, R P; Greber, U F (2000). The first step of adenovirus type 2 disassembly occurs at the cell surface, independently of endocytosis and escape to the cytosol. Journal of Virology, 74(15):7085-7095.

Müller, B; Basler, K (2000). The repressor and activator forms of Cubitus interruptus control Hedgehog target genes through common generic gli-binding sites. Development, 127(14):2999-3007.

Rick, J M; Horschke, I; Neuhauss, S C F (2000). Optokinetic behavior is reversed in achiasmatic mutant zebrafish larvae. Current Biology, 10(10):595-598.

Fitzli, D; Stoeckli, E T; Kunz, S; Siribour, K; Rader, C; Kunz, B; Kozlov, S V; Buchstaller, A; Lane, R P; Suter, D M; Dreyer, W J; Sonderegger, P (2000). A direct interaction of axonin-1 with NgCAM-related cell adhesion molecule (NrCAM) results in guidance, but not growth of commissural axons. Journal of Cell Biology, 149(4):951-968.

Stidwill, R P; Greber, U F (2000). Intracellular Virus Trafficking Reveals Physiological Characteristics of the Cytoskeleton. News in Physiological Sciences, 15(2):67-71.

Fröhli-Hoier, E; Mohler, W A; Kim, S K; Hajnal, A (2000). The Caenorhabditis elegans APC-related gene apr-1 is required for epithelial cell migration and Hox gene expression. Genes and Development, 14(7):874-886.

Su, H P; Brugnera, E; Van Criekinge, W; Smits, E; Hengartner, M; Bogaert, T; Ravichandran, K S (2000). Identification and characterization of a dimerization domain in CED-6, an adapter protein involved in engulfment of apoptotic cells. Journal of Biological Chemistry, 275(13):9542-9549.

Gartner, A; Milstein, S; Ahmed, S; Hodgkin, J; Hengartner, M O (2000). A conserved checkpoint pathway mediates DNA damage--induced apoptosis and cell cycle arrest in C. elegans. Molecular Cell, 5(3):435-443.

Sivasankaran, R; Calleja, M; Morata, G; Basler, K (2000). The Wingless target gene Dfz3 encodes a new member of the Drosophila Frizzled family. Mechanisms of Development, 91(1-2):427-431.

Dahmann, C; Basler, K (2000). Opposing transcriptional outputs of Hedgehog signaling and engrailed control compartmental cell sorting at the Drosophila A/P boundary. Cell, 100(4):411-422.

Nakano, M Y; Greber, U F (2000). Quantitative microscopy of fluorescent adenovirus entry. Journal of Structural Biology, 129(1):57-68.

Chen, H; Bagri, A; Zupicich, J A; Zou, Y; Stoeckli, E T; Pleasure, S J; Lowenstein, D H; Skarnes, W C; Chédotal, A; Tessier-Lavigne, M (2000). Neuropilin-2 regulates the development of selective cranial and sensory nerves and hippocampal mossy fiber projections. Neuron, 25(1):43-56.

Perrin, F E; Stoeckli, E T (2000). Use of lipophilic dyes in studies of axonal pathfinding in vivo. Microscopy Research and Technique, 48(1):25-31.

Hengartner, M O; Bryant, J A (2000). Apoptotic cell death: from worms to wombats ... but what about the weeds? Symposia of the Society for Experimental Biology, 52:1-12.

Hofmann, E R; Milstein, S; Hengartner, M O (2000). DNA-damage-induced checkpoint pathways in the nematode Caenorhabditis elegans. Cold Spring Harbor Symposia on Quantitative Biology, 64:467-473.

von Zelewsky, T; Palladino, F; Brunschwig, K; Tobler, H; Hajnal, A; Müller, F (2000). The C. elegans Mi-2 chromatin-remodelling proteins function in vulval cell fate determination. Development, 127(24):5277-5284.

1999

Burke, R; Nellen, D; Bellotto, M; Hafen, E; Senti, K A; Dickson, B J; Basler, K (1999). Dispatched, a novel sterol-sensing domain protein dedicated to the release of cholesterol-modified hedgehog from signaling cells. Cell, 99(7):803-815.

Bopp, D; Schütt, C; Puro, J; Huang, H; Nöthiger, R (1999). Recombination and disjunction in female germ cells of Drosophila depend on the germline activity of the gene sex-lethal. Development, 126(24):5785-5794.

