Header

UZH-Logo

Maintenance Infos

Items where Subject is "Special Collections > SystemsX.ch"

Navigate back| Up a level
Export as
Number of items at this level: 284.

Hu, Chengzhi; Munglani, Gautam; Vogler, Hannes; Ndinyanka Fabrice, Tohnyui; Shamsudhin, Naveen; Wittel, Falk K; Ringli, Christoph; Grossniklaus, Ueli; Herrmann, Hans J; Nelson, Bradley J (2017). Characterization of size-dependent mechanical properties of tip-growing cells using a lab-on-chip device. Lab on a chip, 17(1):82-90.

Burri, Jan T; Chengzhi, Hu; Shamsudhin, Naveen; Wang, Xueqi; Vogler, Hannes; Grossniklaus, Ueli; Nelson, Bradley J (2016). Dual-axis Cellular Force Microscope for mechanical characterization of living plant cells. In: Automation Science and Engineering (CASE), 2016 IEEE International Conference on, Fort Worth, Texas, 21 August 2016 - 25 August 2016, 942-947.

Shamsudhin, Naveen; Atakan, Huseyin Baris; Laubli, Nino; Vogler, Hannes; Hu, Chengzhi; Sebastian, Abu; Grossniklaus, Ueli; Nelson, Bradley J (2016). Probing the micromechanics of the fastest growing plant cell — The pollen tube. In: Engineering in Medicine and Biology Society (EMBC), 2016 IEEE 38th Annual International Conference of the, Lake Buena Vista (Orlando), Florida USA, 16 August 2016 - 20 August 2016, 461-464.

Shamsudhin, Naveen; Laeubli, Nino; Atakan, Huseyin Baris; Vogler, Hannes; Hu, Chengzhi; Haeberle, Walter; Sebastian, Abu; Grossniklaus, Ueli; Nelson, Bradley J (2016). Massively Parallelized Pollen Tube Guidance and Mechanical Measurements on a Lab-on-a-Chip Platform. PLoS ONE, 11(12):e0168138.

Spühler, Isabelle A; Conley, Gaurasundar M; Scheffold, Frank; Sprecher, Simon G (2016). Super resolution imaging of genetically labeled synapses in drosophila brain tissue. Frontiers in Cellular Neuroscience:10:142.

Smith, Kevin; Li, Yunpeng; Piccinini, Filippo; Csucs, Gabor; Balazs, Csaba; Bevilacqua, Alessandro; Horvath, Peter (2015). CIDRE: an illumination-correction method for optical microscopy. Nature Methods, 12(5):404-406.

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Bonde, Marie Mi; Voegeli, Sylvia; Baudrimont, Antoine; Seraphin, Bertrand; Becskei, Attila (2014). Quantification of pre-mRNA escape rate and synergy in splicing. Nucleic Acids Research, 42(20):12847-12860.

Sévin, Daniel C; Sauer, Uwe (2014). Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. Nature Chemical Biology, 10(4):266-272.

Quinodoz, Mathieu; Gobet, Cédric; Naef, Felix; Gustafson, Kyle B (2014). Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology, 15(6):R85.

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning (2014). Cryo-electron microscopy of membrane proteins. Methods in Molecular Biology, 1117:325-41.

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas (2014). Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy. Analytical Chemistry, 86(10):4680-4687.

Gilardi, Federica; Migliavacca, Eugenia; Naldi, Aurélien; Baruchet, Michaël; Canella, Donatella; Le Martelot, Gwendal; Guex, Nicolas; Desvergne, Béatrice (2014). Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals. PLoS Genetics, 10(3):e1004155.

Kowal, Julia; Chami, Mohamed; Baumgartner, Paul; Arheit, Marcel; Chiu, Po-Lin; Rangl, Martina; Scheuring, Simon; Schröder, Gunnar F; Nimigean, Crina M; Stahlberg, Henning (2014). Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nature Communications, 5:3106.

Feller, Chrystel; Gabriel, Jean-Pierre; Mazza, Christian; Yerly, Florence (2014). Pattern formation in auxin flux. Journal of Mathematical Biology, 68(4):879-909.

Bonhoure, N; Bounova, G; Bernasconi, D; Praz, V; Lammers, F; Canella, D; Willis, I M; Herr, W; Hernandez, N; Delorenzi, M; Hernandez, N; Delorenzi, M; Deplancke, B; Desvergne, B; Guex, N; Herr, W; Naef, F; Rougemont, J; Schibler, U; Andersin, T; Cousin, P; Gilardi, F; Gos, P; Lammers, F; Raghav, S; Villeneuve, D; Fabbretti, R; Vlegel, V; Xenarios, I; Migliavacca, E; Praz, V; David, F; Jarosz, Y; Kuznetsov, D; Liechti, R; Martin, O; Delafontaine, J; Cajan, J; Gustafson, K; Krier, I; Leleu, M; Molina, N; Naldi, A; Rib, L; Symul, L; Bounova, G (2014). Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Research, 24(7):1157-1168.

Bernard, Thomas; Bridge, Alan; Morgat, Anne; Moretti, Sébastien; Xenarios, Ioannis; Pagni, Marco (2014). Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics, 15(1):123-135.

Moharana, Kedar; Zabeau, Lennart; Peelman, Frank; Ringler, Philippe; Stahlberg, Henning; Tavernier, Jan; Savvides, Savvas N (2014). Structural and mechanistic paradigm of leptin receptor activation revealed by complexes with wild-type and antagonist leptins. Structure, 22(6):866-877.

Baresic, M; Salatino, S; Kupr, B; van Nimwegen, E; Handschin, C (2014). Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1 in the regulation of the hypoxic gene program. Molecular and Cellular Biology, 34(16):2996-3012.

Ramakrishnan, Chandrasekhar; Bieri, Andrej; Sauter, Nora; Roizard, Sophie; Ringler, Philippe; Müller, Shirley A; Goldie, Kenneth N; Enimanev, Kaloyan; Stahlberg, Henning; Rinn, Bernd; Braun, Thomas (2014). openBEB: open biological experiment browser for correlative measurements. BMC Bioinformatics, 15:84.

Leppänen, Veli-Matti; Tvorogov, Denis; Kisko, Kaisa; Prota, Andrea E; Jeltsch, Michael; Anisimov, Andrey; Markovic-Mueller, Sandra; Stuttfeld, Edward; Goldie, Kenneth N; Ballmer-Hofer, Kurt; Alitalo, Kari (2013). Structural and mechanistic insights into VEGF receptor 3 ligand binding and activation. Proceedings of the National Academy of Sciences of the United States of America, 110(32):12960-12965.

Woodruff, Kristina; Fidalgo, Luis M; Gobaa, Samy; Lutolf, Matthias P; Maerkl, Sebastian J (2013). Live Mammalian Cell Arrays. Nature Methods, 10(6):550-552.

Arnold, Phil; Schöler, Anne; Pachkov, Mikhail; Balwierz, Piotr J; Jørgensen, Helle; Stadler, Michael B; van Nimwegen, Erik; Schübeler, Dirk (2013). Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Research, 23:60-73.

Loizides-Mangold, Ursula (2013). On the future of mass-spectrometry-based lipidomics. FEBS Journal, 280:2817-2829.

Andreasen, Sidsel Ø; Chong, Siow-Feng; Wohl, Benjamin M; Goldie, Kenneth N; Zelikin, Alexander N (2013). Poly(vinyl alcohol) physical hydrogel nanoparticles, not polymer solutions, exert inhibition of nitric oxide synthesis in cultured macrophages. Biomacromolecules, 14(5):1687-95.

Sunnåker, Mikael; Zamora-Sillero, Elias; Dechant, Reinhard; Ludwig, Christina; Busetto, Alberto Giovanni; Wagner, Andreas; Stelling, Joerg (2013). Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism. Science Signaling, 6(277):ra41.

de Mazancourt, Claire; Isbell, Forest; Larocque, Allen; Berendse, Frank; De Luca, Enrica; Grace, James B; Haegeman, Bart; Polley, H Wayne; Roscher, Christiane; Schmid, Bernhard; Tilman, David; van Ruijven, Jasper; Weigelt, Alexandra; Wilsey, Brian J; Loreau, Michel (2013). Predicting ecosystem stability from community composition and biodiversity. Ecology Letters, 16(5):617-625.

