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2023

Vintschger, Ella; Kraemer, Dennis; Joset, Pascal; Horn, Anselm H C; Rauch, Anita; Sticht, Heinrich; Bachmann-Gagescu, Ruxandra (2023). Challenges for the implementation of next generation sequencing-based expanded carrier screening: Lessons learned from the ciliopathies. European Journal of Human Genetics, 31(8):953-961.

Alves, Victoria Cunha; Figueiro-Silva, Joana; Ferrer, Isidre; Carro, Eva (2023). Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer’s disease. Cellular and Molecular Life Sciences, 80(8):196.

Fan, Zheng; Ardicoglu, Raphaela; Batavia, Aashil A; Rust, Ruslan; von Ziegler, Lukas; Waag, Rebecca; Zhang, Jing; Desgeorges, Thibaut; Sturman, Oliver; Dang, Hairuo; Weber, Rebecca; Roszkowski, Martin; Moor, Andreas E; Schwab, Martin E; Germain, Pierre-Luc; Bohacek, Johannes; De Bock, Katrien (2023). The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions. Angiogenesis, 26(3):385-407.

Vladimirov, Nikita; Voigt, Fabian F; Naert, Thomas; Araujo, Gabriela R; Cai, Ruiyao; Reuss, Anna Maria; Zhao, Shan; Schmid, Patricia; Hildebrand, Sven; Schaettin, Martina; Groos, Dominik; Mateos, José María; Bethge, Philipp; Yamamoto, Taiyo; Aerne, Valentino; Roebroeck, Alard; Ertürk, Ali; Aguzzi, Adriano; Ziegler, Urs; Stoeckli, Esther; Baudis, Laura; Lienkamp, Soeren S; Helmchen, Fritjof (2023). The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples. www.biorxiv.org: BioRxiv.

Asadollahi, Reza; Delvendahl, Igor; Muff, Rebecca; Tan, Ge; Rodríguez, Daymé González; Turan, Soeren; Russo, Martina; Oneda, Beatrice; Joset, Pascal; Boonsawat, Paranchai; Masood, Rahim; Mocera, Martina; Ivanovski, Ivan; Baumer Wolz, Alessandra; Bachmann-Gagescu, Ruxandra; Schlapbach, Ralph; Rehrauer, Hubert; Steindl, Katharina; Begemann, Anaïs; Reis, André; Winkler, Jürgen; Winner, Beate; Müller, Martin; Rauch, Anita (2023). Pathogenic SCN2A variants cause early-stage dysfunction in patient-derived neurons. Human Molecular Genetics, 32(13):2192-2204.

Blackburn, Patrick R; Ebstein, Frédéric; Hsieh, Tzung-Chien; Motta, Marialetizia; Radio, Francesca Clementina; Herkert, Johanna C; Rinne, Tuula; Thiffault, Isabelle; Rapp, Michele; Alders, Mariel; Maas, Saskia; Gérard, Bénédicte; Smol, Thomas; Vincent-Delorme, Catherine; Cogné, Benjamin; Isidor, Bertrand; Vincent, Marie; Bachmann-Gagescu, Ruxandra; Rauch, Anita; Joset, Pascal; Ferrero, Giovanni Battista; Ciolfi, Andrea; Husson, Thomas; Guerrot, Anne-Marie; Bacino, Carlos; Macmurdo, Colleen; Thompson, Stephanie S; Rosenfeld, Jill A; Faivre, Laurence; Mau-Them, Frederic Tran; et al (2023). Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. medRxiv 23290941, Cold Spring Harbor Laboratory.

Petkidis, Anthony; Andriasyan, Vardan; Greber, Urs F (2023). Label-free microscopy for virus infections. Microscopy, 72(3):204-212.

Fazilaty, Hassan (2023). Restoration of embryonic gene expression patterns in tissue regeneration and disease. Nature Reviews. Molecular Cell Biology, 24(6):375-376.

Martín-González, Natalia; Gómez-González, Alfonso; Hernando-Pérez, Mercedes; Bauer, Michael; Greber, Urs F; San Martín, Carmen; de Pablo, Pedro J (2023). Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles. Science Advances, 9(14):eade9910.

Carrero, Laura; Antequera, Desireé; Alcalde, Ignacio; Megías, Diego; Figueiro-Silva, Joana; Merayo-Lloves, Jesús; Municio, Cristins; Carro, Eva (2023). Disturbed circadian rhythm and retinal degeneration in a mouse model of Alzheimer’s disease. Acta Neuropathologica Communications, 11(1):55.

Voigt, Fabian F; Reuss, Anna Maria; Naert, Thomas; Hildebrand, Sven; Schaettin, Martina; Hotz, Adriana L; Whitehead, Lachlan; Bahl, Armin; Neuhauss, Stephan C F; Roebroeck, Alard; Stoeckli, Esther T; Lienkamp, Soeren S; Aguzzi, Adriano; Helmchen, Fritjof (2023). Reflective multi-immersion microscope objectives inspired by the Schmidt telescope. Nature Biotechnology:Epub ahead of print.

Gurtner, Alessandra; Borrelli, Costanza; Gonzalez-Perez, Ignacio; Bach, Karsten; Acar, Ilhan E; Núñez, Nicolás G; Crepaz, Daniel; Handler, Kristina; Vu, Vivian P; Lafzi, Atefeh; Stirm, Kristin; Raju, Deeksha; Gschwend, Julia; Basler, Konrad; Schneider, Christoph; Slack, Emma; Valenta, Tomas; Becher, Burkhard; Krebs, Philippe; Moor, Andreas E; Arnold, Isabelle C (2023). Active eosinophils regulate host defense and immune responses in colitis. Nature, 615(7950):151-157.

Ladewig, Markus S; Jacobsen, Julius O B; Wagner, Alex H; Danis, Daniel; El Kassaby, Baha; Gargano, Michael; Groza, Tudor; Baudis, Michael; Steinhaus, Robin; Seelow, Dominik; Bechrakis, Nikolaos E; Mungall, Christopher J; Schofield, Paul N; Elemento, Olivier; Smith, Lindsay; McMurry, Julie A; Munoz‐Torres, Monica; Haendel, Melissa A; Robinson, Peter N (2023). GA4GH Phenopackets: A Practical Introduction. Advanced Genetics, 4(1):2200016.

Doncheva, Nadezhda T; Morris, John H; Holze, Henrietta; Kirsch, Rebecca; Nastou, Katerina C; Cuesta-Astroz, Yesid; Rattei, Thomas; Szklarczyk, Damian; von Mering, Christian; Jensen, Lars J (2023). Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research, 22(2):637-646.

Hiatt, Susan M; Trajkova, Slavica; Sebastiano, Matteo Rossi; Partridge, E Christopher; et al; Bachmann-Gagescu, Ruxandra; Rauch, Anita (2023). Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype. American Journal of Human Genetics, 110(2):215-227.

Laganenka, Leanid; Lee, Jae-Woo; Malfertheiner, Lukas; Dieterich, Cora Lisbeth; Fuchs, Lea; Piel, Jörn; von Mering, Christian; Sourjik, Victor; Hardt, Wolf-Dietrich (2023). Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nature Microbiology, 8(2):204-217.

Moret, Michael; Pachon Angona, Irene; Cotos, Leandro; Yan, Shen; Atz, Kenneth; Brunner, Cyrill; Baumgartner, Martin; Grisoni, Francesca; Schneider, Gisbert (2023). Leveraging molecular structure and bioactivity with chemical language models for de novo drug design. Nature Communications, 14(1):114.

Szklarczyk, Damian; Kirsch, Rebecca; Koutrouli, Mikaela; Nastou, Katerina; Mehryary, Farrokh; Hachilif, Radja; Gable, Annika L; Fang, Tao; Doncheva, Nadezhda T; Pyysalo, Sampo; Bork, Peer; Jensen, Lars J; von Mering, Christian (2023). The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research, 51(D1):D638-D646.

Hernández-Plaza, Ana; Szklarczyk, Damian; Botas, Jorge; Cantalapiedra, Carlos P; Giner-Lamia, Joaquín; Mende, Daniel R; Kirsch, Rebecca; Rattei, Thomas; Letunic, Ivica; Jensen, Lars J; Bork, Peer; von Mering, Christian; Huerta-Cepas, Jaime (2023). eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research, 51(D1):D389-D394.

Fullam, Anthony; Letunic, Ivica; Schmidt, Thomas S B; Ducarmon, Quinten R; Karcher, Nicolai; Khedkar, Supriya; Kuhn, Michael; Larralde, Martin; Maistrenko, Oleksandr M; Malfertheiner, Lukas; Milanese, Alessio; Rodrigues, Joao Frederico Matias; Sanchis-López, Claudia; Schudoma, Christian; Szklarczyk, Damian; Sunagawa, Shinichi; Zeller, Georg; Huerta-Cepas, Jaime; von Mering, Christian; Bork, Peer; Mende, Daniel R (2023). proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research, 51(D1):D760-D766.

Häfliger, Janine; Schwarzfischer, Marlene; Atrott, Kirstin; Stanzel, Claudia; Morsy, Yasser; Wawrzyniak, Marcin; Lang, Silvia; Valenta, Tomas; Basler, Konrad; Rogler, Gerhard; Scharl, Michael; Spalinger, Marianne R (2023). Glycoprotein (GP)96 is essential for maintaining intestinal epithelial architecture by supporting its self-renewal capacity. Cellular and Molecular Gastroenterology and Hepatology, 15(3):717-739.

Dumoulin, Alexandre; Stoeckli, Esther T (2023). Looking for Guidance - Models and Methods to Study Axonal Navigation. Neuroscience, 508:30-39.

Karakulak, Tülay; Szklarczyk, Damian; Saylan, Cemil Can; Moch, Holger; von Mering, Christian; Kahraman, Abdullah (2023). CanIsoNet: a database to study the functional impact of isoform switching events in diseases. Bioinformatics advances, 3(1):vbad050.

Huang, Qingyao; Baudis, Michael (2023). Candidate targets of copy number deletion events across 17 cancer types. Frontiers in Genetics, 13:1017657.

2022

Neuhauss, Stephan C F (2022). Editorial: Insights in methods and model organisms: 2021. Frontiers in Molecular Neuroscience, 15:1104424.

Maruyama, Takamitsu; Hasegawa, Daigaku; Valenta, Tomas; Haigh, Jody; Bouchard, Maxime; Basler, Konrad; Hsu, Wei (2022). GATA3 mediates nonclassical β-catenin signaling in skeletal cell fate determination and ectopic chondrogenesis. Science Advances, 8(48):eadd6172.

Prummel, Karin D; Crowell, Helena L; Nieuwenhuize, Susan; Brombacher, Eline C; Daetwyler, Stephan; Soneson, Charlotte; Kresoja-Rakic, Jelena; Kocere, Agnese; Ronner, Manuel; Ernst, Alexander; Labbaf, Zahra; Clouthier, David E; Firulli, Anthony B; Sánchez-Iranzo, Héctor; Naganathan, Sundar R; O’Rourke, Rebecca; Raz, Erez; Mercader, Nadia; Burger, Alexa; Felley-Bosco, Emanuela; Huisken, Jan; Robinson, Mark D; Mosimann, Christian (2022). Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma. Nature Communications, 13(1):1677.

Masek, Markus; Etard, Christelle; Hofmann, Claudia; Hülsmeier, Andreas J; Zang, Jingjing; Takamiya, Masanari; Gesemann, Matthias; Neuhauss, Stephan C F; Hornemann, Thorsten; Strähle, Uwe; Bachmann-Gagescu, Ruxandra (2022). Loss of the Bardet-Biedl protein Bbs1 alters photoreceptor outer segment protein and lipid composition. Nature Communications, 13:1282.

Möller, Katrin; Brambach, Max; Villani, Ambra; Gallo, Elisa; Gilmour, Darren; Peri, Francesca (2022). A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo. eLife, 11:e82094.

Pelisek, Jaroslav; Reutersberg, Benedikt; Greber, Urs F; Zimmermann, Alexander (2022). Vascular dysfunction in COVID-19 patients: update on SARS-CoV-2 infection of endothelial cells and the role of long non-coding RNAs. Clinical Science, 136(21):1571-1590.

Durrer, Jan; Agrawal, Prajwal; Ozgul, Ali; Neuhauss, Stephan C F; Nama, Nitesh; Ahmed, Daniel (2022). A robot-assisted acoustofluidic end effector. Nature Communications, 13:6370.