Liu, Q A; Hengartner, M O (1999). Human CED-6 encodes a functional homologue of the Caenorhabditis elegans engulfment protein CED-6. Current Biology, 9(22):1347-1350.

Neuhauss, S C F; Biehlmaier, O; Seeliger, M W; Das, T; Kohler, K; Harris, W A; Baier, H (1999). Genetic disorders of vision revealed by a behavioral screen of 400 essential loci in zebrafish. Journal of Neuroscience, 19(19):8603-8615.

Geisler, R; Rauch, G J; Baier, H; van Bebber, F; Bross, L; Dekens, M P; Finger, K; Fricke, C; Gates, M A; Geiger, H; Geiger-Rudolph, S; Gilmour, D; Glaser, S; Gnügge, L; Habeck, H; Hingst, K; Holley, S; Keenan, J; Kirn, A; Knaut, H; Lashkari, D; Maderspacher, F; Martyn, U; Neuhauss, S C F; Neumann, C; Nicolson, T; Pelegri, F; Ray, R; Rick, J M; Roehl, H; Roeser, T; Schauerte, H E; Schier, A F; Schönberger, U; Schönthaler, H B; Schulte-Merker, S; Seydler, C; Talbot, W S; Weiler, C; Nüsslein-Volhard, C; Haffter, P (1999). A radiation hybrid map of the zebrafish genome. Nature Genetics, 23(1):86-89.

Dahmann, C; Basler, K (1999). Compartment boundaries: at the edge of development. Trends in Genetics, 15(8):320-326.

Morata, G; Basler, K (1999). Cells in search of a signal. Nature Cell Biology, 1(3):E60-E61.

Burstyn-Cohen, T; Tzarfaty, V; Frumkin, A; Feinstein, Y; Stoeckli, E T; Klar, A (1999). F-Spondin is required for accurate pathfinding of commissural axons at the floor plate. Neuron, 23(2):233-246.

Fraser, A G; James, C; Evan, G I; Hengartner, M O (1999). Caenorhabditis elegans inhibitor of apoptosis protein (IAP) homologue BIR-1 plays a conserved role in cytokinesis. Current Biology, 9(6):292-301.

Méthot, N; Basler, K (1999). Hedgehog controls limb development by regulating the activities of distinct transcriptional activator and repressor forms of Cubitus interruptus. Cell, 96(6):819-831.

Suomalainen, M; Nakano, M Y; Keller, S; Boucke, K; Stidwill, R P; Greber, U F (1999). Microtubule-dependent plus- and minus end-directed motilities are competing processes for nuclear targeting of adenovirus. Journal of Cell Biology, 144(4):657-672.

Brunner, E; Brunner, D; Fu, W; Hafen, E; Basler, K (1999). The dominant mutation Glazed is a gain-of-function allele of wingless that, similar to loss of APC, interferes with normal eye development. Developmental Biology, 206(2):178-188.

Gumienny, T L; Lambie, E; Hartwieg, E; Horvitz, H R; Hengartner, M O (1999). Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. Development, 126(5):1011-1022.

Liu, Y; Hengartner, M O; Herr, W (1999). Selected elements of herpes simplex virus accessory factor HCF are highly conserved in Caenorhabditis elegans. Molecular and Cellular Biology, 19(1):909-915.

von Mering, C; Basler, K (1999). Distinct and regulated activities of human Gli proteins in Drosophila. Current Biology, 9(22):1319-1322.

Hengartner, M O (1999). Programmed cell death in the nematode C. elegans. Recent Progress in Hormone Research, 54:213-222.

Liu, Q A; Hengartner, M O (1999). The molecular mechanism of programmed cell death in C. elegans. Annals of the New York Academy of Sciences, 887:92-104.

1998

Drummond, I A; Majumdar, A; Hentschel, H; Elger, M; Solnica-Krezel, L; Schier, A F; Neuhauss, S C F; Stemple, D L; Zwartkruis, F; Rangini, Z; Driever, W; Fishman, M C (1998). Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development, 125(23):4655-4667.

Marlow, F; Zwartkruis, F; Malicki, J; Neuhauss, S C F; Abbas, L; Weaver, M; Driever, W; Solnica-Krezel, L (1998). Functional interactions of genes mediating convergent extension, knypek and trilobite, during the partitioning of the eye primordium in zebrafish. Developmental Biology, 203(2):382-399.