Vonaesch, Pascale; Cardini, Steven; Sellin, Mikael E; Goud, Bruno; Hardt, Wolf-Dietrich; Schauer, Kristine (2013). Quantitative insights into actin rearrangements and bacterial target site selection fromSalmonella Typhimurium infection of micropatterned cells. Cellular Microbiology, 15(11):1851-1865.

Shimobayash, Mitsugu; Oppliger, Wolfgang; Moes, Suzette; Jenö, Paul; Hall, Michael N (2013). TORC1-regulated protein kinase Npr1 phosphorylates Orm to stimulate complex sphingolipid synthesis. Molecular Biology of the Cell, 24:870-881.

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.

Weidmann, Simon; Barylyuk, Konstantin; Nespovitaya, Nadezhda; Mädler, Stefanie; Zenobi, Renato (2013). A New, Modular Mass Calibrant for High-Mass MALDI-MS. Analytical Chemistry, 85:3425-3432.

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS ONE, 8(2):1-17.

Prota, Andrea E; Bargsten, Katja; Zurwerra, Didier; Field, Jessica J; Díaz, José Fernando; Altmann, Karl-Heinz; Steinmetz, Michel O (2013). Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science, 339(6119):587-590.

Simicevic, Jovan; Schmid, Adrien W; Gilardoni, Paola A; Zoller, Benjamin; Raghav, Sunil K; Krier, Irina; Gubelmann, Carinne; Lisacek, Frédérique; Naef, Felix; Moniatte, Marc; Deplancke, Bart (2013). Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics. Nature Methods, 10(6):570-576.

Chen, Jerry L; Carta, Stefano; Soldado-Magraner, Joana; Schneider, Bernard L; Helmchen, Fritjof (2013). Behaviour-dependent recruitment of long-range projection neurons in somatosensory cortex. Nature, 499(7458):336-340.

Goepfert, Arnaud; Stanger, Frédéric V; Dehio, Christoph; Schirmer, Tilman (2013). Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold. PLoS ONE, 8(5):e64901.

Paul, Grégory; Cardinale, Janick; Sbalzarini, Ivo F (2013). Coupling Image Restoration and Segmentation: A Generalized Linear Model/Bregman Perspective. International Journal of Computer Vision, 104(1):69-93.

Lemgruber, Leandro; Kudryashev, Mikhail; Dekiwadia, Chaitali; Riglar, David T; Baum, Jake; Stahlberg, Henning; Ralph, Stuart A; Frischknecht, Friedrich (2013). Cryo-electron tomography reveals four-membrane architecture of the Plasmodium apicoplast. Malaria Journal, 12:25.

Pacheco-Villalobos, David; Sankar, Martial; Ljung, Karin; Hardtke, Christian S (2013). Disturbed Local Auxin Homeostasis Enhances Cellular Anisotropy and Reveals Alternative Wiring of Auxin-ethylene Crosstalk in Brachypodium distachyon Seminal Roots. PLoS Genetics, 9(6):e1003564.

Grasso, Luigino; Wyss, Romain; Piguet, Joachim; Werner, Michael; Hassaïne, Ghérici; Hovius, Ruud; Vogel, Horst (2013). Downscaling the analysis of complex transmembrane signaling cascades to closed attoliter volumes. PLoS ONE, 8(8):e70929.

Kudryashev, M; Stenta, M; Schmelz, S; Amstutz, M; Wiesand, U; Castano-Diez, D; Degiacomi, M T; Munnich, S; Bleck, C K; Kowal, J; Diepold, A; Heinz, D W; Dal Peraro, M; Cornelis, G R; Stahlberg, H (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2:e00792-e00792.

Stergiou, Lilli; Bauer, Manuel; Mair, Waltraud; Bausch-Fluck, Damaris; Drayman, Nir; Wollscheid, Bernd; Oppenheim, Ariella; Pelkmans, Lucas (2013). Integrin-Mediated Signaling Induced by Simian Virus 40 Leads to Transient Uncoupling of Cortical Actin and the Plasma Membrane. PLoS ONE, 8(2):e55799.

Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2):e57329.

Sarraf-Zadeh, Ladan; Christen, Stefan; Sauer, Uwe; Cognigni, Paola; Miguel-Aliaga, Irene; Stocker, Hugo; Köhler, Katja; Hafen, Ernst (2013). Local requirement of the Drosophila insulin binding protein imp-L2 in coordinating developmental progression with nutritional conditions. Developmental Biology, 381(1):97-106.

Sbalzarini, Ivo F (2013). Modeling and simulation of biological systems from image data. BioEssays, 35(5):482-490.

Busetto, Alberto Giovanni; Hauser, Alain; Krummenacher, Gabriel; Sunnåker, Mikael; Dimopoulos, Sotiris; Ong, Cheng Soon; Stelling, Jörg; Buhmann, Joachim M (2013). Near-optimal experimental design for model selection in systems biology. Bioinformatics:online.

Steeb, Benjamin; Claudi, Beatrice; Burton, Neil A; Tienz, Petra; Schmidt, Alexander; Farhan, Hesso; Mazé, Alain; Bumann, Dirk (2013). Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence. PLoS Pathogens, 9(4):e1003301.

Hohm, Tim; Preuten, Tobias; Fankhauser, Christian (2013). Phototropism: Translating light into directional growth. American Journal of Botany, 100(1):47-59.

Pessi, Gabriella; Braunwalder, Rubina; Grunau, Alexander; Omasits, Ulrich; Ahrens, Christian H; Eberl, Leo (2013). Response of Burkholderia cenocepacia H111 to Micro-Oxia. PLoS ONE, 8(9):e72939.

Kemmerling, Simon; Arnold, Stefan A; Bircher, Benjamin A; Sauter, Nora; Escobedo, Carlos; Dernick, Gregor; Hierlemann, Andreas; Stahlberg, Henning; Braun, Thomas (2013). Single-cell lysis for visual analysis by electron microscopy. Journal of Structural Biology, 183(3):467-73.

Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer Cell, 23(6):768-83.

Delgado-Gonzalo, R; Unser, M (2013). Spline-based framework for interactive segmentation in biomedical imaging. IRBM, 34(3):235-243.

Schmutz, Christoph; Ahrne, Erik Lennart; Kasper, Christoph Alexander; Tschon, Therese; Sorg, Isabel; Dreier, Roland Felix; Schmidt, Alexander; Arrieumerlou, Cecile (2013). Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Molecular & Cellular Proteomics, 12(10):2952-2968.

Zampar, Guillermo G; Kümmel, Anne; Ewald, Jennifer; Jol, Stefan; Niebel, Bastian; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2013). Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology, 9:online.

Limenitakis, Julien; Oppenheim, Rebecca D; Creek, Darren J; Foth, Bernardo J; Barrett, Michael P; Soldati-Favre, Dominique (2013). The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Molecular Microbiology, 87(4):894-908.

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.

Vogler, Hannes; Draeger, Christian; Weber, Alain; Felekis, Dimitris; Eichenberger, Christof; Routier-Kierzkowska, Anne-Lise; Boisson-Dernier, Aurélien; Ringli, Christoph; Nelson, Bradley J; Smith, Richard S; Grossniklaus, Ueli (2013). The pollen tube: a soft shell with a hard core. The Plant Journal, 73(4):617-627.

Varjosalo, Markku; Keskitalo, Salla; Van Drogen, Audrey; Nurkkala, Helka; Vichalkovski, Anton; Aebersold, Ruedi; Gstaiger, Matthias (2013). The protein interaction landscape of the human CMGC kinase group. Cell Reports, 3(4):1306-20.

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Reh, Lucia; Novy, Karel; Wollscheid, Bernd; Helenius, Ari; Stahlberg, Henning; Mercer, Jason (2013). Vaccinia virus entry is followed by core activation and proteasome-mediated release of the immunomodulatory effector VH1 from lateral bodies. Cell Reports, 4(3):464-476.