Olszewski, Dominik; Georgi, Fanny; Murer, Luca; Andriasyan, Vardan; Kuttler, Fabien; Petkidis, Anthony; Witte, Robert; Yakimovich, Artur; Fischer, Lucy; Rozanova, Alina; Yamauchi, Yohei; Turcatti, Gerardo; Greber, Urs F (2022). High-content, arrayed compound screens with rhinovirus, influenza A virus and herpes simplex virus infections. Scientific Data, 9:610.

Greber, Urs F; Suomalainen, Maarit (2022). Adenovirus Entry - Stability, Uncoating and Nuclear Import. Molecular Microbiology, 118(4):309-320.

Myren‐Svelstad, Sverre; Jamali, Ahmed; Ophus, Sunniva S; D'gama, Percival P; Ostenrath, Anna M; Mutlu, Aytac Kadir; Hoffshagen, Helene Homme; Hotz, Adriana L; Neuhauss, Stephan C F; Jurisch‐Yaksi, Nathalie; Yaksi, Emre (2022). Elevated photic response is followed by a rapid decay and depressed state in ictogenic networks. Epilepsia, 63(10):2543-2560.

Cordovado, Amélie; Schaettin, Martina; Jeanne, Médéric; et al; Stoeckli, Esther T (2022). SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance. Human Molecular Genetics, 31(19):3325-3340.

Gable, Annika L; Szklarczyk, Damian; Lyon, David; Matias Rodrigues, João F; von Mering, Christian (2022). Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments. Briefings in Bioinformatics, 23(5):bbac355.

Özsoy, Çağla; Hotz, Adriana L; Rieser, Nicolas N; Chen, Zhenyue; Deán-Ben, Xosé Luís; Neuhauss, Stephan C F; Razansky, Daniel (2022). Volumetric optoacoustic neurobehavioral tracking of epileptic seizures in freely-swimming zebrafish larvae. Frontiers in Molecular Neuroscience, 15:1004518.

Krieg, Carsten; Weber, Lukas M; Fosso, Bruno; Marzano, Marinella; Hardiman, Gary; Olcina, Monica M; Domingo, Enric; El Aidy, Sahar; Mallah, Khalil; Robinson, Mark D; Guglietta, Silvia (2022). Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy. Journal for ImmunoTherapy of Cancer, 10(9):e004717.

Dean, Kevin M; Chakraborty, Tonmoy; Daetwyler, Stephan; Lin, Jinlong; Garrelts, Gerard; M'Saad, Ons; Mekbib, Hannahmariam T; Voigt, Fabian F; Schaettin, Martina; Stoeckli, Esther T; Helmchen, Fritjof; Bewersdorf, Joerg; Fiolka, Reto (2022). Isotropic imaging across spatial scales with axially swept light-sheet microscopy. Nature Protocols, 17(9):2025-2053.

Caviglia, Sara; Unterweger, Iris A; Gasiūnaitė, Akvilė; Vanoosthuyse, Alexandre E; Cutrale, Francesco; Trinh, Le A; Fraser, Scott E; Neuhauss, Stephan C F; Ober, Elke A (2022). FRaeppli: a multispectral imaging toolbox for cell tracing and dense tissue analysis in zebrafish. Development, 149(16):dev199615.

Kramer, Bernhard A; del Castillo, Jacobo Sarabia; Pelkmans, Lucas (2022). Multimodal perception links cellular state to decision-making in single cells. Science, 377(6606):642-648.

Berry, Scott; Pelkmans, Lucas (2022). Mechanisms of cellular mRNA transcript homeostasis. Trends in Cell Biology, 32(8):655-668.

COVID-19 Host Genetics Initiative (2022). A first update on mapping the human genetic architecture of COVID-19. Nature, 608(7921):E1-E10.

Huang, Qingyao; Baudis, Michael (2022). Candidate targets of copy number deletion events across 17 cancer types. bioRxiv 498080, Cold Spring Harbor Laboratory.

Rusterholz, Tamara D S; Hofmann, Claudia; Bachmann-Gagescu, Ruxandra (2022). Insights Gained From Zebrafish Models for the Ciliopathy Joubert Syndrome. Frontiers in Genetics, 13:939527.

Kannan, Abhilash; Suomalainen, Maarit; Volle, Romain; Bauer, Michael; Amsler, Marco; Trinh, Hung V; Vavassori, Stefano; Schmid, Jana Pachlopnik; Vilhena, Guilherme; Marin-Gonzalez, Alberto; Pérez, Rubén; Franceschini, Andrea; von Mering, Christian; Hemmi, Silvio; Greber, Urs F (2022). Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects. Viruses, 14(7):1407.

Baeriswyl, Thomas; Schaettin, Martina; Leoni, Simone; Dumoulin, Alexandre; Stoeckli, Esther T (2022). Endoglycan Regulates Purkinje Cell Migration by Balancing Cell-Cell Adhesion. Frontiers in Neuroscience, 16:894962.

Mytlis, Avishag; Kumar, Vineet; Qiu, Tao; Deis, Rachael; Hart, Neta; Levy, Karine; Masek, Markus; Shawahny, Amal; Ahmad, Adam; Eitan, Hagai; Nather, Farouq; Adar-Levor, Shai; Birnbaum, Ramon Y; Elia, Natalie; Bachmann-Gagescu, Ruxandra; Roy, Sudipto; Elkouby, Yaniv M (2022). Control of meiotic chromosomal bouquet and germ cell morphogenesis by the zygotene cilium. Science, 376:6599.

Orjuela, Stephany; Parker, Hannah R; Sajibu, Sija; Cereatti, Fabrizio; Sauter, Matthias; Buffoli, Federico; Robinson, Mark D; Marra, Giancarlo (2022). Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing. Epigenetics, 17(6):677-694.

Berry, Scott; Müller, Micha; Rai, Arpan; Pelkmans, Lucas (2022). Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Systems, 13(6):454-470.e15.

Tuschl, Karin; White, Richard J; Trivedi, Chintan; Valdivia, Leonardo E; Niklaus, Stephanie; Bianco, Isaac H; Dadswell, Chris; González-Méndez, Ramón; Sealy, Ian M; Neuhauss, Stephan C F; Houart, Corinne; Rihel, Jason; Wilson, Stephen W; Busch-Nentwich, Elisabeth M (2022). Loss of slc39a14 causes simultaneous manganese hypersensitivity and deficiency in zebrafish. Disease Models & Mechanisms, 15(6):dmm044594.

Jacobsen, Julius O B; Baudis, Michael; Baynam, Gareth S; Beckmann, Jacques S; Beltran, Sergi; Buske, Orion J; et al (2022). The GA4GH Phenopacket schema defines a computable representation of clinical data. Nature Biotechnology, 40(6):817-820.

Fergin, Aleksandra; Boesch, Gabriel; Greter, Nadja R; Berger, Simon; Hajnal, Alex (2022). Tissue-specific inhibition of protein sumoylation uncovers diverse SUMO functions during C. elegans vulval development. PLoS Genetics, 18(6):e1009978.

Righelli, Dario; Weber, Lukas M; Crowell, Helena L; Pardo, Brenda; Collado-Torres, Leonardo; Ghazanfar, Shila; Lun, Aaron T L; Hicks, Stephanie C; Risso, Davide (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11):3128-3131.

Soutschek, Michael; Germade, Tomás; Germain, Pierre-Luc; Schratt, Gerhard (2022). enrichMiR predicts functionally relevant microRNAs based on target collections. Nucleic Acids Research, 50(W1):W280-W289.

Vaccaro, Giuseppe; Dumoulin, Alexandre; Zuñiga, Nikole R; Bandtlow, Christine E; Stoeckli, Esther T (2022). The Nogo-66 Receptors NgR1 and NgR3 Are Required for Commissural Axon Pathfinding. Journal of Neuroscience, 42(20):4087-4100.

Böddeker, Thomas J; Rosowski, Kathryn A; Berchtold, Doris; Emmanouilidis, Leonidas; Han, Yaning; Allain, Frédéric H T; Style, Robert W; Pelkmans, Lucas; Dufresne, Eric R (2022). Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18(5):571-578.

Soutschek, Michael; Gross, Fridolin; Schratt, Gerhard; Germain, Pierre-Luc (2022). scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction. Bioinformatics, 38(9):2466-2473.

Čaušević, Senka; Tackmann, Janko; Sentchilo, Vladimir; von Mering, Christian; van der Meer, Jan Roelof (2022). Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation. mSystems, 7(2):e0016022.

von Ziegler, Lukas M; Floriou-Servou, Amalia; Waag, Rebecca; Das Gupta, Rebecca R; Sturman, Oliver; Gapp, Katharina; Maat, Christina A; Kockmann, Tobias; Lin, Han-Yu; Duss, Sian N; Privitera, Mattia; Hinte, Laura; von Meyenn, Ferdinand; Zeilhofer, Hanns Ulrich; Germain, Pierre-Luc; Bohacek, Johannes (2022). Multiomic profiling of the acute stress response in the mouse hippocampus. Nature Communications, 13:1824.

Böddeker, Thomas J; Rosowski, Kathryn A; Berchtold, Doris; Emmanouilidis, Leonidas; Han, Yaning; Allain, Frédéric H T; Style, Robert W; Pelkmans, Lucas; Dufresne, Eric R (2022). Publisher Correction: Non-specific adhesive forces between filaments and membraneless organelles. Nature Physics, 18(5):601.

Rambla, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Tim; Fromont, Lauren A; Navarro, Arcadi; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita; Spalding, John D; Törnroos, Juha; Vasallo, Claudia; Veal, Colin D; Brookes, Anthony J (2022). Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond. Human Mutation, 43(6):791-799.

Rubinstein, Mark P; Williams, Cameron; Mart, Caroline; Beall, Jonathan; MacPherson, Linda; Azar, Joseph; Swiderska-Syn, Marzena; Manca, Paolo; Gibney, Barry C; Robinson, Mark D; Krieg, Carsten; Hill, Elizabeth G; Taha, Sharif A; Rock, Amy D; Lee, John H; Soon-Shiong, Patrick; Wrangle, John (2022). Phase I Trial Characterizing the Pharmacokinetic Profile of N-803, a Chimeric IL-15 Superagonist, in Healthy Volunteers. Journal of Immunology, 208(6):1362-1370.

Wagner, Johanna; Masek, Markus; Jacobs, Andrea; Soneson, Charlotte; Sivapatham, Sujana; Damond, Nicolas; de Souza, Natalie; Robinson, Mark D; Bodenmiller, Bernd (2022). Mass cytometric and transcriptomic profiling of epithelial-mesenchymal transitions in human mammary cell lines. Scientific Data, 9:44-60.

Lattmann, Evelyn; Deng, Ting; Walser, Michael; Widmer, Patrizia; Rexha-Lambert, Charlotte; Prasad, Vibhu; Eichhoff, Ossia; Daube, Michael; Dummer, Reinhard; Levesque, Mitchell P; Hajnal, Alex (2022). A DNA replication-independent function of pre-replication complex genes during cell invasion in C. elegans. PLoS Biology, 20(2):e3001317.

Murer, Luca; Petkidis, Anthony; Vallet, Thomas; Vignuzzi, Marco; Greber, Urs F (2022). Chemical evolution of Rhinovirus identifies capsid-destabilizing mutations driving low pH-independent genome uncoating. Journal of Virology, 96(2):e0106021.

Hotz, Adriana L; Jamali, Ahmed; Rieser, Nicolas N; Niklaus, Stephanie; Aydin, Ecem; Myren‐Svelstad, Sverre; Lalla, Laetitia; Jurisch‐Yaksi, Nathalie; Yaksi, Emre; Neuhauss, Stephan C F (2022). Loss of glutamate transporter eaat2a leads to aberrant neuronal excitability, recurrent epileptic seizures, and basal hypoactivity. Glia, 70:196-214.

Spiri, Silvan; Berger, Simon; Mereu, Louisa; DeMello, Andrew; Hajnal, Alex (2022). Reciprocal EGFR signaling in the anchor cell ensures precise inter-organ connection during Caenorhabditis elegans vulval morphogenesis. Development, 149(1):dev199900.

Ratti, Emanuele; Germain, Pierre-Luc (2022). A relic of design: against proper functions in biology. Biology & Philosophy, 37:27.