Schweizer, L; Basler, K (1998). Drosophila ciD encodes a hybrid Pangolin/Cubitus interruptus protein that diverts the Wingless into the Hedgehog signaling pathway. Mechanisms of Development, 78(1-2):141-151.

Greber, U F (1998). Virus assembly and disassembly: the adenovirus cysteine protease as a trigger factor. Reviews in Medical Virology, 8(4):213-222.

Hengartner, M (1998). Apoptosis. Death by crowd control. Science, 281(5381):1298-1299.

Liu, Q A; Hengartner, M O (1998). Candidate adaptor protein CED-6 promotes the engulfment of apoptotic cells in C. elegans. Cell, 93(6):961-972.

Lin, X; Hengartner, M O; Kolesnick, R N (1998). Caenorhabditis elegans contains two distinct acid sphingomyelinases. Journal of Biological Chemistry, 273(23):14374-14379.

Heller, A; Steinmann-Zwicky, M (1998). In Drosophila, female gonadal cells repress male-specific gene expression in XX germ cells. Mechanisms of Development, 73(2):203-209.

Meise, M; Hilfiker-Kleiner, D; Dübendorfer, A; Brunner, C; Nöthiger, R; Bopp, D (1998). Sex-lethal, the master sex-determining gene in Drosophila, is not sex-specifically regulated in Musca domestica. Development, 125(8):1487-1494.

Saccone, G; Peluso, I; Artiaco, D; Giordano, E; Bopp, D; Polito, L C (1998). The Ceratitis capitata homologue of the Drosophila sex-determining gene sex-lethal is structurally conserved, but not sex-specifically regulated. Development, 125(8):1495-1500.

Heller, A; Steinmann-Zwicky, M (1998). No premature gene expression in germ cells of embryos deriving from nos females. Mechanisms of Development, 72(1-2):169-173.

Gutch, M J; Flint, A J; Keller, J; Tonks, N K; Hengartner, M O (1998). The Caenorhabditis elegans SH2 domain-containing protein tyrosine phosphatase PTP-2 participates in signal transduction during oogenesis and vulval development. Genes and Development, 12(4):571-585.

Stoeckli, E T; Landmesser, L T (1998). Axon guidance at choice points. Current Opinion in Neurobiology, 8(1):73-79.

Hengartner, M O (1998). Apoptosis. Death cycle and Swiss army knives. Nature, 391(666):441-442.

Talbot, W S; Egan, E S; Gates, M A; Walker, C; Ullmann, B; Neuhauss, S C F; Kimmel, C B; Postlethwait, J H (1998). Genetic analysis of chromosomal rearrangements in the cyclops region of the zebrafish genome. Genetics, 148(1):373-380.

1997

Peter, M E; Heufelder, A E; Hengartner, M O (1997). Advances in apoptosis research. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 94(24):12736-12737.

Stoeckli, E T (1997). Molecular mechanisms of growth cone guidance: stop and go? Cell and Tissue Research, 290(2):441-449.

Lee, R Y; Lobel, L; Hengartner, M; Horvitz, H R; Avery, L (1997). Mutations in the alpha1 subunit of an L-type voltage-activated Ca2+ channel cause myotonia in Caenorhabditis elegans. The EMBO Journal, 16(20):6066-6076.

Greber, U F; Suomalainen, M; Stidwill, R P; Boucke, K; Ebersold, M W; Helenius, A (1997). The role of the nuclear pore complex in adenovirus DNA entry. The EMBO Journal, 16(19):5998-6007.

Hengartner, M O (1997). Apoptosis. CED-4 is a stranger no more. Nature, 388(664):714-715.

Hengartner, M O (1997). Genetic control of programmed cell death and aging in the nematode Caenorhabditis elegans. Experimental Gerontology, 32(4-5):363-374.

Birge, R; Hengartner, M; Lockshin, R; Zakeri, Z (1997). DATELINE: New York--The Cell Death Society's 'Mechanisms of cell death'. Queens College of CUNY, Flushing, New York, 12 October, 1996. Cell Death and Differentiation, 4(4):341-342.