Piccinini, Filippo; Bevilacqua, Alessandro; Smith, Kevin; Horvath, Peter (2013). Vignetting and photo-bleaching correction in automated fluorescence microscopy from an array of overlapping images. In: 10th IEEE International Symposium on Biomedical Imaging (ISBI), San Francisco, CA, U.S.A. , 2013 - 2013.

Blaskovic, Sanja; Blanc, Mathieu; van der Goot, F Gisou (2013). What does S-palmitoylation do to membrane proteins? FEBS Journal, 280(12):2766-2774.

Kiefer, P; Schmitt, U; Vorholt, J A (2013). eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows. Bioinformatics, 29(7):963-964.

Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie (2012). Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway. PLoS ONE, 7(12):e52877.

van der Westen, Rebecca; Hosta-Rigau, Leticia; Sutherland, Duncan S; Goldie, Kenneth N; Albericio, Fernando; Postma, Almar; Städler, Brigitte (2012). Myoblast cell interaction with polydopamine coated liposomes. Biointerphases, 7(1-4):8.

Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J (2012). iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks. Nucleic Acids Research:1-8.

Geertz, Marcel; Shore, David; Maerkl, Sebastian J (2012). Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proceedings of the National Academy of Sciences of the United States of America, 109(41):16540-16545.

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

Weidmann, Simon; Kemmerling, Simon; Mädler, Stefanie; Stahlberg, Henning; Braun, Thomas; Zenobi, Renato (2012). Ionic Liquids as Matrices in MicrofluidicSample Deposition for High-mass Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. European Journal of Mass Spectrometry, 18:279-286.

Schröter, Christian; Ares, Saúl; Morelli, Luis G; Isakova, Alina; Hens, Korneel; Soroldoni, Daniele; Gajewski, Martin; Jülicher, Frank; Maerkl, Sebastian J; Deplancke, Bart; Oates, Andrew C (2012). Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit. PLoS Biology, 10(7):1-20.

Rajkumar, Arun S; Maerkl, Sebastian J (2012). Rapid Synthesis Of Defined Eukaryotic Promoter Libraries. ACS Synthetic Biology, 1:483-490.

Delgado-Gonzalo, Ricard; Chenouard, Nicolas; Unser, Michael (2012). Fast parametric snakes for 3D microscopy. In: IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, 2 May 2012 - 5 May 2012.

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

Snijder, Berend; Sacher, Raphael; Rämö, Pauli; Liberali, Prisca; Mench, Karin; Wolfrum, Nina; Burleigh, Laura; Scott, Cameron C; Verheije, Monique H; Mercer, Jason; Moese, Stefan; Heger, Thomas; Theusner, Kristina; Jurgeit, Andreas; Lamparter, David; Balistreri, Giuseppe; Schelhaas, Mario; De Haan, Cornelis A M; Marjomäki, Varpu; Hyypiä, Timo; Rottier, Peter J M; Sodeik, Beate; Marsh, Mark; Gruenberg, Jean; Amara, Ali; Greber, Urs; Helenius, Ari; Pelkmans, Lucas (2012). Single-cell analysis of population context advances RNAi screening at multiple levels. Molecular Systems Biology, 8(579):1-18.

Canella, Donatella; Bernasconi, David; Gilardi, Federica; LeMartelot, Gwendal; Migliavacca, Eugenia; Praz, Viviane; Cousin, Pascal; Delorenzi, Mauro; Hernandez, Nouria (2012). A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Research, 22:666-680.

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

Geertz, Marcel; Rockel, Sylvie; Maerkl, Sebastian J (2012). A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries. Methods in Molecular Biology, 813:107-123.

Draeger, Christian. A genetic, biochemical, and biomechanical study of plant cell wall dynamics in pollen tubes. 2012, University of Zurich, Faculty of Science.

Mülleder, Michael; Capuano, Floriana; Pir, Pınar; Christen, Stefan; Sauer, Uwe; Oliver, Stephen G; Ralser, Markus (2012). A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nature Biotechnology, 30(12):1176-1178.

Reboux, Sylvain; Schrader, Birte; Sbalzarini, Ivo F (2012). A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics, 231(9):3623-3646.

Gonnet, Pedro; Dimopoulos, Sotiris; Widmer, Lukas; Stelling, Jörg (2012). A specialized ODE integrator for the efficient computation of parameter sensitivities. BMC Systems Biology, 6:46.

Koeppl, Heinz; Zechner, Christoph; Ganguly, Arnab; Pelet, Serge; Peter, Matthias (2012). Accounting for extrinsic variability in the estimation of stochastic rate constants. International Journal of Robust and Nonlinear Control, 22(10):1103-1119.

Pelet, Serge; Dechant, Reinhard; Lee, Sung Sik; van Drogen, Frank; Peter, Matthias (2012). An integrated image analysis platform to quantify signal transduction in single cells. Integrative Biology, 4:1274-82.

Radotić, Ksenija; Roduit, Charles; Simonović, Jasna; Hornitschek, Patricia; Fankhauser, Christian; Mutavdžić, Dragosav; Steinbach, Gabor; Dietler, Giovanni; Kasas, Sandor (2012). Atomic Force Microscopy Stiffness Tomography on Living Arabidopsis thaliana Cells Reveals the Mechanical Properties of Surface and Deep Cell-Wall Layers during Growth. Biophysical Journal, 103(3):386-394.

Routier-Kierzkowska, A -L; Weber, A; Kochova, P; Felekis, D; Nelson, B J; Kuhlemeier, C; Smith, R S (2012). Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics. Plant Physiology, 158(4):1514-1522.

Ojosnegros, S; Delgado-Eckert, E; Beerenwinkel, N (2012). Competition-colonization trade-off promotes coexistence of low-virulence viral strains. Journal of the Royal Society Interface, 9(74):2244-2254.

Kemmerling, Simon; Ziegler, Jörg; Schweighauser, Gabriel; Arnold, Stefan A; Giss, Dominic; Müller, Shirley A; Ringler, Philippe; Goldie, Kenneth N; Goedecke, Nils; Hierlemann, Andreas; Stahlberg, Henning; Engel, Andreas; Braun, Thomas (2012). Connecting μ-fluidics to electron microscopy. Journal of Structural Biology, 177(1):128-134.

Sugihara, Kaori; Chami, Mohamed; Derényi, Imre; Vörös, János; Zambelli, Tomaso (2012). Directed self-assembly of lipid nanotubes from inverted hexagonal structures. ACS Nano, 6(8):6626-6632.

Cardinale, J; Paul, G; Sbalzarini, I F (2012). Discrete region competition for unknown numbers of connected regions. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(8):3531-3545.

Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F; Grima, Ramon (2012). Discreteness-induced concentration inversion in mesoscopic chemical systems. Nature Communications, 3:779.

Hosta-Rigau, Leticia; Jensen, Bettina E B; Fjeldsø, Kit S; Postma, Almar; Li, Guoxin; Goldie, Kenneth N; Albericio, Fernando; Zelikin, Alexander N; Städler, Brigitte (2012). Drug Delivery: Surface-Adhered Composite Poly(Vinyl Alcohol) Physical Hydrogels: Polymersome-Aided Delivery of Therapeutic Small Molecules. Advanced Healthcare Materials, 1(6):791-5.

Delgado-Gonzalo, R; Thévenaz, P; Unser, M (2012). Exponential splines and minimal-support bases for curve representation. Computer Aided Geometric Design, 29(2):109-128.

Awile, Omar; Büyükkeçeci, Ferit; Reboux, Sylvain; Sbalzarini, Ivo F (2012). Fast neighbor lists for adaptive-resolution particle simulations. Computer Physics Communications, 183(5):1073-1081.

Ramdya, Pavan; Schaffter, Thomas; Floreano, Dario; Benton, Richard (2012). Fluorescence Behavioral Imaging (FBI) Tracks Identity in Heterogeneous Groups of Drosophila. PLoS ONE, 7(11):e48381.

Le Martelot, Gwendal; Canella, Donatella; Symul, Laura; Migliavacca, Eugenia; Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix (2012). Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biology, 10(11):e1001442.

Loizides-Mangold, Ursula; David, Fabrice P A; Nesatyy, Victor J; Kinoshita, Taroh; Riezman, Howard (2012). Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels. Journal of Lipid Research, 53(8):1522-34.