Burja, Blaž; Paul, Dominique; Tastanova, Aizhan; Edalat, Sam Galen; Gerber, Reto; Houtman, Miranda; Elhai, Muriel; Bürki, Kristina; Staeger, Ramon; Restivo, Gaetana; Lang, Ramon; Sodin-Šemrl, Snežna; Lakota, Katja; Tomšič, Matija; Levesque, Mitchell P; Distler, Oliver; Rotar, Žiga; Robinson, Mark D; Frank-Bertoncelj, Mojca (2022). An Optimized Tissue Dissociation Protocol for Single-Cell RNA Sequencing Analysis of Fresh and Cultured Human Skin Biopsies. Frontiers in Cell and Developmental Biology, 10:872688.

Volle, Romain; Murer, Luca; Petkidis, Anthony; Andriasyan, Vardan; Savi, Alessandro; Bircher, Cornelia; Meili, Nicole; Fischer, Lucy; Sequeira, Daniela Policarpo; Mark, Daniela Katharina; Gomez-Gonzalez, Alfonso; Greber, Urs F (2022). Methylene blue, Mycophenolic acid, Posaconazole, and Niclosamide inhibit SARS-CoV-2 Omicron variant BA.1 infection of human airway epithelial organoids. Current Research in Microbial Sciences, 3:100158.

Sikorski, Johannes; Baumgartner, Vanessa; Birkhofer, Klaus; Boeddinghaus, Runa S; Bunk, Boyke; Fischer, Markus; Fösel, Bärbel U; Friedrich, Michael W; Göker, Markus; Hölzel, Norbert; Huang, Sixing; Huber, Katharina J; Kandeler, Ellen; Klaus, Valentin H; Kleinebecker, Till; Marhan, Sven; von Mering, Christian; Oelmann, Yvonne; Prati, Daniel; Regan, Kathleen M; Richter-Heitmann, Tim; Rodrigues, João F Matias; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Schurig, Elisabeth; Solly, Emily F; Wolters, Volkmar; Overmann, Jörg (2022). The Evolution of Ecological Diversity in Acidobacteria. Frontiers in Microbiology, 13:715637.

2021

Bauer, Michael; Gomez-Gonzalez, Alfonso; Suomalainen, Maarit; Schilling, Nicolas; Hemmi, Silvio; Greber, Urs F (2021). A viral ubiquitination switch attenuates innate immunity and triggers nuclear import of virion DNA and infection. Science Advances, 7(51):eabl7150.

Bieri, Manuela; Hendrickx, Rodinde; Bauer, Michael; Yu, Bin; Jetzer, Tania; Dreier, Birgit; Mittl, Peer R E; Sobek, Jens; Plückthun, Andreas; Greber, Urs F; Hemmi, Silvio (2021). The RGD-binding integrins αvβ6 and αvβ8 are receptors for mouse adenovirus-1 and -3 infection. PLoS Pathogens, 17(12):e1010083.

Bai, Yu; Caussinus, Emmanuel; Leo, Stefano; Bosshardt, Fritz; Myachina, Faina; Rot, Gregor; Robinson, Mark D; Lehner, Christian F (2021). A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. BMC Genomics, 22:771.

Milosavljevic, Stefan; Kuo, Tony; Decarli, Samuele; Mohn, Lucas; Sese, Jun; Shimizu, Kentaro K; Shimizu-Inatsugi, Rie; Robinson, Mark D (2021). ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw. BMC Genomics, 22:547.

Gerber, Reto; Robinson, Mark D (2021). Censcyt: censored covariates in differential abundance analysis in cytometry. BMC Bioinformatics, 22(1):235.

Garbelli, Marco; Neuhauss, Stephan C F (2021). Color vision: Parsing spectral information for opponent color vision in the fish retina. Current Biology, 31(23):R1525-R1527.

Borrelli, Costanza; Valenta, Tomas; Handler, Kristina; Vélez, Karelia; Gurtner, Alessandra; Moro, Giulia; Lafzi, Atefeh; De Vargas Roditi, Laura; Hausmann, George; Arnold, Isabelle C; Moor, Andreas E; Basler, Konrad (2021). Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells. Nature Communications, 12:1368.

Schmeing, Stephan; Robinson, Mark D (2021). ReSeq simulates realistic Illumina high-throughput sequencing data. Genome Biology, 22:67.

Sahadevan, Sonu; Hembach, Katharina M; Tantardini, Elena; Pérez-Berlanga, Manuela; Hruska-Plochan, Marian; Megat, Salim; Weber, Julien; Schwarz, Petra; Dupuis, Luc; Robinson, Mark D; De Rossi, Pierre; Polymenidou, Magdalini (2021). Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nature Communications, 12(1):3027.

Greber, Urs F (2021). Two years into COVID-19 – Lessons in SARS-CoV-2 and a perspective from papers in FEBS Letters. FEBS letters, 595(23):2847-2853.

COVID-19 Host Genetics Initiative (2021). Mapping the human genetic architecture of COVID-19. Nature, 600(7889):472-477.

Landínez Macías, María Paula; Urwyler, Olivier (2021). The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System. Frontiers in Molecular Neuroscience, 7:755686.

Jacobsen, Julius O B; Baudis, Michael; Baynam, Gareth S; Beckmann, Jacques S; Beltran, Sergi; et al (2021). The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine. medRxiv 21266944, Cold Spring Harbor Laboratory.

Glasauer, Stella M K; Triemer, Therese; Neef, Anne B; Neuhauss, Stephan C F; Luedtke, Nathan W (2021). DNA template strand segregation in developing zebrafish. Cell Chemical Biology, 28(11):1638-1647.e4.

Rehm, Heidi L; Page, Angela J H; Smith, Lindsay; Adams, Jeremy B; Alterovitz, Gil; Babb, Lawrence J; Barkley, Maxmillian P; Baudis, Michael; Beauvais, Michael J S; Beck, Tim; Beckmann, Jacques S; Beltran, Sergi; Bernick, David; Bernier, Alexander; Bonfield, James K; Boughtwood, Tiffany F; Bourque, Guillaume; Bowers, Sarion R; Brookes, Anthony J; Brudno, Michael; Brush, Matthew H; Bujold, David; Burdett, Tony; Buske, Orion J; Cabili, Moran N; Cameron, Daniel L; Carroll, Robert J; Casas-Silva, Esmeralda; Chakravarty, Debyani; Chaudhari, Bimal P; et al (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell, 1(2):100029.

Thorogood, Adrian; Rehm, Heidi L; Goodhand, Peter; Page, Angela J H; Joly, Yann; Baudis, Michael; Rambla, Jordi; Navarro, Arcadi; Nyronen, Tommi H; Linden, Mikael; Dove, Edward S; Fiume, Marc; Brudno, Michael; Cline, Melissa S; Birney, Ewan (2021). International federation of genomic medicine databases using GA4GH standards. Cell, 1(2):100032.

Wagner, Alex H; Babb, Lawrence; Alterovitz, Gil; Baudis, Michael; et al (2021). The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification. Cell Genomics, 1(2):100027.

Schlegel, Domino K; Ramkumar, Srinivasagan; von Lintig, Johannes; Neuhauss, Stephan C F (2021). Disturbed retinoid metabolism upon loss of rlbp1a impairs cone function and leads to subretinal lipid deposits and photoreceptor degeneration in the zebrafish retina. eLife, 10:e71473.

Wong, Mie; Gilmour, Darren (2021). Going your own way: Self-guidance mechanisms in cell migration. Current Opinion in Cell Biology, 72:116-123.

Wälchli, Thomas; Bisschop, Jeroen; Miettinen, Arttu; Ulmann-Schuler, Alexandra; Hintermüller, Christoph; Meyer, Eric P; Krucker, Thomas; Wälchli, Regula; Monnier, Philippe P; Carmeliet, Peter; Vogel, Johannes; Stampanoni, Marco (2021). Hierarchical imaging and computational analysis of three-dimensional vascular network architecture in the entire postnatal and adult mouse brain. Nature Protocols, 16(10):4564-4610.

Zang, Jingjing; Gesemann, Matthias; Keim, Jennifer; Samardzija, Marijana; Grimm, Christian; Neuhauss, Stephan C F (2021). Circadian regulation of vertebrate cone photoreceptor function. eLife, 10:e68903.

Prasad, Vibhu; Greber, Urs F (2021). The endoplasmic reticulum unfolded protein response – homeostasis, cell death and evolution in virus infections. FEMS Microbiology Reviews, 45(5):fuab016.

Zang, Jingjing; Neuhauss, Stephan C F (2021). Biochemistry and physiology of zebrafish photoreceptors. Pflügers Archiv : European Journal of Physiology, 473(9):1569-1585.

Doumpas, Nikolaos; Söderholm, Simon; Narula, Smarth; Moreira, Steven; Doble, Bradley W; Cantù, Claudio; Basler, Konrad (2021). TCF/LEF regulation of the topologically associated domain ADI promotes mESCs to exit the pluripotent ground state. Cell Reports, 36(11):109705.

Landínez-Macías, María; Qi, Weihong; Bratus-Neuenschwander, Anna; Müller, Martin; Urwyler, Olivier (2021). The RNA-binding protein Musashi controls axon compartment-specific synaptic connectivity through ptp69D mRNA poly(A)-tailing. Cell Reports, 36(11):109713.

Suomalainen, Maarit; Greber, Urs F (2021). Virus Infection Variability by Single-Cell Profiling. Viruses, 13(8):1568.

Dulla, Kalyan; Slijkerman, Ralph; van Diepen, Hester C; Albert, Silvia; Dona, Margo; et al; Zang, Jingjing; Neuhauss, Stephan C F (2021). Antisense oligonucleotide-based treatment of retinitis pigmentosa caused by USH2A exon 13 mutations. Molecular Therapy, 29(8):2441-2455.

Diener, Johanna; Baggiolini, Arianna; Pernebrink, Mattias; Dalcher, Damian; Lerra, Luigi; Cheng, Phil F; Varum, Sandra; Häusel, Jessica; Stierli, Salome; Treier, Mathias; Studer, Lorenz; Basler, Konrad; Levesque, Mitchell P; Dummer, Reinhard; Santoro, Raffaella; Cantù, Claudio; Sommer, Lukas (2021). Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4. Nature Communications, 12(1):5056.

Fazilaty, Hassan; Brügger, Michael David; Valenta, Tomas; Szczerba, Barbara M; Berkova, Linda; Doumpas, Nikolaos; Hausmann, George; Scharl, Michael; Basler, Konrad (2021). Tracing colonic embryonic transcriptional profiles and their reactivation upon intestinal damage. Cell Reports, 36(5):109484.

Huang, Qingyao; Carrio-Cordo, Paula; Gao, Bo; Paloots, Rahel; Baudis, Michael (2021). The Progenetix oncogenomic resource in 2021. bioRxiv 428237v2, Cold Spring Harbor Laboratory.

Huang, Qingyao; Carrio-Cordo, Paula; Gao, Bo; Paloots, Rahel; Baudis, Michael (2021). The Progenetix oncogenomic resource in 2021. Database, 2021:baab043.

Berger, Simon; Spiri, Silvan; deMello, Andrew; Hajnal, Alex (2021). Microfluidic-based imaging of complete Caenorhabditis elegans larval development. Development, 148(18):online.

Masek, Markus; Etard, Christelle; Hofmann, Claudia; Hülsmeier, Andreas J; Zang, Jingjing; Takamiya, Masanari; Gesemann, Matthias; Neuhauss, Stephan; Hornemann, Thorsten; Strähle, Uwe; Bachmann-Gagescu, Ruxandra (2021). The Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition. ArXiv.org 452166, Cornell University.

Kita, Katarzyna; Albergaria, Catarina; Machado, Ana S; Carey, Megan R; Müller, Martin; Delvendahl, Igor (2021). GluA4 facilitates cerebellar expansion coding and enables associative memory formation. eLife, 10:online.

Dumoulin, Alexandre; Zuñiga, Nikole R; Stoeckli, Esther T (2021). Axon guidance at the spinal cord midline-A live imaging perspective. Journal of Comparative Neurology, 529(10):2517-2538.

Zareba, Joanna; Peri, Francesca (2021). Microglial ‘fat shaming’ in development and disease. Current Opinion in Cell Biology, 73:105-109.

Höller, Christian; Schnoering, Gabriel; Eghlidi, Hadi; Suomalainen, Maarit; Greber, Urs F; Poulikakos, Dimos (2021). On-chip transporting arresting and characterizing individual nano-objects in biological ionic liquids. Science Advances, 7(27):eabd8758.