Fazeli, A; Dickinson, S L; Hermiston, M L; Tighe, R V; Steen, R G; Small, C G; Stoeckli, E T; Keino-Masu, K; Masu, M; Rayburn, H; Simons, J; Bronson, R T; Gordon, J I; Tessier-Lavigne, M; Weinberg, R A (1997). Phenotype of mice lacking functional Deleted in colorectal cancer (Dcc) gene. Nature, 386(6627):796-804.

Spector, M S; Desnoyers, S; Hoeppner, D J; Hengartner, M O (1997). Interaction between the C. elegans cell-death regulators CED-9 and CED-4. Nature, 385(6617):653-656.

Stoeckli, E T; Sonderegger, P; Pollerberg, G E; Landmesser, L T (1997). Interference with axonin-1 and NrCAM interactions unmasks a floor-plate activity inhibitory for commissural axons. Neuron, 18(2):209-221.

Burke, R; Basler, K (1997). Hedgehog signaling in Drosophila eye and limb development - conserved machinery, divergent roles? Current Opinion in Neurobiology, 7(1):55-61.

Schier, A F; Neuhauss, S C F; Helde, K A; Talbot, W S; Driever, W (1997). The one-eyed pinhead gene functions in mesoderm and endoderm formation in zebrafish and interacts with no tail. Development, 124(2):327-342.

Weber, R G; Boström, J; Wolter, M; Baudis, M; Collins, V P; Reifenberger, G; Lichter, P (1997). Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: toward a genetic model of meningioma progression. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 94(26):14719-14724.

Hengartner, M O (1997). Apoptosis and the shape of death. Genesis, 21(4):245-248.

Desnoyers, S; Hengartner, M O (1997). Genetics of apoptosis. Advances in Pharmacology, 41:35-56.

Werner, C A; Döhner, H; Joos, S; Trümper, L H; Baudis, M; Barth, T F; Ott, G; Möller, P; Lichter, P; Bentz, M (1997). High-level DNA amplifications are common genetic aberrations in B-cell neoplasms. American Journal of Pathology, 151(2):335-342.

Hajnal, A; Whitfield, C W; Kim, S K (1997). Inhibition of Caenorhabditis elegans vulval induction by gap-1 and by let-23 receptor tyrosine kinase. Genes and Development, 11(20):2715-2728.

Spector, M S; Hengartner, M O (1997). Orderly dismantling of a cell. Apoptosis, 2(3):343-346.

1996

Driever, W; Solnica-Krezel, L; Schier, A F; Neuhauss, S C F; Malicki, J; Stemple, D L; Stainier, D Y; Zwartkruis, F J T; Abdelilah, S; Rangini, Z; Belak, J; Boggs, C (1996). A genetic screen for mutations affecting embryogenesis in zebrafish. Development, 123:47-46.

Solnica-Krezel, L; Stemple, D L; Mountcastle-Shah, E; Rangini, Z; Neuhauss, S C F; Malicki, J; Schier, A F; Stainier, D Y; Zwartkruis, F J T; Abdelilah, S; Driever, W (1996). Mutations affecting cell fates and cellular rearrangements during gastrulation in zebrafish. Development, 123:67-80.

Neuhauss, S C F; Solnica-Krezel, L; Schier, A F; Zwartkruis, F J T; Stemple, D L; Malicki, J; Abdelilah, S; Stainier, D Y; Driever, W (1996). Mutations affecting craniofacial development in zebrafish. Development, 123:357-367.

Stemple, D L; Solnica-Krezel, L; Zwartkruis, F J T; Neuhauss, S C F; Schier, A F; Malicki, J; Stainier, D Y; Abdelilah, S; Rangini, Z; Mountcastle-Shah, E; Driever, W (1996). Mutations affecting development of the notochord in zebrafish. Development, 123:117-128.

Malicki, J; Schier, A F; Solnica-Krezel, L; Stemple, D L; Neuhauss, S C F; Stainier, D Y; Abdelilah, S; Rangini, Z; Zwartkruis, F; Driever, W (1996). Mutations affecting development of the zebrafish ear. Development, 123:275-283.

Malicki, J; Neuhauss, S C F; Schier, A F; Solnica-Krezel, L; Stemple, D L; Stainier, D Y; Abdelilah, S; Zwartkruis, F J T; Rangini, Z; Driever, W (1996). Mutations affecting development of the zebrafish retina. Development, 123(UNSPEC):263-273.