Samol, I; Shapiguzov, A; Ingelsson, B; Fucile, G; Crevecoeur, M; Vener, A V; Rochaix, J -D; Goldschmidt-Clermont, M (2012). Identification of a Photosystem II Phosphatase Involved in Light Acclimation in Arabidopsis. Plant Cell, 24(6):2596-2609.

Barat, Somedutta; Willer, Yvonne; Rizos, Konstantin; Claudi, Beatrice; Mazé, Alain; Schemmer, Anne K; Kirchhoff, Dennis; Schmidt, Alexander; Burton, Neil; Bumann, Dirk (2012). Immunity to Intracellular Salmonella Depends on Surface-associated Antigens. PLoS Pathogens, 8(10):e1002966.

Kango-Singh, Madhuri; Nienhaus, Ulrike; Aegerter-Wilmsen, Tinri; Aegerter, Christof M (2012). In-vivo imaging of the drosophila wing imaginal disc over time: Novel insights on growth and boundary formation. PLoS ONE, 7(10):e47594.

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

Lim, L; Jackson-Lewis, V; Wong, L C; Shui, G H; Goh, A X H; Kesavapany, S; Jenner, A M; Fivaz, M; Przedborski, S; Wenk, M R (2012). Lanosterol induces mitochondrial uncoupling and protects dopaminergic neurons from cell death in a model for Parkinson's disease. Cell Death and Differentiation, 19(3):416-27.

Chitwood, D H; Headland, L R; Ranjan, A; Martinez, C C; Braybrook, S A; Koenig, D P; Kuhlemeier, C; Smith, R S; Sinha, N R (2012). Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning. Plant Cell, 24(6):2318-2327.

Kudryashev, Mikhail; Castaño-Díez, Daniel; Stahlberg, Henning (2012). Limiting factors in single particle cryo electron tomography. Computational and Structural Biotechnology Journal, 1(2):online.

Zhu, Zhen; Frey, Olivier; Ottoz, Diana Silvia; Rudolf, Fabian; Hierlemann, Andreas (2012). Microfluidic single-cell cultivation chip with controllable immobilization and selective release of yeast cells. Lab on a chip, 12(5):906-15.

Schmidt, A; Bachmann, R; Kometer, M; Csomor, P A; Stephan, K E; Seifritz, E; Vollenweider, F X (2012). Mismatch negativity encoding of prediction errors predicts S-ketamine-induced cognitive impairments. Neuropsychopharmacology, 37(4):865-875.

Misselwitz, Benjamin; Barrett, Naomi; Kreibich, Saskia; Vonaesch, Pascale; Andritschke, Daniel; Rout, Samuel; Weidner, Kerstin; Sormaz, Milos; Songhet, Pascal; Horvath, Peter; Chabria, Mamta; Vogel, Viola; Spori, Doris M; Jenny, Patrick; Hardt, Wolf-Dietrich (2012). Near surface swimming of Salmonella Typhimurium explains target-site selection and cooperative invasion. PLoS Pathogens, 8(7):e1002810.

Stoeber, Miriam; Stoeck, Ina Karen; Hänni, Christine; Bleck, Christopher Karl Ernst; Balistreri, Giuseppe; Helenius, Ari (2012). Oligomers of the ATPase EHD2 confine caveolae to the plasma membrane through association with actin. EMBO Journal Online, 31(10):2350-64.

Schultze, S M; Hemmings, B A; Niessen, M; Tschopp, O (2012). PI3K/AKT, MAPK and AMPK signalling: protein kinases in glucose homeostasis. Expert Reviews in Molecular Medicine, 14:e1.

Guenot, B; Bayer, E; Kierzkowski, D; Smith, R S; Mandel, T; Zadnikova, P; Benkova, E; Kuhlemeier, C (2012). PIN1-Independent Leaf Initiation in Arabidopsis. Plant Physiology, 159(4):1501-1510.

Lakkaraju, Asvin Kk; Abrami, Laurence; Lemmin, Thomas; Blaskovic, Sanja; Kunz, Béatrice; Kihara, Akio; Dal Peraro, Matteo; van der Goot, Françoise Gisou (2012). Palmitoylated calnexin is a key component of the ribosome-translocon complex. EMBO Journal Online, 31(7):1823-35.

Lesur, Antoine; Varesio, Emmanuel; Domon, Bruno; Hopfgartner, Gérard (2012). Peptides Quantification by Liquid Chromatography with Matrix-Assisted Laser Desorption/Ionization and Selected Reaction Monitoring Detection. Journal of Proteome Research, 11(10):4972-4982.

Langer, D; Helmchen, F (2012). Post hoc immunostaining of GABAergic neuronal subtypes following in vivo two-photon calcium imaging in mouse neocortex. Pflügers Archiv: European Journal of Physiology (Pflugers Archiv), 463(2):339-354.

Beerenwinkel, Niko; Siebourg, Juliane (2012). Probability, Statistics, and Computational Science. Methods in Molecular Biology, 855:77-110.

Waldmeier, Lorenz; Meyer-Schaller, Nathalie; Diepenbruck, Maren; Christofori, Gerhard (2012). Py2T murine breast cancer cells, a versatile model of TGFβ-induced EMT in vitro and in vivo. PLoS ONE, 7(11):e48651.

Lee, Sung Sik; Horvath, Peter; Pelet, Serge; Hegemann, Björn; Lee, Luke P; Peter, Matthias (2012). Quantitative and dynamic assay of single cell chemotaxis. Integrative Biology, 4(4):381.

Mercer, Jason; Snijder, Berend; Sacher, Raphael; Burkard, Christine; Bleck, Christopher Karl Ernst; Stahlberg, Henning; Pelkmans, Lucas; Helenius, Ari (2012). RNAi Screening Reveals Proteasome- and Cullin3-Dependent Stages in Vaccinia Virus Infection. Cell Reports, 2(4):1036-1047.

Tsuchimatsu, Takashi; Kaiser, Pascal; Yew, Chow-Lih; Bachelier, Julien B; Shimizu, Kentaro K (2012). Recent loss of self-incompatibility by degradation of the male component in allotetraploid Arabidopsis kamchatica. PLoS Genetics, 8(7):e1002838.

Fiscella, Michele; Farrow, Karl; Jones, Ian L; Jäckel, David; Müller, Jan; Frey, Urs; Bakkum, Douglas J; Hantz, Péter; Roska, Botond; Hierlemann, Andreas (2012). Recording from defined populations of retinal ganglion cells using a high-density CMOS-integrated microelectrode array with real-time switchable electrode selection. Journal of Neuroscience Methods, 211(1):103-113.

Kueng, Stephanie; Tsai-Pflugfelder, Monika; Oppikofer, Mariano; Ferreira, Helder C; Roberts, Emma; Tsai, Chinyen; Roloff, Tim-Christoph; Sack, Ragna; Gasser, Susan M (2012). Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states. PLoS Genetics, 8(5):e1002727.

Brankatschk, B; Wichert, S P; Johnson, S D; Schaad, O; Rossner, M J; Gruenberg, J (2012). Regulation of the EGF Transcriptional Response by Endocytic Sorting. Science Signaling, 5(215):ra21.

Oliveira, Ana Paula; Ludwig, Christina; Picotti, Paola; Kogadeeva, Maria; Aebersold, Ruedi; Sauer, Uwe (2012). Regulation of yeast central metabolism by enzyme phosphorylation. Molecular Systems Biology, 8:online.

Ghielmetti, Giulia; Aegerter, Christof M (2012). Scattered light fluorescence microscopy in three dimensions. Optics Express, 20(4):3744-3752.

Schulz, Kristina; Sydekum, Esther; Krueppel, Roland; Engelbrecht, Christoph J; Schlegel, Felix; Schröter, Aileen; Rudin, Markus; Helmchen, Fritjof (2012). Simultaneous BOLD fMRI and fiber-optic calcium recording in rat neocortex. Nature Methods, 9(6):597-602.

Delgado-Gonzalo, Ricard; Thévenaz, Philippe; Seelamantula, Chandra Sekhar; Unser, Michael (2012). Snakes with an ellipse-reproducing property. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society, 21(3):1258-71.

Jol, Stefan J; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias (2012). System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Computational Biology, 8(3):e1002415.