Greber, Urs F; Gomez-Gonzalez, Alfonso (2021). Adenovirus – a blueprint for gene delivery. Current Opinion in Virology, 48:49-56.

Lütge, Almut; Zyprych-Walczak, Joanna; Brykczynska Kunzmann, Urszula; Crowell, Helena L; Calini, Daniela; Malhotra, Dheeraj; Soneson, Charlotte; Robinson, Mark D (2021). CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life science alliance, 4(6):e202001004.

Andriasyan, Vardan; Yakimovich, Artur; Petkidis, Anthony; Georgi, Fanny; Witte, Robert; Puntener, Daniel; Greber, Urs F (2021). Microscopy deep learning predicts virus infections and reveals mechanics of lytic-infected cells. iScience, 24(6):102543.

Gao, Bo; Baudis, Michael (2021). Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Frontiers in Genetics, 12:654887.

Huang, Ruizhu; Soneson, Charlotte; Germain, Pierre-Luc; Schmidt, Thomas S B; von Mering, Christian; Robinson, Mark D (2021). treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses. Genome Biology, 22:157.

Dmitrijeva, Marija; Kahlert, Christian R; Feigelman, Rounak; Kleiner, Rebekka L; Nolte, Oliver; Albrich, Werner C; Baty, Florent; von Mering, Christian (2021). Strain-Resolved Dynamics of the Lung Microbiome in Patients with Cystic Fibrosis. mBio, 12(2):e02863-20.

Seyffert, Michael; Georgi, Fanny; Tobler, Kurt; Bourqui, Laurent; Anfossi, Michela; Michaelsen, Kevin; Vogt, Bernd; Greber, Urs F; Fraefel, Cornel (2021). The HSV-1 Transcription Factor ICP4 Confers Liquid-Like Properties to Viral Replication Compartments. International Journal of Molecular Sciences, 22(9):4447.

Viegas, Filipe O; Neuhauss, Stephan C F (2021). A Metabolic Landscape for Maintaining Retina Integrity and Function. Frontiers in Molecular Neuroscience, 14:656000.

Yusifov, Elkhan; Dumoulin, Alexandre; Stoeckli, Esther T (2021). Investigating Primary Cilia during Peripheral Nervous System Formation. International Journal of Molecular Sciences, 22(6):3176.

Baeriswyl, Thomas; Dumoulin, Alexandre; Schaettin, Martina; Tsapara, Georgia; Niederkofler, Vera; Helbling, Denise; Avilés, Evelyn; Frei, Jeannine A; Wilson, Nicole H; Gesemann, Matthias; Kunz, Beat; Stoeckli, Esther T (2021). Endoglycan plays a role in axon guidance by modulating cell adhesion. eLife, 10:e64767.

Carrio-Cordo, Paula; Baudis, Michael (2021). Copy number variant heterogeneity among cancer types reflects inconsistent concordance with diagnostic classifications. bioRxiv 433348, Cold Spring Harbor Laboratory.

Brücher, Dominik; Kirchhammer, Nicole; Smith, Sheena N; Schumacher, Jatina; Schumacher, Nina; Kolibius, Jonas; Freitag, Patrick C; Schmid, Markus; Weiss, Fabian; Keller, Corina; Grove, Melanie; Greber, Urs F; Zippelius, Alfred; Plückthun, Andreas (2021). iMATCH: an integrated modular assembly system for therapeutic combination high-capacity adenovirus gene therapy. Molecular Therapy - Methods & Clinical Development, 20:572-586.

Mytils, Avishag; Kumar, Vineet; Tao, Qiu; Deis, Rachael; Levy, Karine; Masek, Markus; Eitan, Hagai; Nather, Farouq; Shawahny, Amal; Bachmann-Gagescu, Ruxandra; Roy, Sudipto; Elkouby, Yaniv M (2021). Ciliary control of meiotic chromosomal pairing mechanics and germ cell morphogenesis. bioRxiv 430249, Cold Spring Harbor Laboratory.

Bottes, Sara; Jaeger, Baptiste N; Pilz, Gregor-Alexander; Jörg, David J; Cole, John Darby; Kruse, Merit; Harris, Lachlan; Korobeynyk, Vladislav I; Mallona, Izaskun; Helmchen, Fritjof; Guillemot, François; Simons, Benjamin D; Jessberger, Sebastian (2021). Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging. Nature Neuroscience, 24(2):225-233.

Alon, Shahar; Goodwin, Daniel R; Sinha, Anubhav; Wassie, Asmamaw T; Chen, Fei; et al; IMAXT Consortium; Bodenmiller, Bernd; Kuett, L; Tietscher, S; Windhager, Jonas (2021). Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science, 371(6528):eaax2656.

Wagner, Alex H; Babb, Lawrence; Alterovitz, Gil; Baudis, Michael; et al (2021). The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation. bioRxiv 426843, Cold Spring Harbor Laboratory.

Dilshat, Ramile; Fock, Valerie; Kenny, Colin; Gerritsen, Ilse; Lasseur, Romain Maurice Jacques; Travnickova, Jana; Eichhoff, Ossia M; Cerny, Philipp; Möller, Katrin; Sigurbjörnsdóttir, Sara; Kirty, Kritika; Einarsdottir, Berglind Ósk; Cheng, Phil F; Levesque, Mitchell; Cornell, Robert A; Patton, E Elizabeth; Larue, Lionel; de Tayrac, Marie; Magnúsdóttir, Erna; Ögmundsdóttir, Margrét Helga; Steingrimsson, Eirikur (2021). MITF reprograms the extracellular matrix and focal adhesion in melanoma. eLife, 10:e63093.

Mallona, Izaskun; Ilie, Ioana Mariuca; Karemaker, Ino Dominiek; Butz, Stefan; Manzo, Massimiliano; Caflisch, Amedeo; Baubec, Tuncay (2021). Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1):145-157.

Wang, Yuluan; Soneson, Charlotte; Malinowska, Anna L; Laski, Artur; Ghosh, Souvik; Kanitz, Alexander; Gebert, Luca F R; Robinson, Mark D; Hall, Jonathan (2021). MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Nucleic Acids Research, 49(1):25-37.

Szklarczyk, Damian; Gable, Annika L; Nastou, Katerina C; Lyon, David; Kirsch, Rebecca; Pyysalo, Sampo; Doncheva, Nadezhda T; Legeay, Marc; Fang, Tao; Bork, Peer; Jensen, Lars J; von Mering, Christian (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research, 49(D1):D605-D612.

Chevrier, Stéphane; Zurbuchen, Yves; Cervia, Carlo; Adamo, Sarah; Raeber, Miro E; de Souza, Natalie; Sivapatham, Sujana; Jacobs, Andrea; Bachli, Esther; Rudiger, Alain; Stüssi-Helbling, Melina; Huber, Lars C; Schaer, Dominik J; Nilsson, Jakob; Boyman, Onur; Bodenmiller, Bernd (2021). A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Reports Medicine, 2(1):100166.

Germain, Pierre-Luc; Lun, Aaron; Garcia Meixide, Carlos; Macnair, Will; Robinson, Mark D (2021). Doublet identification in single-cell sequencing data using scDblFinder. F1000Research, 10:979.

Gerber, Reto; Robinson, Mark D (2021). pubassistant.ch: consolidating publication profiles of researchers. F1000Research, 10:989.

2020

Marin-Gonzalez, Alberto; Aicart-Ramos, Clara; Marin-Baquero, Mikel; Martín-González, Alejandro; Suomalainen, Maarit; Kannan, Abhilash; Vilhena, J G; Greber, Urs F; Moreno-Herrero, Fernando; Pérez, Rubén (2020). Double-stranded RNA bending by AU-tract sequences. Nucleic Acids Research, 48(22):12917-12928.

Brügger, Michael David; Valenta, Tomas; Fazilaty, Hassan; Hausmann, George; Basler, Konrad (2020). Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis. PLoS Biology, 18(12):e3001032.

Cascione, Luciano; Aresu, Luca; Baudis, Michael; Bertoni, Francesco (2020). DNA Copy Number Changes in Diffuse Large B Cell Lymphomas. Frontiers in Oncology, 10:584095.

Georgi, Fanny; Kuttler, Fabien; Murer, Luca; Andriasyan, Vardan; Witte, Robert; Yakimovich, Artur; Turcatti, Gerardo; Greber, Urs F (2020). A high-content image-based drug screen of clinical compounds against cell transmission of adenovirus. Scientific Data, 7(1):265.

Lang, Judith; Bohn, Patrick; Bhat, Hilal; Jastrow, Holger; Walkenfort, Bernd; Cansiz, Feyza; Fink, Julian; Bauer, Michael; Olszewski, Dominik; Greber, Urs F; et al (2020). Acid ceramidase of macrophages traps herpes simplex virus in multivesicular bodies and protects from severe disease. Nature Communications, 11:1338.

Tiberi, Simone; Robinson, Mark D (2020). BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty. Genome Biology, 21:69.

de Medeiros, Gustavo; Kromm, Dimitri; Balazs, Balint; Norlin, Nils; Günther, Stefan; Izquierdo, Emiliano; Ronchi, Paolo; Komoto, Shinya; Krzic, Uros; Schwab, Yannick; Peri, Francesca; de Renzis, Stefano; Leptin, Maria; Rauzi, Matteo; Hufnagel, Lars (2020). Cell and tissue manipulation with ultrashort infrared laser pulses in light-sheet microscopy. Scientific Reports, 10:1942.

Primo, Pasquale; Meccariello, Angela; Inghilterra, Maria Grazia; Gravina, Andrea; Del Corsano, Giuseppe; Volpe, Gennaro; Sollazzo, Germano; Aceto, Serena; Robinson, Mark D; Salvemini, Marco; Saccone, Giuseppe (2020). Targeting the autosomal Ceratitis capitata transformer gene using Cas9 or dCas9 to masculinize XX individuals without inducing mutations. BMC Genetics, 21(Suppl 2):150.

Crowell, Helena L; Soneson, Charlotte; Germain, Pierre-Luc; Calini, Daniela; Collin, Ludovic; Raposo, Catarina; Malhotra, Dheeraj; Robinson, Mark D (2020). muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data. Nature Communications, 11:6077.

Germain, Pierre-Luc; Sonrel, Anthony; Robinson, Mark D (2020). pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools. Genome Biology, 21(1):227.

Schreier, Verena N; Loehr, Morten O; Deng, Ting; Lattmann, Evelyn; Hajnal, Alex; Neuhauss, Stephan C F; Luedtke, Nathan W (2020). Fluorescent dATP for DNA Synthesis In Vivo. ACS Chemical Biology, 15(11):2996-3003.

Gesemann, Matthias; Neuhauss, Stephan C F (2020). Selective Gene Loss of Visual and Olfactory Guanylyl Cyclase Genes Following the Two Rounds of Vertebrate-Specific Whole-Genome Duplications. Genome Biology and Evolution, 12(11):2153-2167.

Daly, James L; Simonetti, Boris; Klein, Katja; Chen, Kai-En; Williamson, Maia Kavanagh; Antón-Plágaro, Carlos; Shoemark, Deborah K; Simón-Gracia, Lorena; Bauer, Michael; Hollandi, Reka; Greber, Urs F; Horvath, Peter; Sessions, Richard B; Helenius, Ari; Hiscox, Julian A; Teesalu, Tambet; Matthews, David A; Davidson, Andrew D; Collins, Brett M; Cullen, Peter J; Yamauchi, Yohei (2020). Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science, 370(6518):861-865.

Huang, Ruizhu; Soneson, Charlotte; Ernst, Felix G M; Rue-Albrecht, Kevin C; Yu, Guangchuang; Hicks, Stephanie C; Robinson, Mark D (2020). TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research, 9:1246.

Salgado, David; Armean, Irina M; Baudis, Michael; et al (2020). The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research, 9:1229.

Suomalainen, Maarit; Prasad, Vibhu; Kannan, Abhilash; Greber, Urs F (2020). Cell-to-cell and genome-to-genome variability of adenovirus transcription tuned by the cell cycle. Journal of Cell Science:jcs.252544.

Ballesteros-Álvarez, Josué; Dilshat, Ramile; Fock, Valerie; Möller, Katrín; Karl, Ludwig; Larue, Lionel; Ögmundsdóttir, Margrét Helga; Steingrímsson, Eiríkur (2020). MITF and TFEB cross-regulation in melanoma cells. PLoS ONE, 15(9):e0238546.

