Publications by WingX

 

2013

  • Handke B, Poernbacher I, Goetze S, Ahrens DH, Omasits U, Marty F, Simigdala N, Meyer I, Wollscheid B, Brunner E, Hafen E, Lehner DF The hemolymph proteome of fed and starved Drosophila larvae. PloS One, in press.
  • Schluck T et al. Mechanical Control of Organ Size in the Development of the Drosophila Wing Disc. PloS One, in press.
  • Sbalzarini IF: Modeling and simulation of biological systems from image data. Bioessays. 2013 May;35(5):482-90. Pubmed
  • Zartman J, Restrepo S, Basler K: A high-throughput template for optimizing Drosophila organ culture with response-surface methods. Development. 2013 Feb;140(3):667-74. Pubmed
  • 2012

    • Ramdya P, Schaffter T, Floreano D, Benton R: Fluorescence behavioral imaging (FBI) tracks identity in heterogeneous groups of Drosophila. PLoS One. 2012;7(11):e48381. Epub 2012 Nov 7. Pubmed
    • Ochoa-Espinosa A, Affolter M: Branching morphogenesis: from cells to organs and back. Cold Spring Harb Perspect Biol. 2012 Oct 1;4(10). Pubmed
    • Nienhaus U, Aegerter-Wilmsen T, Aegerter CM: In-vivo imaging of the Drosophila wing imaginal disc over time: novel insights on growth and boundary formation. PLoS One. 2012;7(10):e47594. Epub 2012 Oct 16. Pubmed
    • Aegerter-Wilmsen T, Heimlicher MB, Smith AC, Barbier de Reuille P, Smith RS, Aegerter CM, Basler K: Integrating force-sensing and signaling pathways in a model for the regulation of wing imaginal disc size. Development. 2012 Sep;139(17):3221-31. Epub 2012 Jul 25. Pubmed
    • Ramaswamy R, González-Segredo N, Sbalzarini IF, Grima R: Discreteness-induced concentraiton inversion in mesoscopic chemical systems. Nat Commun, 3:779, 2012. Pubmed
    • Cardinale J, Paul G, Sbalzarini IF: Discrete region competition for unknown numbers of connected regions. IEEE Trans Image Process. 2012 Apr 3. [Epub ahead of print] Pubmed
    • Ghielmetti G, Aegerter CM: Scattered light fluorescence microscopy in three dimensions. Opt Express. 2012 Feb 13;20(4):3744-52. Pubmed
    • Müller CL, Ramaswamy R, Sbalzarini IF: Global parameter identification of stochastic reaction networks from single trajectories. Adv Exp Med Biol. 2012;736:477-98. Pubmed
    • Schwank G, Restrepo S, Yang SF, Basler K: Comment on “Dynamics of Dpp signaling and proliferation control”.Science. 2012 Jan 27;335(6067):401; author reply 401. Pubmed