Lee, S S; Vizcarra, I A; Huberts, D H E W; Lee, L P; Heinemann, M (2012). Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform. Proceedings of the National Academy of Sciences of the United States of America, 109(13):4916-4920.

Rouilly, Vincent; Pujadas, Eva; Hullár, Béla; Balázs, Csabas; Kunszt, Peter; Podvinec, Michael (2012). iBRAIN2: Automated analysis and data handling for RNAi screens. In: Gesing, Sandra; Glatard, Tristan; Olabarriaga, Silvia Delgado; Solomonides, Tony; Silverstein, Jonathan C; Montagnat, Johan; Gaignard, Alban; Krefting, Dagmar. HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences. s.n.: IOS Press, 205-213.

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

Loewith, Robbie; Hall, Michael N (2011). Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control. Genetics, 189:1177 -1201.

Zhu, Z; Frey, O; Hierlemann, A (2011). Microfluidic single-cell culture chip for individual trapping, cultivation, and selective release of yeast cells. In: 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences, Seattle, Washington, USA, 2 October 2011 - 6 October 2011.

Baumgartner, Thomas; Knoch, Daria; Hotz, Philine; Eisenegger, Christoph; Fehr, Ernst (2011). Dorsolateral and ventromedial prefrontal cortex orchestrate normative choice. Nature Neuroscience, 14(11):1468-1474.

Hamaratoglu, Fisun; Morton de Lachapelle, Aitana; Pyrowolakis, George; Bergmann, Sven; Affolter, Markus (2011). Dpp signaling activity requires pentagone to scale with tissue size in the growing drosophila wing imaginal disc. PLoS Biology, 9:1-17.

Daunizeau, J; David, Olivier; Stephan, K E (2011). Dynamic causal modelling: A critical review of the biophysical and statistical foundations. NeuroImage, 58(2):312-322.

Zamora-Sillero, E; Hafner, M; Ibig, A; Stelling, J; Wagner, A (2011). Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Systems Biology, 5:142.

Blumer, Clemens; Vivien, Cyprien; Oertner, Thomas G; Vetter, Thomas (2011). Fluorescence Image Segmentation by using Digitally Reconstructed Fluorescence Images. In: Microscopic Image Analysis with Applications in Biology, Heidelberg, Germany, 2 September 2011 - 2 September 2011.

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

Raman, K; Wagner, A (2011). Evolvability and robustness in a complex signalling circuit. Molecular BioSystems, 7(4):1081-1092.

Paul, Grégory; Müller, Christian L; Sbalzarini, Ivo F (2011). Sensitivity analysis from evolutionary algorithm search paths. In: EVOLVE, Workshop on Probability, Set Oriented Numerics and Evolutionary Computation, Luxembourg, 25 May 2011 - 27 May 2011.

Eisenegger, Christoph; Haushofer, Johannes; Fehr, Ernst (2011). The role of testosterone in social interaction. Trends in Cognitive Sciences, 15(6):263-271.

Delgado-Gonzalo, Ricard; Chenouard, Nicolas; Unser, Michael (2011). A new hybrid Bayesian-variational particle filter with application to mitotic cell tracking. In: International Symposium on Biomedical Imaging, Chicago, IL, 30 March 2011 - 2 April 2011.

Zinzalla, Vittoria; Stracka, Daniele; Oppliger, Wolfgang; Hall, Michael N (2011). Activation of mTORC2 by Association with the Ribosome. Cell, 144:757-768.

Maerkl, Sebastian J (2011). Next generation microfluidic platforms for high-throughput protein biochemistry. Current Opinion in Biotechnology, 22(1):59-65.

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

Mathys, Christoph; Daunizeau, J; Friston, Karl J; Stephan, K E (2011). A Bayesian foundation for individual learning under uncertainty. Frontiers in Human Neuroscience, 5:39.

Geier, Florian; Fengos, Georgios; Iber, Dagmar (2011). A Computational Analysis of the Dynamic Roles of Talin, Dok1, and PIPKI for Integrin Activation. PLoS ONE, 6(11):e24808.

Huberts, Daphne H E W; Niebel, Bastian; Heinemann, Matthias (2011). A flux-sensing mechanism could regulate the switch between respiration and fermentation. FEMS Yeast Research, 12(2):118-128.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays. Journal of Chemical Physics, 134(1):014106.

Lissina, Elena; Young, Brian; Urbanus, Malene L; Guan, Xue Li; Lowenson, Jonathan; Hoon, Shawn; Baryshnikova, Anastasia; Riezman, Isabelle; Michaut, Magali; Riezman, Howard; Cowen, Leah E; Wenk, Markus R; Clarke, Steven G; Giaever, Guri; Nislow, Corey (2011). A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genetics, 7(10):e1002332.

Bailly-Bechet, Marc; Benecke, Arndt; Hardt, Wolf Dietrich; Lanza, Valentina; Sturm, Alexander; Zecchina, Riccardo (2011). An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology, 63(4):637-662.

Moran, Rosalyn J; Symmonds, Mkael; Stephan, K E; Friston, Karl J; Dolan, Raymond J (2011). An in vivo assay of synaptic function mediating human cognition. Current Biology, 21(15):1320-1325.

Gonzalez, German; Fusco, Ludovico; Benmansour, Fethallah; Fua, Pascal; Pertz, Olivier; Smith, Kevin (2011). Automated quantification of morphodynamics for high-throughput live cell time-lapse dataset. Lausanne, Switzerland: EPF Lausanne.

Truttmann, Matthias C; Guye, Patrick; Dehio, Christoph (2011). BID-F1 and BID-F2 Domains of Bartonella henselae Effector Protein BepF Trigger Together with BepC the Formation of Invasome Structures. PLoS ONE, 6(10):e25106.

Hector, A; Bell, T; Hautier, Y; Isbell, F; Kéry, M; Reich, P B; van Ruijven, J; Schmid, B (2011). BUGS in the analysis of biodiversity experiments: species richness and composition are of similar importance for grassland productivity. PLoS ONE, 6(3):e17434.

Truttmann, M C; Misselwitz, B; Huser, S; Hardt, W-D; Critchley, D R; Dehio, C (2011). Bartonella henselae engages inside-out and outside-in signaling by integrin 1 and talin1 during invasome-mediated bacterial uptake. Journal of Cell Science, 124(21):3591-3602.

Schoen, Ingmar; Ries, Jonas; Klotzsch, Enrico; Ewers, Helge; Vogel, Viola (2011). Binding-activated localization microscopy of DNA structures. Nano letters, 11(9):4008-4011.

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

Costenoble, Roeland; Picotti, Paola; Reiter, Lukas; Stallmach, Robert; Heinemann, Matthias; Sauer, Uwe; Aebersold, Ruedi (2011). Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology, 7:464.

Schroder, G; Schuelein, R; Quebatte, M; Dehio, C (2011). Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae. Proceedings of the National Academy of Sciences of the United States of America, 108(35):14643-14648.

Moran, Rosalyn J; Stephan, Klaas E; Dolan, Raymond J; Friston, Karl J (2011). Consistent spectral predictors for dynamic causal models of steady-state responses. NeuroImage, 55(4):1694-1708.

Hermes, Jens P; Sander, Fabian; Peterle, Torsten; Cioffi, Carla; Ringler, Philippe; Pfohl, Thomas; Mayor, Marcel (2011). Direct control of the spatial arrangement of gold nanoparticles in organic-inorganic hybrid superstructures. Small, 7(7):920-9.

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

Moran, Rosalyn J; Jung, Fabienne; Kumagai, Tetsuya; Endepols, Heike; Graf, Rudolf; Dolan, Raymond J; Friston, Karl J; Stephan, Klaas E; Tittgemeyer, Marc (2011). Dynamic causal models and physiological inference: A validation study using isoflurane anaesthesia in rodents. PLoS ONE, 6(8):e22790.

Bottier, Celine; Gabella, Chiara; Vianay, Benoît; Buscemi, Lara; Sbalzarini, Ivo F; Meister, Jean-Jacques; Verkhovsky, Alexander B (2011). Dynamic measurement of the height and volume of migrating cells by a novel fluorescence microscopy technique. Lab on a chip, 11:3855-3863.