Kahraman, Abdullah; Karakulak, Tülay; Szklarczyk, Damian; von Mering, Christian (2020). Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network. Scientific Reports, 10:14453.

Saxena, Meera; Kalathur, Ravi KR; Rubinstein, Natalia; Vettiger, Andrea; Sugiyama, Nami; Neutzner, Melanie; Coto-Llerena, Mairene; Kancherla, Venkatesh; Ercan, Caner; Piscuoglio, Salvatore; Fischer, Jonas; Fagiani, Ernesta; Cantù, Claudio; Basler, Konrad; Christofori, Gerhard (2020). A Pygopus 2-histone interaction is critical for cancer cell de-differentiation and progression in malignant breast cancer. Cancer Research, 80(17):3631-3648.

Gao, Bo; Baudis, Michael (2020). Minimum error calibration and normalization for genomic copy number analysis. Genomics, 112(5):3331-3341.

Hanya, Goro; Tackmann, Janko; Sawada, Akiko; Lee, Wanyi; Pokharel, Sanjeeta Sharma; de Castro Maciel, Valdevino Gisele; Toge, Akito; Kuroki, Kota; Otsuka, Ryoma; Mabuchi, Ryoma; Liu, Jie; Hatakeyama, Masaomi; Yamasaki, Eri; von Mering, Christian; Shimizu-Inatsugi, Rie; Hayakawa, Takashi; Shimizu, Kentaro K; Ushida, Kazunari (2020). Fermentation Ability of Gut Microbiota of Wild Japanese Macaques in the Highland and Lowland Yakushima: In Vitro Fermentation Assay and Genetic Analyses. Microbial Ecology, 80(2):459-474.

Georgi, Fanny; Andriasyan, Vardan; Witte, Robert; Murer, Luca; Hemmi, Silvio; Yu, Lisa; Grove, Melanie; Meili, Nicole; Kuttler, Fabien; Yakimovich, Artur; Turcatti, Gerardo; Greber, Urs F (2020). The FDA-approved drug Nelfinavir inhibits lytic cell-free, but not cell-associated non-lytic transmission of human adenovirus. Antimicrobial Agents and Chemotherapy, 64(9):e01002-20.

Hernando-Pérez, Mercedes; Martín-González, Natalia; Pérez-Illana, Marta; Suomalainen, Maarit; Condezo, Gabriela N; Ostapchuk, Philomena; Gallardo, José; Menéndez, Margarita; Greber, Urs F; Hearing, Patrick; de Pablo, Pedro J; San Martín, Carmen (2020). Dynamic competition for hexon binding between core protein VII and lytic protein VI promotes adenovirus maturation and entry. Proceedings of the National Academy of Sciences of the United States of America, 117(24):13699-13707.

Greber, Urs F (2020). Adenoviruses – Infection, pathogenesis and therapy. FEBS letters, 594(12):1818-1827.

Hartmann, Jonas; Wong, Mie; Gallo, Elisa; Gilmour, Darren (2020). An image-based data-driven analysis of cellular architecture in a developing tissue. eLife, 9:e55913.

Mereu, Louisa; Morf, Matthias K; Spiri, Silvan; Gutierrez, Peter; Escobar-Restrepo, Juan M; Daube, Michael; Walser, Michael; Hajnal, Alex (2020). Polarized epidermal growth factor secretion ensures robust vulval cell fate specification in Caenorhabditis elegans. Development, 147(11):dev175760.

Haller, Otto; Kochs, Georg (2020). Mx genes: host determinants controlling influenza virus infection and trans-species transmission. Human Genetics, 139(6-7):695-705.

Chambers, Joseph M; Wingert, Rebecca A (2020). New zebrafish model for monitoring proximal tubule physiology in genetic and acquired renal Fanconi syndromes. Kidney International, 97(6):1097-1099.

Malan-Müller, Stefanie; de Souza, Vladimir B C; Daniels, Willie M U; Seedat, Soraya; Robinson, Mark D; Hemmings, Sîan M J (2020). Shedding Light on the Transcriptomic Dark Matter in Biological Psychiatry: Role of Long Noncoding RNAs in D-cycloserine-Induced Fear Extinction in Posttraumatic Stress Disorder. Omics : a journal of integrative biology, 24(6):352-369.

Georgi, Fanny; Greber, Urs F (2020). The Adenovirus Death Protein – A small membrane protein controls cell lysis and disease. FEBS letters, 594(12):1861-1878.

Chen, Zhiyong; Luciani, Alessandro; Mateos, José María; Barmettler, Gery; Giles, Rachel H; Neuhauss, Stephan C F; Devuyst, Olivier (2020). Transgenic zebrafish modeling low-molecular-weight proteinuria and lysosomal storage diseases. Kidney International, 97(6):1150-1163.

Latour, Brooke L; Van De Weghe, Julie C; Rusterholz, Tamara D S; Letteboer, Stef J F; Gomez, Arianna; Shaheen, Ranad; Gesemann, Matthias; Karamzade, Arezou; Asadollahi, Mostafa; Barroso-Gil, Miguel; Chitre, Manali; Grout, Megan E; van Reeuwijk, Jeroen; van Beersum, Sylvia E C; Miller, Caitlin V; Dempsey, Jennifer C; Morsy, Heba; Bamshad, Michael J; Nickerson, Deborah A; Neuhauss, Stephan C F; Boldt, Karsten; Ueffing, Marius; Keramatipour, Mohammad; Sayer, John A; Alkuraya, Fowzan S; Bachmann-Gagescu, Ruxandra; Roepman, Ronald; Doherty, Dan (2020). Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome. Journal of Clinical Investigation, 130(8):4423-4439.

Borrelli, Costanza; Valenta, Tomas; Handler, Kristina; Vélez, Karelia; Moro, Giulia; Lafzi, Atefeh; de Vargas Roditi, Laura; Hausmann, George; Moor, Andreas E; Basler, Konrad (2020). Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells. bioRxiv 103499, Cold Spring Harbor Laboratory.

Bosch, Pablo Sanchez; Pepperl, Julia; Basler, Konrad (2020). Anchor away – A fast, reliable and reversible technique to inhibit proteins in Drosophila melanogaster. G3 : Genes, Genomes, Genetics, 10(5):1745-1752.

Wong, Mie; Gilmour, Darren (2020). Getting back on track: exploiting canalization to uncover the mechanisms of developmental robustness. Current Opinion in Genetics & Development, 63:53-60.

Prasad, Vibhu; Suomalainen, Maarit; Jasiqi, Yllza; Hemmi, Silvio; Hearing, Patrick; Hosie, Louise; Burgert, Hans-Gerhard; Greber, Urs F (2020). The UPR sensor IRE1α and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections. Nature Communications, 11:1997.

Zimmerli, Dario; Borrelli, Costanza; Jauregi-Miguel, Amaia; Söderholm, Simon; Brütsch, Salome; Doumpas, Nikolaos; Reichmuth, Jan; Murphy-Seiler, Fabienne; Aguet, Michel; Basler, Konrad; Moor, Andreas E; Cantù, Claudio (2020). TBX3 acts as tissue-specific component of the Wnt/β-catenin enhanceosome. bioRxiv 053561, Cold Spring Harbor Laboratory.

Ruffell, Daniela (2020). Coronavirus SARS‐CoV‐2: filtering fact from fiction in the infodemic. FEBS letters, 594(7):1127-1131.

Cannac, Fabien; Qi, Chao; Falschlunger, Julia; Hausmann, George; Basler, Konrad; Korkhov, Volodymyr M (2020). Cryo-EM structure of the hedgehog release protein dispatched. Science Advances, 6(16):eaay7928.

Huang, Qingyao; Baudis, Michael (2020). Enabling population assignment from cancer genomes with SNP2pop. Scientific Reports, 10:4846.

Rai, Arpan; Pelkmans, Lucas (2020). Liquid droplets in the skin. Science, 367(6483):1193-1194.

Deng, Ting; Stempor, Przemyslaw; Appert, Alex; Daube, Michael; Ahringer, Julie; Hajnal, Alex; Lattmann, Evelyn (2020). The Caenorhabditis elegans homolog of the Evi1 proto-oncogene, egl-43, coordinates G1 cell cycle arrest with pro-invasive gene expression during anchor cell invasion. PLoS Genetics, 16(3):e1008470.

Ali, Zaheer; Zang, Jingjing; Lagali, Neil; Schmitner, Nicole; Salvenmoser, Willi; Mukwaya, Anthony; Neuhauss, Stephan C F; Jensen, Lasse D; Kimmel, Robin A (2020). Photoreceptor degeneration accompanies vascular changes in a Zebrafish model of diabetic retinopathy. Investigative Ophthalmology & Visual Science [IOVS], 61(2):43.

Wong, Mie; Newton, Lionel R; Hartmann, Jonas; Hennrich, Marco L; Wachsmuth, Malte; Ronchi, Paolo; Guzmán-Herrera, Alejandra; Schwab, Yannick; Gavin, Anne-Claude; Gilmour, Darren (2020). Dynamic buffering of extracellular chemokine by a dedicated scavenger pathway enables robust adaptation during directed tissue migration. Developmental Cell, 52(4):492-508.e10.

Bruns, Dominique; Gawehn, Erik; Kumar, Karthiga Santhana; Schneider, Petra; Baumgartner, Martin; Schneider, Gisbert (2020). Identification of Synthetic Activators of Cancer Cell Migration by Hybrid Deep Learning. Chembiochem, 21(4):500-507.

Haag, Andrea; Walser, Michael; Henggeler, Adrian; Hajnal, Alex (2020). The CHORD protein CHP-1 regulates EGF receptor trafficking and signaling in C. elegans and in human cells. eLife, 9:e50986.

Straub, Isabelle; Witter, Laurens; Eshra, Abdelmoneim; Hoidis, Miriam; Byczkowicz, Niklas; Maas, Sebastian; Delvendahl, Igor; Dorgans, Kevin; Savier, Elise; Bechmann, Ingo; Krueger, Martin; Isope, Philippe; Hallermann, Stefan (2020). Gradients in the mammalian cerebellar cortex enable Fourier-like transformation and improve storing capacity. eLife, 9:e51771.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793):82-93.

Cianciolo Cosentino, Chiara; Berto, Alessandro; Pelletier, Stéphane; Hari, Michelle; Loffing, Johannes; Neuhauss, Stephan C F; Doye, Valérie (2020). Author correction: Moderate Nucleoporin 133 deficiency leads to glomerular damage in zebrafish. Scientific Reports, 10(1):756.

Konietzka, Jan; Fritz, Maximilian; Spiri, Silvan; McWhirter, Rebecca; Leha, Andreas; Palumbos, Sierra; Costa, Wagner Steuer; Oranth, Alexandra; Gottschalk, Alexander; Miller, David M; Hajnal, Alex; Bringmann, Henrik (2020). Epidermal Growth Factor Signaling Promotes Sleep through a Combined Series and Parallel Neural Circuit. Current Biology, 30(1):1-16.e13.

Knop, Janin; Spilgies, Lisanne M; Rufli, Stefanie; Reinhart, Ramona; Vasilikos, Lazaros; Yabal, Monica; Owsley, Erika; Jost, Philipp J; Marsh, Rebecca A; Wajant, Harald; Robinson, Mark D; Kaufmann, Thomas; Wong, W Wei-Lynn (2020). Correction: TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death and Disease, 11(1):56.

Carrio-Cordo, Paula; Acheson, Elise; Huang, Qingyao; Baudis, Michael (2020). Geographic assessment of cancer genome profiling studies. Database, 2020:baaa009.

Frank, C Andrew; James, Thomas D; Müller, Martin (2020). Homeostatic control of Drosophila neuromuscular junction function. Synapse - Wiley-Blackwell, 74(1):23783-23789.

Carrio-Cordo, Paula; Baudis, Michael (2020). Mountains and Chasms: Surveying the Oncogenomic Publication Landscape. Oncology, 98(Suppl. 6):332-343.

Putora, Paul Martin; Baudis, Michael; Beadle, Beth M; El Naqa, Issam; Giordano, Frank A; Nicolay, Nils H (2020). Oncology Informatics: Status Quo and Outlook. Oncology, 98(Suppl. 6):329-331.

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Crowell, Helena L; Chevrier, Stéphane; Jacobs, Andrea; Sivapatham, Sujana; Bodenmiller, Bernd; Robinson, Mark D; et al; Kölzer, Viktor (2020). An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Research, 9:1263.