    2011

    • Ramaswamy R, Sbalzarini IF: Exact on-lattice stochastic reaction-diffusion simulations using partial-propensity methods. J Chem Phys. 2011 Dec 28;135(24):244103. Pubmed
    • Caussinus E, Kanca O, Affolter M: Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nat Struct Mol Biol. Nat Struct Mol Biol. 2011 Dec 11;19(1):117-21. Pubmed
    • Ramaswamy R, Sbalzarini IF: Intrinsic noise alters the frequency spectrum of mesoscopic oscillatory chemical reaction systems. Sci Rep. 2011;1:154. Epub 2011 Nov 11. Pubmed
    • Dalessi S, Neves A, Bergmann S: Modeling morphogen gradient formation from arbitrary realistically shaped sources. J Theor Biol. 2012 Feb 7;294C:130-138. Epub 2011 Nov 10. Pubmed
    • Zielke N, Kim KJ, Tran V, Shibutani ST, Bravo MJ, Nagarajan S, van Straaten M, Woods B, von Dassow G, Rottig C, Lehner CF, Grewal SS, Duronio RJ, Edgar BA: Control of Drosophila endocycles by E2F and CRL4(CDT2).Nature. 2011 Oct 30;480(7375):123-7. doi: 10.1038/nature10579. Pubmed
    • Restrepo S, Basler K: Morphogen gradients: expand and repress. Curr Biol. 2011 Oct 11;21(19):R815-7. Pubmed
    • Vermot J, Affolter M: Modeling new conceptual interpretations of development. Development. 2011 Oct;138(19):4111-5. Pubmed
    • Hamaratoglu F, de Lachapelle AM, Pyrowolakis G, Bergmann S, Affolter M: Dpp signaling activity requires Pentagone to scale with tissue size in the growing Drosophila wing imaginal disc. PLoS Biol. 2011 Oct;9(10):e1001182. Epub 2011 Oct 25. Pubmed
    • Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M: Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology. 2011 Nov 8;7:547. doi: 10.1038/msb.2011.79. Pubmed
    • Schwank G, Dalessi S, Yang SF, Yagi R, de Lachapelle AM, Affolter M, Bergmann S, Basler K: Formation of the long range Dpp morphogen gradient. PLoS Biol. 2011 Jul;9(7):e1001111. Epub 2011 Jul 26. Pubmed
    • Vuilleumier R, Affolter M, Pyrowolakis G: Pentagone: patrolling BMP morphogen signaling. Fly (Austin). 2011 Jul-Sep;5(3):210-4. Epub 2011 Jul 1. Pubmed
    • Schaffter T, Marbach D, Floreano D: GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics. 2011 Aug 15;27(16):2263-70. Epub 2011 Jun 22. Pubmed
    • Paul G, Müller CL, Sbalzarini IF: Sensitivity analysis from evolutionary algorithm search paths. In Proc. EVOLVE, Workshop on Probability, Set Oriented Numerics and Evolutionary Computation, Luxembourg, May 2011. Link
    • Willecke M, Toggweiler J, and Basler K: Loss of PI3K blocks cell-cycle progression in a Drosophila tumor model. Oncogene. 2011 Sep 29;30(39):4067-74. doi: 10.1038/onc.2011.125. Epub 2011 Apr 25. Pubmed
    • Koumoutsakos P, Bayati B, Milde F, Tauriello G: Particle simulations of morphogenesis. Math Mod Meth Appl S. 2011 Apr;21:955–1006, Apr. 2011. DOI Link
    • Affolter M, Basler K: Cytonemes show their colors. Science. 2011 Apr 15;332(6027):312-3. Pubmed
    • Schilling S, Willecke M, Aegerter-Wilmsen T, Cirpka OA, Basler K, von Mering C: 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 Comput Biol. 2011 Apr;7(4):e1002025. Epub 2011 Apr 7. Pubmed
    • Ramaswamy R, Sbalzarini IF, González-Segredo N: Noise-induced modulation of the relaxation kinetics around a non-equilibrium steady state of non-linear chemical reaction networks. PLoS One. 2011 Jan 28;6(1):e16045. Pubmed
    • Schwank G, Tauriello G, Yagi R, Kranz E, Koumoutsakos P, Basler K: Antagonistic growth regulation by Dpp and Fat drives uniform cell proliferation. Dev Cell. 2011 Jan 18;20(1):123-30. Pubmed
    • Ramaswamy R, Sbalzarini IF: A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays. J Chem Phys. 2011 Jan 7;134(1):014106. Pubmed
    • Bayati B, Chatelain P, Koumoutsakos P: Adaptive mesh refinement for stochastic reaction-diffusion processes.Journal of Computational Physics Volume 230, Issue 1, 1 January 2011, Pages 13-26. DOI Link
    • Petrov V, Aegerter CM: Integrating Mechanical Control Theory into Models of Biological Development. J Mech Med Biol. 2011; 11(4):713-34. DOI Link