Pack, M; Solnica-Krezel, L; Malicki, J; Neuhauss, S C F; Schier, A F; Stemple, D L; Driever, W; Fishman, M C (1996). Mutations affecting development of zebrafish digestive organs. Development, 123(UNSPECIFIE):321-328.

Abdelilah, S; Mountcastle-Shah, E; Harvey, M; Solnica-Krezel, L; Schier, A F; Stemple, D L; Malicki, J; Neuhauss, S C F; Zwartkruis, F J T; Stainier, D Y; Rangini, Z; Driever, W (1996). Mutations affecting neural survival in the zebrafish Danio rerio. Development, 123(1):217-227.

Schier, A F; Neuhauss, S C F; Harvey, M; Malicki, J; Solnica-Krezel, L; Stainier, D Y; Zwartkruis, F J T; Abdelilah, S; Stemple, D L; Rangini, Z; Yang, H; Driever, W (1996). Mutations affecting the development of the embryonic zebrafish brain. Development, 123(UNSPECIFIE):165-178.

Stainier, D Y; Fouquet, B; Chen, J N; Warren, K S; Weinstein, B M; Meiler, S E; Mohideen, M A; Neuhauss, S C F; Solnica-Krezel, L; Schier, A F; Zwartkruis, F J T; Stemple, D L; Malicki, J; Driever, W; Fishman, M C (1996). Mutations affecting the formation and function of the cardiovascular system in the zebrafish embryo. Development, 123(UNSPECIFIE):285-292.

Staab, S; Heller, A; Steinmann-Zwicky, M (1996). Somatic sex-determining signals act on XX germ cells in Drosophila embryos. Development, 122(12):4065-4071.

Zecca, M; Basler, K; Struhl, G (1996). Direct and long-range action of a wingless morphogen gradient. Cell, 87(5):833-844.

Burke, R; Basler, K (1996). Hedgehog-dependent patterning in the Drosophila eye can occur in the absence of Dpp signaling. Developmental Biology, 179(2):360-368.

Metzstein, M M; Hengartner, M O; Tsung, N; Ellis, R E; Horvitz, H R (1996). Transcriptional regulator of programmed cell death encoded by Caenorhabditis elegans gene ces-2. Nature, 382(6591):545-547.

Stoeckli, E T; Ziegler, U; Bleiker, A J; Groscurth, P; Sonderegger, P (1996). Clustering and functional cooperation of Ng-CAM and axonin-1 in the substratum-contact area of growth cones. Developmental Biology, 177(1):15-29.

Page, A P; MacNiven, K; Hengartner, M O (1996). Cloning and biochemical characterization of the cyclophilin homologues from the free-living nematode Caenorhabditis elegans. Biochemical Journal, 317(1):179-185.

Burke, R; Basler, K (1996). Dpp receptors are autonomously required for cell proliferation in the entire developing Drosophila wing. Development, 122(7):2261-2269.

Domínguez, M; Brunner, M; Hafen, E; Basler, K (1996). Sending and receiving the hedgehog signal: control by the Drosophila Gli protein Cubitus interruptus. Science, 272(5268):1621-1625.

Nellen, D; Burke, R; Struhl, G; Basler, K (1996). Direct and long-range action of a DPP morphogen gradient. Cell, 85(3):357-368.

Greber, U F; Kasamatsu, H (1996). Nuclear targeting of SV40 and adenovirus. Trends in Cell Biology, 6(5):189-195.

Greber, U F; Webster, P; Weber, J; Helenius, A (1996). The role of the adenovirus protease on virus entry into cells. The EMBO Journal, 15(8):1766-1777.

Hoeppner, D J; Hengartner, M O; Fisher, D E (1996). Programmed cell death: from development to disease. Biochimica et Biophysica Acta, 1242(3):217-220.

Bopp, D; Calhoun, G; Horabin, J I; Samuels, M; Schedl, P (1996). Sex-specific control of Sex-lethal is a conserved mechanism for sex determination in the genus Drosophila. Development, 122(3):971-982.

Hengartner, M O (1996). Programmed cell death in invertebrates. Current Opinion in Genetics & Development, 6(1):34-38.

Hoskins, R; Hajnal, A F; Harp, S A; Kim, S K (1996). The C. elegans vulval induction gene l