Shaul, Merav E; Eyal, Ophir; Guglietta, Silvia; Aloni, Pazzit; Zlotnik, Asaf; Forkosh, Ester; Levy, Liran; Weber, Lukas M; Levin, Yonathan; Pomerantz, Alon; Nechushtan, Hovav; Eruslanov, Evgeniy; Singhal, Sunil; Robinson, Mark D; Krieg, Carsten; Fridlender, Zvi G (2020). Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis. FASEB Journal, 34(3):4204-4218.

Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J; Hicks, Stephanie C; Robinson, Mark D; et al (2020). Eleven grand challenges in single-cell data science. Genome Biology, 21:31.

Tsapara, Georgia; Andermatt, Irwin; Stoeckli, Esther T (2020). Gene Silencing in Chicken Brain Development. In: Sprecher, Simon G. Brain Development. Humana, New York, NY: Springer, 439-456.

Lattmann, Evelyn; Deng, Ting; Hajnal, Alex (2020). To Divide or Invade: A Look Behind the Scenes of the Proliferation-Invasion Interplay in the Caenorhabditis elegans Anchor Cell. Frontiers in Cell and Developmental Biology, 8:616051.

Greber, Urs F (2020). Virale Pandemien - Gedanken aus der Grundlagenforschung. Zürich: Forschung für Leben.

2019

Kramer, Bernhard A; Pelkmans, Lucas (2019). Cellular state determines the multimodal signaling response of single cells. bioRxiv 880930, Cold Spring Harbor Laboratory.

Schlegel, Domino K; Glasauer, Stella M K; Mateos, José M; Barmettler, Gery; Ziegler, Urs; Neuhauss, Stephan C F (2019). A New Zebrafish Model for CACNA2D4-Dysfunction. Investigative Ophthalmology & Visual Science [IOVS], 60(15):5124-5135.

Geirsdottir, Laufey; David, Eyal; Keren-Shaul, Hadas; et al; Peri, Francesca (2019). Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program. Cell, 179(7):1609-1622.e16.

Freyre, Christophe A C; Rauher, Pascal C; Ejsing, Christer S; Klemm, Robin W (2019). MIGA2 Links Mitochondria, the ER, and Lipid Droplets and Promotes De Novo Lipogenesis in Adipocytes. Molecular Cell, 76(5):811-825.e14.

Kabakci, Zeynep; Käppeli, Simon; Cantù, Claudio; Jensen, Lasse D; König, Christiane; Toggweiler, Janine; Gentili, Christian; Ribaudo, Giovanni; Zagotto, Giuseppe; Basler, Konrad; Pinna, Lorenzo A; Cozza, Giorgio; Ferrari, Stefano (2019). Pharmacophore-guided discovery of CDC25 inhibitors causing cell cycle arrest and tumor regression. Scientific Reports, 9(1):1335.

Bauer, Michael; Flatt, Justin W; Seiler, Daria; Cardel, Bettina; Emmenlauer, Mario; Boucke, Karin; Suomalainen, Maarit; Hemmi, Silvio; Greber, Urs F (2019). The E3 Ubiquitin Ligase Mind Bomb 1 Controls Adenovirus Genome Release at the Nuclear Pore Complex. Cell Reports, 29(12):3785-3795.e8.

Heller, Davide; Szklarczyk, Damian; von Mering, Christian (2019). Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies. BMC Bioinformatics, 20(1):228.

Delvendahl, Igor; Kita, Katarzyna; Müller, Martin (2019). Rapid and sustained homeostatic control of presynaptic exocytosis at a central synapse. Proceedings of the National Academy of Sciences of the United States of America, 116(47):23783-23789.

Saunders, Gary; Baudis, Michael; Becker, Regina; Beltran, Sergi; Béroud, Christophe; Birney, Ewan; Brooksbank, Cath; Brunak, Søren; Van den Bulcke, Marc; Drysdale, Rachel; Capella-Gutierrez, Salvador; Flicek, Paul; Florindi, Francesco; Goodhand, Peter; Gut, Ivo; Heringa, Jaap; Holub, Petr; Hooyberghs, Jef; Juty, Nick; Keane, Thomas M; Korbel, Jan O; Lappalainen, Ilkka; Leskosek, Brane; Matthijs, Gert; Mayrhofer, Michaela Th; Metspalu, Andres; Navarro, Arcadi; Newhouse, Steven; Nyrönen, Tommi; Page, Angela; et al (2019). Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics, 20(11):693-701.

Núñez-León, Daniel; Aguirre-Fernández, Gabriel; Steiner, Andrea; Nagashima, Hiroshi; Jensen, Per; Stoeckli, Esther; Schneider, Richard A; Sánchez-Villagra, Marcelo R (2019). Morphological diversity of integumentary traits in fowl domestication: Insights from disparity analysis and embryonic development. Developmental Dynamics, 248(11):1044-1058.

Heimlicher, Maria B; Bächler, Mirjam; Liu, Minghua; Ibeneche-Nnewihe, Chieze; Florin, Ernst-Ludwig; Hoenger, Andreas; Brunner, Damian (2019). Reversible solidification of fission yeast cytoplasm after prolonged nutrient starvation. Journal of Cell Science, 132(21):jcs231688.

Voigt, Fabian F; Kirschenbaum, Daniel; Platonova, Evgenia; Pagès, Stéphane; Campbell, Robert A A; Kastli, Rahel; Schaettin, Martina; Egolf, Ladan; van der Bourg, Alexander; Bethge, Philipp; Haenraets, Karen; Frézel, Noémie; Topilko, Thomas; Perin, Paola; Hillier, Daniel; Hildebrand, Sven; Schueth, Anna; Roebroeck, Alard; Roska, Botond; Stoeckli, Esther T; Pizzala, Roberto; Renier, Nicolas; Zeilhofer, Hanns Ulrich; Karayannis, Theofanis; Ziegler, Urs; Batti, Laura; Holtmaat, Anthony; Lüscher, Christian; Aguzzi, Adriano; Helmchen, Fritjof (2019). The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nature Methods, 16(11):1105-1108.

Robinson, Mark D; Vitek, Olga (2019). Benchmarking comes of age. Genome Biology, 20(1):205.

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

Meccariello, Angela; Salvemini, Marco; Primo, Pasquale; Hall, Brantley; Koskinioti, Panagiota; Dalíková, Martina; Gravina, Andrea; Gucciardino, Michela Anna; Forlenza, Federica; Gregoriou, Maria-Eleni; Ippolito, Domenica; Monti, Simona Maria; Petrella, Valeria; Perrotta, Maryanna Martina; Schmeing, Stephan; Ruggiero, Alessia; Scolari, Francesca; Giordano, Ennio; Tsoumani, Konstantina T; Marec, František; Windbichler, Nikolai; Arunkumar, Kallare P; Bourtzis, Kostas; Mathiopoulos, Kostas D; Ragoussis, Jiannis; Vitagliano, Luigi; Tu, Zhijian; Papathanos, Philippos Aris; Robinson, Mark D; Saccone, Giuseppe (2019). Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. Science, 365(6460):1457-1460.

Tackmann, Janko; Matias Rodrigues, João Frederico; von Mering, Christian (2019). Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data. Cell Systems, 9(3):286-296.e8.

Knop, Janin; Spilgies, Lisanne M; Rufli, Stefanie; Reinhart, Ramona; Vasilikos, Lazaros; Yabal, Monica; Owsley, Erika; Jost, Philipp J; Marsh, Rebecca A; Wajant, Harald; Robinson, Mark D; Kaufmann, Thomas; Wong, W Wei-Lynn (2019). TNFR2 induced priming of the inflammasome leads to a RIPK1-dependent cell death in the absence of XIAP. Cell Death and Disease, 10(10):700.

Choobdar, Sarvenaz; Ahsen, Mehmet E; Crawford, Jake; Tomasoni, Mattia; Fang, Tao; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv; von Mering, C; Subramanian, Aravind; Zhang, Jitao D; Stolovitzky, Gustavo; Kutalik, Zoltán; Lage, Kasper; Slonim, Donna K; Saez-Rodriguez, Julio; Cowen, Lenore J; Bergmann, Sven; Marbach, Daniel (2019). Assessment of network module identification across complex diseases. Nature Methods, 16(9):843-852.

Soneson, Charlotte; Yao, Yao; Bratus-Neuenschwander, Anna; Patrignani, Andrea; Robinson, Mark D; Hussain, Shobbir (2019). A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nature Communications, 10(1):3359.

Van den Berge, Koen; Hembach, Katharina M; Soneson, Charlotte; Tiberi, Simone; Clement, Lieven; Love, Michael I; Patro, Rob; Robinson, Mark D (2019). RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis. Annual Review of Biomedical Data Science, 2(1):139-173.

Son, Jae Hak; Kohlbrenner, Tea; Heinze, Svenia; Beukeboom, Leo W; Bopp, Daniel; Meisel, Richard P (2019). Minimal Effects of Proto-Y Chromosomes on House Fly Gene Expression in Spite of Evidence That Selection Maintains Stable Polygenic Sex Determination. Genetics, 213(1):313-327.

Orjuela, Stephany; Huang, Ruizhu; Hembach, Katharina M; Robinson, Mark D; Soneson, Charlotte (2019). ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data. G3 : Genes, Genomes, Genetics, 9(7):2089-2096.

D'Agati, Gianluca; Cabello, Elena María; Frontzek, Karl; Rushing, Elisabeth J; Klemm, Robin; Robinson, Mark D; White, Richard M; Mosimann, Christian; Burger, Alexa (2019). Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish. Disease Models & Mechanisms, 12(7):dmm039545.

Krattinger, Simon G; Kang, Joohyun; Bräunlich, Stephanie; Boni, Rainer; Chauhan, Harsh; Selter, Liselotte L; Robinson, Mark D; Schmid, Marc W; Wiederhold, Elena; Hensel, Goetz; Kumlehn, Jochen; Sucher, Justine; Martinoia, Enrico; Keller, Beat (2019). Abscisic acid is a substrate of the ABC transporter encoded by the durable wheat disease resistance gene Lr34. New Phytologist, 223(2):853-866.

Weber, Lukas M; Saelens, Wouter; Cannoodt, Robrecht; Soneson, Charlotte; Hapfelmeier, Alexander; Gardner, Paul P; Boulesteix, Anne-Laure; Saeys, Yvan; Robinson, Mark D (2019). Essential guidelines for computational method benchmarking. Genome Biology, 20:125.

Mariani, Samanta Antonella; Li, Zhuan; Rice, Siobhan; Krieg, Carsten; Fragkogianni, Stamatina; Robinson, Mark D; Vink, Chris Sebastiaan; Pollard, Jeffrey William; Dzierzak, Elaine (2019). Pro-inflammatory Aorta-Associated Macrophages Are Involved in Embryonic Development of Hematopoietic Stem Cells. Immunity, 50(6):1439-1452.e5.

Kaiser, Julia; Maibach, Martina; Salpeter, Iris; Hagenbuch, Niels; de Souza, Vladimir B C; Robinson, Mark D; Schwab, Martin E (2019). The Spinal Transcriptome after Cortical Stroke: In Search of Molecular Factors Regulating Spontaneous Recovery in the Spinal Cord. Journal of Neuroscience, 39(24):4714-4726.

Modic, Miha; Grosch, Markus; Rot, Gregor; Schirge, Silvia; Lepko, Tjasa; Yamazaki, Tomohiro; Lee, Flora C Y; Rusha, Ejona; Shaposhnikov, Dmitry; Palo, Michael; Merl-Pham, Juliane; Cacchiarelli, Davide; Rogelj, Boris; Hauck, Stefanie M; von Mering, Christian; Meissner, Alexander; Lickert, Heiko; Hirose, Tetsuro; Ule, Jernej; Drukker, Micha (2019). Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Molecular Cell, 74(5):951-965.e13.

Lun, Xiao-Kang; Szklarczyk, Damian; Gábor, Attila; Dobberstein, Nadine; Zanotelli, Vito Riccardo Tomaso; Saez-Rodriguez, Julio; von Mering, Christian; Bodenmiller, Bernd (2019). Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Molecular Cell, 74(5):1086-1102.e5.

Brunner, Erich; Yagi, Ryohei; Debrunner, Marc; Beck-Schneider, Dezirae; Burger, Alexa; Escher, Eliane; Mosimann, Christian; Hausmann, George; Basler, Konrad (2019). CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Science Alliance, 2(3):e201800267.