    2010

    • Bayati B, Owhadi H, Koumoutsakos P: A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA). J Chem Phys. 2010 Dec 28;133(24):244117. Pubmed
    • Bergdorf M, Sbalzarini IF, Koumoutsakos P: A Lagrangian particle method for reaction-diffusion systems on deforming surfaces. 2010 Nov;61(5):649-63. Epub 2009 Dec 18. Pubmed
    • Szabad J: Putting together rather than taking apart. EMBO Rep. 2010 Dec;11(12):904-6. Epub 2010 Nov 19. Pubmed
    • de Lachapelle AM, Bergmann S: Pre-steady and stable morphogen gradients: can they coexist? Molecular Systems Biology 6: 428; published online 16 November 2010. DOI Link
    • Ahrens CH, Brunner E, Qeli E, Basler K, Aebersold R: Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol. 2010 Nov;11(11):789-801. Epub 2010 Oct 14. Pubmed
    • Leiva L: Kräftemessen am Anfang des Lebens. Neue Zürcher Zeitung, 13. Oktober 2010. Link
    • Polyansky A, Ramaswamy R, Volynsky PE, Sbalzarini IF, Marrink SJ, Efremov RG: Antimicrobial peptides induce growth of phosphatidylglycerol domains in a model bacterial membrane. J. Phys. Chem. Lett., 1:3108–3111, 2010. Epub 2010 October 11. DOI Link
    • Ramaswamy R, Sbalzarini IF: Fast Exact Stochastic Simulation Algorithms Using Partial Propensities. AIP Conf. Proc. 1281, pp. 1338-1341. ICNAAM 19–25 September 2010. DOI Link
    • Yagi R, Mayer F, Basler K: Refined LexA transactivators and their use in combination with the Drosophila Gal4 system. Proc Natl Acad Sci USA 2010 Sept 14;107(37):16166-71. Epub 2010 Aug 30. Pubmed
    • Helmuth JA, Paul G, Sbalzarini IF: Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics. 2010 Jul 7;11:372. Pubmed
    • Müller CL, Sbalzarini IF: Gaussian Adaptation as a unifying framework for continuous black-box optimization and adaptive Monte Carlo sampling. In Proc. IEEE Congress on Evolutionary Computation (CEC), pages 2594–2601, Barcelona, Spain, July 2010. DOI Link
    • Schluck T, Aegerter CM: Photo-elastic properties of the wing imaginal disc of Drosophila. Eur Phys J E Soft Matter. 2010 Oct;33(2):111-5. Epub 2010 May 28. Pubmed
    • Vuilleumier R, Springhorn A, Patterson L, Koidl S, Hammerschmidt M, Affolter M, Pyrowolakis G:Control of Dpp morphogen signalling by a secreted feedback regulator.Nat Cell Biol. 2010 Jun;12(6):611-7. Epub 2010 May 9. Pubmed
    • Nature Research Highlights: Microscopy: See through tissue. Nature 465, 12 (06 May 2010), Published online 05 May 2010. DOI Link
    • Vellekoop I, Aegerter CM: Scattered light fluorescence microscopy: imaging through turbid layers. Opt Lett. 2010 Apr 15;35(8):1245-7. Pubmed
    • Müller CL, Sbalzarini IF: Gaussian adaptation revisited — an entropic view on covariance matrix adaptation. In Proc. EvoStar, volume 6024 of Lecture Notes in Computer Science, pages 432–441, Istanbul, Turkey, April 2010. Springer. DOI Link
    • Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G: Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. Pubmed
    • Schrader B, Reboux S, Sbalzarini IF: Discretization correction of general integral PSE operators in particle methods. J. Comput. Phys., 229:4159–4182, 2010 June. Epub 2010 Feb 14. DOI Link
    • de Lachapelle AM, Bergmann S: Precision and scaling in morphogen gradient read-out. Mol Syst Biol. 2010;6:351. Epub 2010 Mar 9. Pubmed
    • Aegerter-Wilmsen T, Smith SC, Christen AJ, Aegerter CM, Hafen E, Basler K: Exploring the effects of mechanical feedback on epithelial topology. Development. 2010 Feb;137(3):499-504. Pubmed
    • Vellekoop IM, Aegerter CM: Focusing light through living tissue. SPIE proceedings 2010 Feb;7554:755430. DOI Link
    • Baumgartner R, Poernbacher I, Buser N, Hafen E, Stocker H:The WW domain protein Kibra acts upstream of Hippo in Drosophila.Dev Cell. 2010 Feb 16;18(2):309-16. Pubmed
    • Ramaswamy R, Sbalzarini IF: A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks.J Chem Phys. 2010 Jan 28;132(4):044102. Pubmed
    • Schwank G, Basler K: Regulation of organ growth by morphogen gradients. Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a001669. Pubmed
    • 2009

