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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.
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.
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.
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.
Schwank, G; Yang, S F; Restrepo, S; Basler, K (2012). Comment on "Dynamics of dpp signaling and proliferation control". Science, 335(6067):401.
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.
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.
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.
Ghielmetti, Giulia; Aegerter, Christof M (2012). Scattered light fluorescence microscopy in three dimensions. Optics Express, 20(4):3744-3752.
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.
Hamaratoglu, Fisun; de Lachapelle, Aitana Morton; 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.
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.
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.
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.
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.
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.
Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. Journal of Chemical Physics, 135(24):244103.
Schaffter, Thomas; Marbach, Daniel; Floreano, Dario (2011). GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics, 27(16):2263-2270.
Müller, Christian L; Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories. In: Goryanin, Igor I; Goryachev, Andrew B. Advances in Systems Biology. New York, NY: Springer, 477-498.
Ramaswamy, Rajesh; Sbalzarini, Ivo F (2011). Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Scientific Reports, 1:154.
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.
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.
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.
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.
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. American Institute of Physics, 1338-1341.
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.
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.
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. Spie - The International Society For Optical Engineering, 755430 (10 pp.).
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.
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.
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.
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.
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.
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.
Hamaratoglu, F; Basler, K; Affolter, M (2009). Confronting morphogen gradients: how important are they for growth? Science Signaling, 2(94):pe67.
Köhler, K; Brunner, E; Xue, L Guan; Boucke, K; Greber, U F; Mohanty, S; Barth, J M I; 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.
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.
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.
Gebäck, T; Koumoutsakos, P (2009). Edge detection in microscopy images using curvelets. BMC bioinformatics, 10:75.
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.
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.