Gug, G; Huang, Q; Chiticariu, E; Solovan, C; Baudis, Michael (2019). DNA copy number imbalances in primary cutaneous lymphomas. Journal of the European Academy of Dermatology and Venerology, 33(6):1062-1075.

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

Maxeiner, Sabrina; Grolleman, Judith; Schmid, Tobias; Kammenga, Jan; Hajnal, Alex (2019). The hypoxia-response pathway modulates RAS/MAPK-mediated cell fate decisions in Caenorhabditis elegans. Life Science Alliance, 2(3):e201800255.

Bachmann-Gagescu, Ruxandra; Neuhauss, Stephan C F (2019). The photoreceptor cilium and its diseases. Current Opinion in Genetics & Development, 56:22-33.

Spalinger, Marianne R; Schmidt, Thomas S B; Schwarzfischer, Marlene; Hering, Larissa; Atrott, Kirstin; Lang, Silvia; Gottier, Claudia; Geirnaert, Annelies; Lacroix, Christophe; Dai, Xuezhi; Rawlings, David J; Chan, Andrew C; von Mering, Christian; Rogler, Gerhard; Scharl, Michael (2019). Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner. Journal of Clinical Investigation, 129(6):2527-2541.

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

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

Tackmann, Janko. Wiring the Microbial Web of Earth – New Approaches for Scalable Computational Prediction of Interpretable Microbial Ecosystem Structure. 2019, University of Zurich, Faculty of Science.

Urwyler, Olivier; Izadifar, Azadeh; Vandenbogaerde, Sofie; Sachse, Sonja; Misbaer, Anke; Schmucker, Dietmar (2019). Branch-restricted localization of phosphatase Prl-1 specifies axonal synaptogenesis domains. Science, 364(6439):eaau9952.

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

Herzog, Chiara; Pons Garcia, Laura; Keatinge, Marcus; Greenald, David; Moritz, Christian; Peri, Francesca; Herrgen, Leah (2019). Rapid clearance of cellular debris by microglia limits secondary neuronal cell death after brain injury in vivo. Development, 146(9):dev174698.

Chatterjee, Bithi; Deng, Yun; Holler, Angelika; Núñez, Nicolás Gonzalo; Azzi, Tarik; Vanoaica, Liliana Danusia; Müller, Anne; Zdimerova, Hana; Antsiferova, Olga; Zbinden, Andrea; Capaul, Riccarda; Dreyer, Johannes H; Nadal, David; Becher, Burkhard; Robinson, Mark D; Stauss, Hans; Münz, Christian (2019). CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo. PLoS Pathogens, 15(5):e1007748.

Sun, Michael Shoujie; Weber, Joe; Blattner, Ariane C; Chaurasia, Soumya; Lehner, Christian F (2019). MNM and SNM maintain but do not establish achiasmate homolog conjunction during Drosophila male meiosis. PLoS Genetics, 15(5):e1008162.

Cheng, Hung-Wei; Onder, Lucas; Novkovic, Mario; Soneson, Charlotte; Lütge, Mechthild; Pikor, Natalia; Scandella, Elke; Robinson, Mark D; Miyazaki, Jun-Ichi; Tersteegen, Anne; Sorg, Ursula; Pfeffer, Klaus; Rülicke, Thomas; Hehlgans, Thomas; Ludewig, Burkhard (2019). Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp. Nature Communications, 10(1):1739.

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

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

Shokri, Leila; Inukai, Sachi; Hafner, Antonina; Weinand, Kathryn; Hens, Korneel; Vedenko, Anastasia; Gisselbrecht, Stephen S; Dainese, Riccardo; Bischof, Johannes; Furger, Edy; Feuz, Jean-Daniel; Basler, Konrad; Deplancke, Bart; Bulyk, Martha L (2019). A Comprehensive Drosophila melanogaster Transcription Factor Interactome. Cell Reports, 27(3):955-970.e7.

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

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

Fiume, Marc; Cupak, Miroslav; Keenan, Stephen; Rambla, Jordi; de la Torre, Sabela; Dyke, Stephanie O M; Brookes, Anthony J; Carey, Knox; Lloyd, David; Goodhand, Peter; Haeussler, Maximilian; Baudis, Michael; Stockinger, Heinz; Dolman, Lena; Lappalainen, Ilkka; Törnroos, Juha; Linden, Mikael; Spalding, J Dylan; Ur-Rehman, Saif; Page, Angela; Flicek, Paul; Sherry, Stephen; Haussler, David; Varma, Susheel; Saunders, Gary; Scollen, Serena (2019). Federated discovery and sharing of genomic data using Beacons. Nature Biotechnology, 37(3):220-224.

Delvendahl, Igor; Müller, Martin (2019). Homeostatic plasticity—a presynaptic perspective. Current Opinion in Neurobiology, 54:155-162.

Soneson, Charlotte; Love, Michael I; Patro, Rob; Hussain, Shobbir; Malhotra, Dheeraj; Robinson, Mark D (2019). A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs. Life Science Alliance, 2(1):e201800175.

Liu, Minghua; Heimlicher, Maria B; Bächler, Mirjam; Ibeneche-Nnewihe, Chieze C; Florin, Ernst-Ludwig; Brunner, Damian; Hoenger, Andreas (2019). Glucose starvation triggers filamentous septin assemblies in anS. pombeseptin-2 deletion mutant. Biology Open, 8(1):bio037622.

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

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

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

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

Bick, Jochen T; Zeng, Shuqin; Robinson, Mark D; Ulbrich, Susanne E; Bauersachs, Stefan (2019). Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. Database, 2019:86.

Nowicka, Malgorzata; Krieg, Carsten; Crowell, Helena L; Weber, Lukas M; Hartmann, Felix J; Guglietta, Silvia; Becher, Burkhard; Levesque, Mitchell P; Robinson, Mark D (2019). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research, 6:748.

Greber, Urs F (2019). Editorial: Physical Virology and the Nature of Virus Infections. In: Greber, Urs F. Physical Virology : Virus Structure and Mechanics. Cham: Springer, 1-11.

Weber, Lukas M; Soneson, Charlotte (2019). HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. F1000Research, 8:1459.

Bruns, Dominique; Merk, Daniel; Santhana Kumar, Karthiga; Baumgartner, Martin; Schneider, Gisbert (2019). Synthetic Activators of Cell Migration Designed by Constructive Machine Learning. ChemistryOpen, 8(10):1303-1308.

Weber, Lukas M; Nowicka, Malgorzata; Soneson, Charlotte; Robinson, Mark D (2019). diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering. Communications Biology, 2:183.

2018

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

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

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

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

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

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

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

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

Parker, Hannah R; Orjuela, Stephany; Martinho Oliveira, Andreia; Cereatti, Fabrizio; Sauter, Matthias; Heinrich, Henriette; Tanzi, Giulia; Weber, Achim; Komminoth, Paul; Vavricka, Stephan; Albanese, Luca; Buffoli, Federico; Robinson, Mark D; Marra, Giancarlo (2018). The proto CpG island methylator phenotype of sessile serrated adenomas/polyps. Epigenetics, 13(10/11):1088-1105.

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

Krieg, Carsten; Nowicka, Malgorzata; Guglietta, Silvia; Schindler, Sabrina; Hartmann, Felix J; Weber, Lukas M; Dummer, Reinhard; Robinson, Mark D; Levesque, Mitchell P; Becher, Burkhard (2018). Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nature Medicine, 24(11):1773-1775.

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

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

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

Wang, Yidong; Lu, Pengfei; Wu, Bingruo; Riascos-Bernal, Dario F; Sibinga, Nicholas E S; Valenta, Tomas; Basler, Konrad; Zhou, Bin (2018). Myocardial β-Catenin-BMP2 signaling promotes mesenchymal cell proliferation during endocardial cushion formation. Journal of Molecular and Cellular Cardiology, 123:150-158.

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

Villiger, Lukas; Grisch-Chan, Hiu Man; Lindsay, Helen; Ringnalda, Femke; Pogliano, Chiara B; Allegri, Gabriella; Fingerhut, Ralph; Häberle, Johannes; Matos, Joao; Robinson, Mark D; Thöny, Beat; Schwank, Gerald (2018). Treatment of a metabolic liver disease by in vivo genome base editing in adult mice. Nature Medicine, 24(10):1519-1525.

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

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

Gug, Georgiana; Huang, Qingyao; Chiticariu, Elena; Solovan, Caius; Baudis, Michael (2018). DNA copy number imbalances in primary cutaneous lymphomas (PCL). bioRxiv 417766, Cold Spring Harbor Laboratory.

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

Ojeda Naharros, Irene; Cristian, Flavia B; Zang, Jingjing; Gesemann, Matthias; Ingham, Philip W; Neuhauss, Stephan C F; Bachmann-Gagescu, Ruxandra (2018). Publisher Correction: The ciliopathy protein TALPID3/KIAA0586 acts upstream of Rab8 activation in zebrafish photoreceptor outer segment formation and maintenance. Scientific Reports, 8:12534.

Bick, Jochen T; Flöter, Veronika L; Robinson, Mark D; Bauersachs, Stefan; Ulbrich, Susanne E (2018). Small RNA-seq analysis of single porcine blastocysts revealed that maternal estradiol-17beta exposure does not affect miRNA isoform (isomiR) expression. BMC Genomics, 19(1):590.

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

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

Huang, Qingyao; Baudis, Michael (2018). Enabling population assignment from cancer genomes with SNP2pop. bioRxiv 368647, Cold Spring Harbor Laboratory.

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

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

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

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

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

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

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

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

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

Savic, Natasa; Ringnalda, Femke Cas; Lindsay, Helen; Berk, Christian; Bargsten, Katja; Li, Yizhou; Neri, Dario; Robinson, Mark D; Ciaudo, Constance; Hall, Jonathan; Jinek, Martin; Schwank, Gerald (2018). Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. eLife, 7:33761.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Praz, Coraline R; Menardo, Fabrizio; Robinson, Mark D; Müller, Marion C; Wicker, Thomas; Bourras, Salim; Keller, Beat (2018). Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. Frontiers in Plant Science, 9:49.

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

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

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

Duò, Angelo; Robinson, Mark D; Soneson, Charlotte (2018). A systematic performance evaluation of clustering methods for single-cell RNA-seq data. F1000Research, 7:1141.

Wrangle, John M; Velcheti, Vamsidhar; Patel, Manish R; Garrett-Mayer, Elizabeth; Hill, Elizabeth G; Ravenel, James G; et al; Robinson, Mark D; Rubinstein, Mark P (2018). ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial. Lancet Oncology, 19(5):694-704.

Gut, Gabriele. Advancements in image-based molecular profiling of single cells. 2018, University of Zurich, Faculty of Science.

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

Soneson, Charlotte; Robinson, Mark D (2018). Bias, robustness and scalability in single-cell differential expression analysis. Nature Methods, 15(4):255-261.

Badugu, Amarendra. Cell shape and tissue mechanics in the Drosophila wing disc. 2018, University of Zurich, Faculty of Science.

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

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

Littringer, Katharina; Moresi, Claudia; Rakebrandt, Nikolas; Zhou, Xiaobei; Schorer, Michelle; Dolowschiak, Tamas; Kirchner, Florian; Rost, Felix; Keller, Christian W; McHugh, Donal; LeibundGut-Landmann, Salomé; Robinson, Mark D; Joller, Nicole (2018). Common features of regulatory T cell specialization during Th1 responses. Frontiers in Immunology, 9:1344.

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

Bieri, Manuela. Development of mouse adenovirus reporter viruses and studies on mouse adenovirus-2 and -3 receptor candidates. 2018, University of Zurich, Faculty of Science.

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

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

Perez-Shibayama, Christian; Gil-Cruz, Cristina; Cheng, Hung-Wei; Onder, Lucas; Printz, Andrea; Mörbe, Urs; Novkovic, Mario; Li, Conglei; Lopez-Macias, Constantino; Buechler, Matthew B; Turley, Shannon J; Mack, Matthias; Soneson, Charlotte; Robinson, Mark D; Scandella, Elke; Gommerman, Jennifer; Ludewig, Burkhard (2018). Fibroblastic reticular cells initiate immune responses in visceral adipose tissues and secure peritoneal immunity. Science Immunology, 3(26):eaar4539.

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

Niklaus, Stephanie. Glutamate homeostasis in the zebrafish outer retina. 2018, University of Zurich, Faculty of Science.