Dima, Danai; Stephan, Klaas E; Roiser, Jonathan P; Friston, Karl J; Frangou, Sophia (2011). Effective connectivity during processing of facial affect: Evidence for multiple parallel pathways. Journal of Neuroscience, 31(40):14378-14385.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.

Helmuth, Jo A; Reboux, Sylvain; Sbalzarini, Ivo F (2011). Exact stochastic simulations of intra-cellular transport by mechanically coupled molecular motors. Journal of Computer Science, 2(4):324-334.

Grewe, B F; Voigt, F F; van 't Hoff, M; Helmchen, F (2011). Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens. Biomedical Optics Express, 2(7):2035-2046.

Pelet, Serge; Peter, Matthias (2011). Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells. In: Koeppl, Heinz; Densmore, Douglas; Setti, Gianluca; di Bernardo, Mario. Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology. New York, USA: Springer, 369-394.

Schaffter, Thomas; Marbach, Daniel; Floreano, Dario (2011). GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics, 27(16):2263-2270.

Li, Baojuan; Daunizeau, Jean; Stephan, Klaas E; Penny, Will; Hu, Dewen; Friston, Karl J (2011). Generalised filtering and stochastic DCM for fMRI. NeuroImage, 58(2):442-457.

Müller, Christian L; Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories. Advances in Experimental Medicine and Biology, 736:477-498.

Ambühl, Mark E; Brepsant, Charles; Meister, Jean-Jacques; Verkhovsky, Alexander B; Sbalzarini, Ivo F (2011). High-resolution cell outline segmentation and tracking from phase-contrast microscopy images. Journal of Microscopy, 245(2):161-170.

Dudkina, N V; Kudryashev, M; Stahlberg, H; Boekema, E J (2011). Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America, 108(37):15196-15200.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Scientific Reports, 1:154.

Chumbley, J R; Flandin, G; Bach, D R; Daunizeau, Jean; Fehr, Ernst; Dolan, R J; Friston, K J (2011). Learning and generalization under ambiguity: An fMRI Study. PLoS Computational Biology, 8(1):e1002346.

Cheng, Danni; Jenner, Andrew M; Shui, Guanghou; Cheong, Wei Fun; Mitchell, Todd W; Nealon, Jessica R; Kim, Woojin S; McCann, Heather; Wenk, Markus R; Halliday, Glenda M; Garner, Brett (2011). Lipid pathway alterations in Parkinson's disease primary visual cortex. PLoS ONE, 6(2):e17299.

Azzouzi, I; Moest, H; Winkler, J; Fauchère, J C; Gerber, A P; Wollscheid, B; Stoffel, M; Schmugge, M; Speer, O (2011). MicroRNA-96 directly inhibits γ-Globin expression in human erythropoiesis. PLoS ONE, 6(7):e22838.

Brodersen, Kay H; Haiss, Florent; Ong, Cheng S; Jung, Fabienne; Tittgemeyer, Marc; Buhmann, Joachim M; Weber, Bruno; Stephan, Klaas E (2011). Model-based feature construction for multivariate decoding. NeuroImage, 56(2):601-615.

Glatter, Timo; Schittenhelm, Ralf B; Rinner, Oliver; Roguska, Katarzyna; Wepf, Alexander; Jünger, Martin A; Köhler, Katja; Jevtov, Irena; Choi, Hyungwon; Schmidt, Alexander; Nesvizhskii, Alexey I; Stocker, Hugo; Hafen, Ernst; Aebersold, Ruedi; Gstaiger, Matthias (2011). Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology, 7:547.

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

Kiefer, Patrick; Delmotte, Nathanaël; Vorholt, Julia A (2011). Nanoscale Ion-Pair Reversed-Phase HPLC−MS for Sensitive Metabolome Analysis. Analytical Chemistry, 83(3):850-855.

Friston, Karl J; Li, Baojuan; Daunizeau, Jean; Stephan, Klaas E (2011). Network discovery with DCM. NeuroImage, 56(3):1202-1221.

Ramaswamy, Rajesh; Sbalzarini, Ivo F; González-Segredo, Nélido (2011). Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks. PLoS ONE, 6(1):e16045.

Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph (2011). Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella. PLoS Genetics, 7(2):e1001296.

Koumoutsakos, P; Bayati, B; Milde, F; Tauriello, G (2011). Particle simulations of morphogenesis. Mathematical Models and Methods in Applied Sciences, 21(Supp. 1):955-1006.

Schultze, S M; Jensen, J; Hemmings, B A; Tschopp, O; Niessen, M (2011). Promiscuous affairs of PKB/AKT isoforms in metabolism. Archives of Physiology and Biochemistry, 117(2):70-77.

Felekis, D (2011). Quantifying growth mechanics of living, growing plant cells in situ using microrobotics. Micro & Nano Letters, 6(5):311.

Brankatschk, Ben; Pons, Véronique; Parton, Robert G; Gruenberg, Jean (2011). Role of SNX16 in the dynamics of tubulo-cisternal membrane domains of late endosomes. PLoS ONE, 6(7):e21771.

Misselwitz, Benjamin; Kreibich, Saskia K; Rout, Samuel; Stecher, Bärbel; Periaswamy, Balamurugan; Hardt, Wolf-Dietrich (2011). Salmonella enterica Serovar Typhimurium Binds to HeLa Cells via Fim-Mediated Reversible Adhesion and Irreversible Type Three Secretion System 1-Mediated Docking. Infection and Immunity, 79(1):330-341.

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

Papadopoulou, Aikaterini S; Dooley, James; Linterman, Michelle A; Pierson, Wim; Ucar, Olga; Kyewski, Bruno; Zuklys, Saulius; Hollander, Georg A; Matthys, Patrick; Gray, Daniel H D; De Strooper, Bart; Liston, Adrian (2011). The thymic epithelial microRNA network elevates the threshold for infection-associated thymic involution via miR-29a mediated suppression of the IFN-α receptor. Nature Immunology, 13(2):181-187.

Pelet, S; Rudolf, F; Nadal-Ribelles, M; de Nadal, E; Posas, F; Peter, M (2011). Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science, 332(6030):732-735.

Lütcke, H; Helmchen, F (2011). Two-photon imaging and analysis of neural network dynamics. Reports on Progress in Physics, 74(8):086602.

Schmidt, Florian Ingo; Bleck, Christopher Karl Ernst; Helenius, Ari; Mercer, Jason (2011). Vaccinia extracellular virions enter cells by macropinocytosis and acid-activated membrane rupture. EMBO Journal Online, 30(17):3647-3661.

Milias-Argeitis, Andreas; Porreca, Riccardo; Summers, Sean; Lygeros, John (2010). Bayesian model selection for the yeast GATA-factor network: a comparison of computational approaches. In: 49th IEEE Conference on Decision and Control, Atlanta, GA, 15 December 2010 - 17 December 2010, 3379-84.

Porreca, Riccardo; Cinquemani, Eugenio; Lygeros, John; Ferrari-Trecate, Giancarlo (2010). Structural identification of unate-like genetic network models from time-lapse protein concentration measurements. In: 49th IEEE Conference on Decision and Control, Atlanta, GA, 15 December 2010 - 17 December 2010, 2529-34.

Daunizeau, J; den Ouden, H E M; Pessiglione, M; Kiebel, S J; Stephan, K E; Friston, K J (2010). Observing the observer (I): Meta-bayesian models of learning and decision-making. PLoS ONE, 5(12):e15554.

Daunizeau, J; den Ouden, H E M; Pessiglione, M; Kiebel, S J; Friston, K J; Stephan, K E (2010). Observing the observer (II): Deciding when to decide. PLoS ONE, 5(12):e15555.

Blanchoud, Simon; Budirahardja, Yemima; Naef, Felix; Gönczy, Pierre (2010). ASSET: A Robust Algorithm for the Automated Segmentation and Standardization of Early Caenorhabditis elegans Embryos. Developmental Dynamics, 239:3285-3296.

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

Baranek, Sophie; Bezler, Alexandra; Adamczyk, Christian; Gönczy, Pierre; Renaud, Philippe (2010). Temperature gradient stimulation for cell division in C. Elegans Embryos on chip. In: 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences , Groningen, Netherlands, 3 October 2010 - 7 October 2010.

Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N (2010). The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates. Molecular Biology of the Cell, 21:3475-3486.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2010). Fast Exact Stochastic Simulation Algorithms Using Partial Propensities. In: International Conference of Numerical Analysis and Applied Mathematics, Rhodes, Greece, 19 September 2010 - 25 September 2010, 1338-1341.

Awile, Omar; Demirel, Ömer; Sbalzarini, Ivo F; Simos, Theodore E; Psihoyios, George; Tsitouras, Ch (2010). Toward an Object-Oriented Core of the PPM Library. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM), Rhodes, Greece, 19 September 2010 - 25 September 2010, 1313-1316.

Geertz, Marcel; Maerkl, Sebastian J (2010). Experimental strategies for studying transcription factor-DNA binding specificities. Briefings in Functional Genomics:1-12.

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

Rohr, Rudolf Philippe; Scherer, Heike; Kehrli, Patrik; Mazza, Christian; Bersier, Louis-Félix (2010). Modeling Food Webs: Exploring Unexplained Structure Using Latent Traits. The American Naturalist, 176:170-177.

Kozak, K; Bauch, A; Pylak, T; Rinn, B (2010). Towards a comprehensive open source platform for management and analysis of High Content Screening data. European Pharmaceutical Review, 4:34-38.

Müller, Christian L; Sbalzarini, Ivo F (2010). Gaussian Adaptation as a unifying framework for continuous black-box optimization and adaptive Monte Carlo sampling. In: 2010 IEEE Congress on Evolutionary Computation (CEC), Barcelona, Spain, 18 July 2010 - 23 July 2010, 1-8.

Lütcke, H; Murayama, M; Hahn, T; Margolis, D J; Astori, S; Meyer zum Alten Borgloh, S; Göbel, W; Yang, Y; Tang, W; Kügler, S; Sprengler, R; Nagai, T; Miyawaki, A; Larkum, M E; Helmchen, F; Hasan, M T (2010). Optical recording of neuronal activity with a genetically-encoded calcium indicator in anesthetized and freely moving mice. Frontiers in Neural Circuits, 4:9.

Delgado-Gonzalo, Ricard; Dénervaud, Nicolas; Maerkl, Sebastian J; Unser, Michael (2010). Multi-target tracking of packed yeast cells. In: IEEE International Symposium on Biomedical Imaging, Rotterdam, Netherlands, 14 April 2010 - 17 April 2010.

Roiser, J P; Stephan, K E; den Ouden, H E M; Friston, K J; Joyce, E M (2010). Adaptive and aberrant reward prediction signals in the human brain. NeuroImage, 50(2):657-664.

Penny, W D; Stephan, K E; Daunizeau, J; Rosa, M J; Friston, K J; Schofield, T M; Leff, A P (2010). Comparing families of dynamic causal models. PLoS Computational Biology, 6(3):e1000709.

Stephan, K E; Penny, W D; Moran, R J; den Ouden, H E M; Daunizeau, J; Friston, K J (2010). Ten simple rules for dynamic causal modeling. NeuroImage, 49(4):3099-3109.

Tan, K R; Brown, M; Labouèbe, G; Yvon, C; Creton, C; Fritschy, J M; Rudolph, U; Lüscher, C (2010). Neural bases for addictive properties of benzodiazepines. Nature, 463(7282):769-774.

Guitart-Masip, M; Bunzeck, N; Stephan, K E; Dolan, R J; Düzel, E (2010). Contextual novelty changes reward representations in the striatum. Journal of Neuroscience, 30(5):1721-1726.

Vellekoop, I M; Aegerter, C M (2010). Focusing light through living tissue. In: Optical coherence tomography and coherence domain optical methods in biomedicine XIV, San Francisco, CA, USA, 25 January 2010 - 27 January 2010, 755430 (10 pp.).

Eisenegger, Christoph; Naef, Michael; Snozzi, R; Heinrichs, Markus; Fehr, Ernst (2010). Prejudice and truth about the effect of testosterone on human bargaining behaviour. Nature, 463(7279):356-359.

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

Bayati, Basil; Owhadi, Houman; Koumoutsakos, Petros (2010). A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA). Journal of Chemical Physics, 133(24):244117.

Ramaswamy, Rajesh; Sbalzarini, Ivo F (2010). A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks. The Journal of chemical physics, 132(4):044102.

Polyansky, Anton A; Ramaswamy, Rajesh; Volynsky, Pavel E; Sbalzarini, Ivo F; Marrink, Siewert J; Efremov, Roman G (2010). Antimicrobial Peptides Induce Growth of Phosphatidylglycerol Domains in a Model Bacterial Membrane. Journal of Physical Chemistry Letters, 1(20):3108-3111.

Helmuth, Jo A; Paul, Grégory; Sbalzarini, Ivo F (2010). Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics, 11(1):372.

Dechant, Reinhard; Binda, Matteo; Lee, Sung Sik; Pelet, Serge; Winderickx, Joris; Peter, Matthias (2010). Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V‐ATPase. EMBO Journal Online, 29(15):2515-2526.

Kümmel, Anne; Ewald, Jennifer Christina; Fendt, Sarah-Maria; Jol, Stefan Jasper; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2010). Differential glucose repression in common yeast strains in response to HXK2 deletion. FEMS Yeast Research, 10(3):322-332.

Schrader, Birte; Reboux, Sylvain; Sbalzarini, Ivo F (2010). Discretization correction of general integral PSE Operators for particle methods. Journal of Computational Physics, 229(11):4159-4182.

Misselwitz, B; Strittmatter, G; Periaswamy, B; Schlumberger, M C; Rout, S; Horvath, P; Kozak, K; Hardt, W D (2010). Enhanced CellClassifier: a multi-class classification tool for microscopy images. BMC Bioinformatics, 11:30.

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

Müller, Christian L; Sbalzarini, Ivo F (2010). Gaussian Adaptation Revisited – An Entropic View on Covariance Matrix Adaptation. Lecture Notes in Computer Science, 6024:432-441.

Grewe, B F; Langer, D; Kasper, H; Kampa, B M; Helmchen, F (2010). High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision. Nature Methods, 7(5):399-405.

Wenk, Markus R (2010). Lipidomics: new tools and applications. Cell, 143(6):888-95.

Schluck, T; Aegerter, C M (2010). Photo-elastic properties of the wing imaginal disc of Drosophila. European Physical Journal E - Soft Matter and Biological Physics, 33(2):111-115.

de Lachapelle, A M; Bergmann, S (2010). Precision and scaling in morphogen gradient read-out. Molecular Systems Biology, 6:351.

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Szabad, János (2010). Putting together rather than taking apart. EMBO Reports, 11(12):904-906.

Marbach, D; Prill, R; Schaffter, T; Mattiussi, C; Floreano, D; Stolovitzky, G (2010). Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 107(14):6286-6291.

Vellekoop, I M; Aegerter, C M (2010). Scattered light fluorescence microscopy: imaging through turbid layers. Optics Letters, 35(8):1245-1247.

Shapiguzov, A; Ingelsson, B; Samol, I; Andres, C; Kessler, F; Rochaix, J -D; Vener, A V; Goldschmidt-Clermont, M (2010). The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 107(10):4782-4787.

Vayssier-Taussat, Muriel; Le Rhun, Danielle; Deng, Hong Kuan; Biville, Francis; Cescau, Sandra; Danchin, Antoine; Marignac, Geneviève; Lenaour, Evelyne; Boulouis, Henri Jean; Mavris, Maria; Arnaud, Lionel; Yang, Huanming; Wang, Jing; Quebatte, Maxime; Engel, Philipp; Saenz, Henri; Dehio, Christoph (2010). The Trw Type IV Secretion System of Bartonella Mediates Host-Specific Adhesion to Erythrocytes. PLoS Pathogens, 6(6):e1000946.

Jol, Stefan J; Kümmel, Anne; Hatzimanikatis, Vassily; Beard, Daniel A; Heinemann, Matthias (2010). Thermodynamic Calculations for Biochemical Transport and Reaction Processes in Metabolic Networks. Biophysical Journal, 99(10):3139-3144.