Krieg, Carsten; Nowicka, Malgorzata; Guglietta, Silvia; Schindler, Sabrina; Hartmann, Felix J; Weber, Lukas M; Dummer, Reinhard; Robinson, Mark D; Levesque, Mitchell P; Becher, Burkhard (2018). High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nature Medicine, 24(2):144-153.

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

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

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

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

Witte, Robert. Investigation of rhinovirus replication through high-content screening and single cell analysis. 2018, University of Zurich, Faculty of Science.

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

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

Atzeni, Francesco. Mechanochemical modelling as an explorative tool to study tissue morphogenesis. 2018, University of Zurich, Faculty of Science.

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

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

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

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

Van den Berge, Koen; Perraudeau, Fanny; Soneson, Charlotte; Love, Michael I; Risso, Davide; Vert, Jean-Philippe; Robinson, Mark D; Dudoit, Sandrine; Clement, Lieven (2018). Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biology, 19:24.

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

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

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

Hoop, Vanessa Maria. Systematic investigation of the roles of Ca²⁺-binding proteins in neurotransmitter release. 2018, University of Zurich, Faculty of Science.

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

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

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

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

Prasad, Vibhu Ranjan. Unfolded protein response in adenovirus infection. 2018, University of Zurich, Faculty of Science.

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

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

2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gilmour, Darren; Rembold, Martina; Leptin, Maria (2017). From morphogen to morphogenesis and back. Nature, 541(7637):311-320.

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

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

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

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

Gulati, Pratiksha. Adoptive therapy with T-cells genetically targeted to tumor associated antigen through the introduction of chimeric antigen receptors (CARs). 2017, University of Zurich, Faculty of Science.

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

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

Mereu, Louisa. Cell polarity shapes the epidermal growth factor morphogen gradient during C. elegans vulval induction and reciprocal epidermal growth factor signaling orients cell polarity to promote vulval morphogenesis. 2017, University of Zurich, Faculty of Science.

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

Franz, Alexandra. Challenging the Wnt signaling dogma: deciphering the role of Armadillo and Pangolin for Wnt/Wg target gene regulation. 2017, University of Zurich, Faculty of Science.

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

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

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

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

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

Zhou, Xiaobei. Improving statistical methods for RNA sequencing data: outliers, boundary conditions, benchmarking and differential transcript expression. 2017, University of Zurich, Faculty of Science.

Kannan, Abhilash. Innate sensing of miRNA mimetics provides broad range antiviral effects. 2017, University of Zurich, Faculty of Science.

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

Ojeda Naharros, Irene. Modelling ciliopathies in the zebrafish: elucidating the role of CC2D2A and TALPID3 in photoreceptor development and function. 2017, University of Zurich, Faculty of Science.

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

Natsiou, Despoina. Role of Notch signaling in cell fate determination of dental epithelial stem/progenitor cells. 2017, University of Zurich, Faculty of Science.

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.

Nowicka, Malgorzata Franciszka. Statistical method development and design of computational pipelines for differential analyses of high-throughput data, including DNA microarrays, RNA sequencing and HDCyto data. 2017, University of Zurich, Faculty of Science.

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

Sanchez Bosch, Pablo. The Dpp morphogen gradient regulates growth and patterning in the Drosophila wing imaginal disc. 2017, University of Zurich, Faculty of Science.

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

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.

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.

Ai, Ni; Cai, Haoyang; Solovan, Caius; Baudis, Michael (2016). CNARA: reliability assessment for genomic copy number profiles. BMC Genomics, 17:799.

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

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

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

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

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

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

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

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

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

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

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

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

Casano, Alessandra Maria; Albert, Marvin; Peri, Francesca (2016). Developmental Apoptosis Mediates Entry and Positioning of Microglia in the Zebrafish Brain. Cell Reports, 16(4):897-906.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Flori, Michael; Schmid, Corina A; Sumrall, Eric T; Tzankov, Alexandar; Law, Charity W; Robinson, Mark D; Müller, Anne (2016). The hematopoietic oncoprotein FOXP1 promotes tumor cell survival in diffuse large B-cell lymphoma by repressing S1PR2 signaling. Blood, 127(11):1438-1448.

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.

Barry, Joseph D; Donà, Erika; Gilmour, Darren; Huber, Wolfgang (2016). TimerQuant: a modelling approach to tandem fluorescent timer design and data interpretation for measuring protein turnover in embryos. Development, 143(1):174-179.

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.

Yang, Qiutan. A touch of lumen morphogenesis in Caenorhabditis elegans: anchor cell invasion guides epithelial invagination. 2016, University of Zurich, Faculty of Science.

Fehr, Alexander G J; Ruetten, M; Seth-Smith, Helena M B; Nufer, Lisbeth; Voegtlin, A; Lehner, Angelika; Greub, Gilbert; Crosier, Philip S; 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.

Pasakarnis, Laurynas. Analysis of acto-myosin network remodelling: towards a comprehensive understanding of tissue closure events. 2016, University of Zurich, Faculty of Science.

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

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

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

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

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

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

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

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

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

Zafar, Sadia; Parviainen, Suvi; Siurala, Mikko; Hemminki, Otto; Havunen, Riikka; Tähtinen, Siri; Bramante, Simona; Vassilev, Lotta; Wang, Hongjie; Lieber, Andre; Hemmi, Silvio; de Gruijl, Tanja; Kanerva, Anna; Hemminki, Akseli (2016). Intravenously usable fully serotype 3 oncolytic adenovirus coding for CD40L as an enabler of dendritic cell therapy. OncoImmunology, 6(2):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.

Kijowski, A R. Organisation of sterol-rich membranes in cell polarisation. 2016, University of Zurich, Faculty of Science.

Battich, Nicolas. Origins and control of single-cell transcript heterogeneity. 2016, University of Zurich, Faculty of Science.

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.

Bode, Heiko Sebastian. Serine palmitoyltransferase and peripheral neuropathy: studies on neuropathy-causing mutations and their biochemical hallmarks. 2016, University of Zurich, Faculty of Science.

Eshwar, Athmanya K. Studying pathogen-host interactions and pathogenesis in Cronobacter and Listeria infections using in vitro and in vivo infection models. 2016, Universität Zürich, Faculty of Science.

Morf, Matthias K. The Caenorhabditis elegans homolog of the Opitz syndrome gene, madd-2/Mid1, regulates anchor cell invasion during vulval development. 2016, University of Zurich, Faculty of Science.

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, Mark D (2015). Loss of the Notch effector RBPJ promotes tumorigenesis. Journal of Experimental Medicine, 212(1):37-52.

de Medeiros, Gustavo; Norlin, Nils; Gunther, Stefan; Albert, Marvin; Panavaite, Laura; Fiuza, Ulla-Maj; Peri, Francesca; Hiiragi, Takashi; Krzic, Uros; Hufnagel, Lars (2015). Confocal multiview light-sheet microscopy. Nature Communications, 6:8881.

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

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

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

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

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

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

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

Gilmour, Darren (2015). Epithelial morphogenesis: stage diving with purpose. Developmental Cell, 35(1):7-8.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Frechin, Mathieu; Stoeger, Thomas; Daetwyler, Stephan; Gehin, Charlotte; Battich, Nico; Damm, Eva-Maria; Stergiou, Lilli; Riezman, Howard; Pelkmans, Lucas (2015). Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour. Nature, 523(7558):88-91.

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

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

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

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

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

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

Scott, Cameron C; Vossio, Stefania; Vacca, Fabrizio; Snijder, Berend; Larios, Jorge; Schaad, Olivier; Guex, Nicolas; Kuznetsov, Dmitry; Martin, Olivier; Chambon, Marc; Turcatti, Gerardo; Pelkmans, Lucas; Gruenberg, Jean (2015). Wnt directs the endosomal flux of LDL-derived cholesterol and lipid droplet homeostasis. EMBO Reports, 16(6):741-752.

Fehr, Alexander; Eshwar, Athmanya K; Neuhauss, Stephan C F; 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.

Rossi, Federico; Casano, Alessandra Maria; Henke, Katrin; Richter, Kerstin; Peri, Francesca (2015). The SLC7A7 Transporter Identifies Microglial Precursors prior to Entry into the Brain. Cell Reports, 11(7):1008-1017.

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

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

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

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

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

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

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

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

Moritz, Christian; Berardi, Francesco; Abate, Carmen; Peri, Francesca (2015). Live imaging reveals a new role for the sigma-1 (σ1) receptor in allowing microglia to leave brain injuries. Neuroscience Letters, 591:13-18.

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.

Casano, Alessandra Maria; Peri, Francesca (2015). Microglia: Multitasking Specialists of the Brain. Developmental Cell, 32(4):469-477.

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

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

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

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

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

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

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

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

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

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

Liberali, Prisca; Snijder, Berend; Pelkmans, Lucas (2015). Single-cell and multivariate approaches in genetic perturbation screens. Nature Reviews. Genetics, 16(1):18-32.

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.

Petrella, V; Aceto, S; Musacchia, F; Colonna, V; Robinson, Mark D; Benes, V; Cicotti, G; Bongiorno, G; Gradoni, L; Volf, P; Salvemini, M (2015). De novo assembly and sex-specific transcriptome profiling in the sand fly Phlebotomus perniciosus (Diptera, Phlebotominae), a major Old World vector of Leishmania infantum. BMC Genomics, 16:847.

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

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

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

Fehr, Alexander G J. Fish as natural host and in vivo model for infections with intracellular bacterial pathogens. 2015, University of Zurich, Faculty of Science.

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.

Grabliauskaite, Kamile. Molecular mechanisms of acinar-to-ductal metaplasia formation during pancreatitis. 2015, University of Zurich, Faculty of Science.

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.

Klein, Carina. The influence of musicianship on background neuronal oscillations: novel perspectives. 2015, University of Zurich, Faculty of Science.

Roiz Lafuente, Daniel Maria. The proteins LIN-39 HOX, LIN-12 NOTCH and LIN-31 forkhead coordinately control the cell cycle of the C. elegans vulva. 2015, University of Zurich, Faculty of Science.

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.

Durdu, Sevi; Iskar, Murat; Revenu, Celine; Schieber, Nicole; Kunze, Andreas; Bork, Peer; Schwab, Yannick; Gilmour, Darren (2014). Luminal signalling links cell communication to tissue architecture during organogenesis. Nature, 515(7525):120-124.

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.

Mazaheri, Fargol; Breus, Oksana; Durdu, Sevi; Haas, Petra; Wittbrodt, Jochen; Gilmour, Darren; Peri, Francesca (2014). Distinct roles for BAI1 and TIM-4 in the engulfment of dying neurons by microglia. Nature Communications, 5:4046.

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.

Revenu, Céline; Streichan, Sebastian; Donà, Erika; Lecaudey, Virginie; Hufnagel, Lars; Gilmour, Darren (2014). Quantitative cell polarity imaging defines leader-to-follower transitions during collective migration and the key role of microtubule-dependent adherens junction formation. Development, 141(6):1282-1291.

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.

Wang, Mingcong. Evolution of protein abundance. 2014, University of Zurich, Faculty of Science.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

Bitomsky, N; Conrad, E; Moritz, C; Polonio-Vallon, T; Sombroek, D; Schultheiss, K; Glas, C; Greiner, V; Herbel, C; Mantovani, F; del Sal, G; Peri, F; Hofmann, T G (2013). Autophosphorylation and Pin1 binding coordinate DNA damage-induced HIPK2 activation and cell death. Proceedings of the National Academy of Sciences of the United States of America, 110(45):E4203-E4212.

Donà, Erika; Barry, Joseph D; Valentin, Guillaume; Quirin, Charlotte; Khmelinskii, Anton; Kunze, Andreas; Durdu, Sevi; Newton, Lionel R; Fernandez-Minan, Ana; Huber, Wolfgang; Knop, Michael; Gilmour, Darren (2013). Directional tissue migration through a self-generated chemokine gradient. Nature, 503(7475):285-289.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Sieger, Dirk; Peri, Francesca (2013). Animal models for studying microglia: The first, the popular, and the new. Glia, 61(1):3-9.

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.

Taneja Raychaudhuri, Nitika. 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, Mark D; Jiricny, J; Buffoli, F; Marra, Giancarlo (2013). Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions. Oncogenesis, 2:e56.

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

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

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

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

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

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

Bluwstein, A; Kumar, N; Léger, K; Traenkle, J; van Oostrum, J; Rehrauer, H; Baudis, Michael; 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.

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