Ehses, J A; Meier, D T; Wueest, S; Rytka, J; Boller, S; Wielinga, P Y; Schraenen, A; Lemaire, K; Debray, S; Van Lommel, L; Pospisilik, J A; Tschopp, O; Schultze, S M; Malipiero, U; Esterbauer, H; Ellingsgaard, H; Rütti, S; Schuit, F C; Lutz, T A; Böni-Schnetzler, M; Konrad, D; Donath, M Y (2010). Toll-like receptor 2-deficient mice are protected from insulin resistance and beta cell dysfunction induced by a high-fat diet. Diabetologia, 53(8):1795-1806.

Fendt, Sarah-Maria; Buescher, Joerg Martin; Rudroff, Florian; Picotti, Paola; Zamboni, Nicola; Sauer, Uwe (2010). Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Molecular Systems Biology, 6:356.

Fendt, Sarah-Maria; Sauer, Uwe (2010). Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates. BMC Systems Biology, 4(1):12.

Fendt, Sarah-Maria; Oliveira, Ana Paula; Christen, Stefan; Picotti, Paola; Dechant, Reinhard Christoph; Sauer, Uwe (2010). Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Molecular Systems Biology, 6:432.

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

Cinquemani, Eugenio; Porreca, Riccardo; Lygeros, John; Ferrari-Trecate, Giancarlo (2009). Canalizing structure of genetic network dynamics: modelling and identification via mixed-integer programming. In: Combined 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference, Shanghai, 15 December 2009 - 18 December 2009, 5618-23.

Delgado-Gonzalo, Ricard; Tafti, Pouya Dehghani; Unser, Michael (2009). Fractional Laplacian Pyramids. In: International Conference on Image Processing, Cairo, Egypt, 7 November 2009 - 10 November 2009.

Stettler, M; Eicke, S; Mettler, T; Messerli, G; Hörtensteiner, S; Zeeman, S C (2009). Blocking the Metabolism of Starch Breakdown Products in Arabidopsis Leaves Triggers Chloroplast Degradation. Molecular Plant, 2(6):1233-1246.

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

Grewe, B F; Helmchen, F (2009). Optical probing of neuronal ensemble activity. Current Opinion in Neurobiology, 19(5):520-529.

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

Bayati, B; Chatelain, P; Koumoutsakos, P (2009). D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics, 228(16):5908-5916.

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

Cardinale, Janick; Rauch, Alexander; Barral, Yves; Székely, Gábor; Sbalzarini, Ivo F (2009). Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, 28 June 2009 - 1 July 2009, 1091-1094.

Baumgärtel, K; Tweedie-Cullen, R Y; Grossmann, J; Gehrig, P; Livingstone-Zatchej, M; Mansuy, I M (2009). Changes in the proteome after neuronal Zif268 overexpression. Journal of Proteome Research, 8(7):3298-3316.

Smith, R S (2009). Modeling plant morphogenesis and growth. In: New Trends in the Physics and Mechanics of Biological Systems. Oxford: Oxford University Press, online.

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

Engelbrecht, C J; Göbel, W; Helmchen, F (2009). Enhanced fluorescence signal in nonlinear microscopy through supplementary fiber-optic light collection. Optics Express, 17(8):6421-6435.

Bragg, J G; Wagner, A (2009). Protein material costs: single atoms can make an evolutionary difference. Trends in Genetics, 25(1):5-8.

Hafner, M; Koeppl, H; Hasler, M; Wagner, A (2009). 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biology, 5(10):e1000534.

Kotte, Oliver; Heinemann, Matthias (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4):519-525.

Ramaswamy, Rajesh; González-Segredo, Nélido; Sbalzarini, Ivo F (2009). A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. The Journal of chemical physics, 130(24):244104.

Mjolsness, E; Orendorff, D; Chatelain, P; Koumoutsakos, P (2009). An exact accelerated stochastic simulation algorithm. The Journal of chemical physics, 130(14):144110.

Morel, Etienne; Gruenberg, Jean (2009). Annexin A2 binding to endosomes and functions in endosomal transport are regulated by tyrosine 23 phosphorylation. Journal of Biological Chemistry, 284(3):1604-1611.

Morel, Etienne; Parton, Robert G; Gruenberg, Jean (2009). Annexin A2-dependent polymerization of actin mediates endosome biogenesis. Developmental cell, 16(3):445-457.

Smith, R S; Bayer, E M (2009). Auxin transport-feedback models of patterning in plants. Plant, Cell and Environment, 32(9):1258-1271.

Falcón, B L; Hashizume, H; Koumoutsakos, P; Chou, J; Bready, J V; Coxon, A; Oliner, J D; McDonald, D M (2009). Contrasting actions of selective inhibitors of angiopoietin-1 and angiopoietin-2 on the normalization of tumor blood vessels. American Journal of Pathology, 175(5):2159-70.

Helmuth, Jo A; Sbalzarini, Ivo F (2009). Deconvolving Active Contours for Fluorescence Microscopy Images. Lecture Notes in Computer Science, 5875:544-553.

Nienhaus, U; Aegerter-Wilmsen, T; Aegerter, C M (2009). Determination of mechanical stress distribution in Drosophila wing discs using photoelasticity. Mechanisms of Development, 126(11-12):942-949.

Boisson-Dernier, A; Roy, S; Kritsas, K; Grobei, M A; Jaciubek, M; Schroeder, J I; Grossniklaus, U (2009). Disruption of the pollen-expressed FERONIA homologs ANXUR1 and ANXUR2 triggers pollen tube discharge. Development, 136(19):3279-3288.

Gebäck, T; Koumoutsakos, P (2009). Edge detection in microscopy images using curvelets. BMC bioinformatics, 10:75.

Guan, Xue Li; Souza, Cleiton M; Pichler, Harald; Dewhurst, Gisèle; Schaad, Olivier; Kajiwara, Kentaro; Wakabayashi, Hirotomo; Ivanova, Tanya; Castillon, Guillaume A; Piccolis, Manuele; Abe, Fumiyoshi; Loewith, Robbie; Funato, Kouichi; Wenk, Markus R; Riezman, Howard (2009). Functional interactions between sphingolipids and sterols in biological membranes regulating cell physiology. Molecular Biology of the Cell, 20(7):2083-95.

Marbach, Daniel; Schaffter, Thomas; Mattiussi, Claudio; Floreano, Dario (2009). Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology, 16(2):229-39.

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

Bayer, E M; Smith, R S; Mandel, T; Nakayama, N; Sauer, M; Prusinkiewicz, P; Kuhlemeier, C (2009). Integration of transport-based models for phyllotaxis and midvein formation. Genes and Development, 23(3):373-384.

Maerkl, Sebastian J (2009). Microfluidic High-Throughput Screening. Integrative Biology, 1:19-29.

Stephan, K E; Tittgemeyer, M; Knösche, T R; Moran, R J; Friston, K J (2009). Tractography-based priors for dynamic causal models. NeuroImage, 47(4):1628-1638.

Ferrada, E; Wagner, A (2008). Protein robustness promotes evolutionary innovations on large evolutionary time-scales. Proceedings of the Royal Society B: Biological Sciences, 275(1643):1595-1602.

Wright, J; Wagner, A (2008). The Systems Biology Research Tool: evolvable open-source software. BMC Systems Biology, 2:55.

Wagner, A (2008). Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B: Biological Sciences, 275(1630):91-100.

Milde, F; Bergdorf, M; Koumoutsakos, P (2008). A hybrid model for three-dimensional simulations of sprouting angiogenesis. Biophysical journal, 95(7):3146-60.

Rossinelli, D; Bayati, B; Koumoutsakos, P (2008). Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems. Chemical Physics Letters, 451(1-3):136 - 140.

Bayati, B; Chatelain, P; Koumoutsakos, P (2008). Multiresolution stochastic simulations of reaction-diffusion processes. Physical Chemistry Chemical Physics (PCCP), 10(39):5963-6.

Wagner, A (2008). Neutralism and selectionism: a network-based reconciliation. Nature Reviews. Genetics, 9(12):965-974.

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

This list was generated on Thu Nov 23 22:19:21 2017 CET.