      • Gazzola M, Burckhardt CJ, Bayati B, Engelke M, Greber UF, Koumoutsakos P:A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus. PLoS Comput Biol. 2009 Dec;5(12):e1000623. Epub 2009 Dec 24. Pubmed
      • Weiss A, Charbonnier E, Ellertsdóttir E, Tsirigos A, Wolf C, Schuh R, Pyrowolakis G, Affolter M:A conserved activation element in BMP signaling during Drosophila development. Nat Struct Mol Biol. 2010 Jan;17(1):69-76. Epub 2009 Dec 13. Pubmed
      • Helmuth JA, Sbalzarini IF: Deconvolving active contours for fluorescence microscopy images. Proc Int Symp Visual Computing (ISVC), Las Vegas, USA, December 2009. Lect. Notes Comput. Sc. 5875:544-553, 2009. DOI Link
      • Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E: Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol. 2009 Nov;7(11):e1000236. Epub 2009 Nov 3. Pubmed
      • Hamaratoglu F, Basler K, Affolter M: Confronting morphogen gradients: how important are they for growth? Sci Signal, 2009 Oct 27;2(94):pe67. Pubmed
      • Falcón BL, Hashizume H, Koumoutsakos P, Chou J, Bready JV, Coxon A, Oliner JD, McDonald DM: Contrasting actions of selective inhibitors of angiopoietin-1 and angiopoietin-2 on the normalization of tumor blood vessels. Am J Pathol. 2009 Nov;175(5):2159-70. Epub 2009 Oct 8. Pubmed
      • Köhler K, Brunner E, Guan XL, Boucke K, Greber UF, Mohanty S, Barth JM, Wenk MR, Hafen E: A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Autophagy. 2009 Oct;5(7):980-90. Epub 2009 Oct 22. Pubmed
      • Bayati B, Chatelain P, Koumoutsakos: D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics. 2009 Sept;228(16):5909-5918. DOI Link
      • Nienhaus U, Aegerter-Wilmsen T, Aegerter CM:Determination of mechanical stress distribution in Drosophila wing discs using photoelasticity. Mech Dev. 2009 Dec;126(11-12):942-9. Epub 2009 Sep 11. Pubmed
      • Ramaswamy R, González-Segredo N, Sbalzarini IF:A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. J Chem Phys. 2009 Jun 28;130(24):244104. Pubmed
      • Cardinale J, Rauch A, Barral Y, Székely G, Sbalzarini IF:Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking. Proc IEEE Intl Symposium Biomedical Imaging (ISBI), pages 1091-1094, Boston, USA, June 2009. DOI Link
      • Mjolsness E, Orendorff D, Chatelain P, Koumoutsakos P:An exact accelerated stochastic simulation algorithm. J Chem Phys. 2009 Apr 14;130(14):144110. Pubmed
      • Gebäck T, Schulz MM, Koumoutsakos P, Detmar M:TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays. Biotechniques. 2009 Apr;46(4):265-74. Pubmed
      • Helmuth JA, Burckhardt CJ, Greber UF, Sbalzarini IF:Shape reconstruction of subcellular structures from live cell fluorescence microscopy images.J Struct Biol. 2009 Jul;167(1):1-10. Epub 2009 Apr 7. Pubmed
      • Gebäck T, Koumoutsakos P:Edge detection in microscopy images using curvelets.BMC Bioinformatics. 2009 Mar 3;10:75. Pubmed
      • Marbach D, Schaffter T, Mattiussi C, Floreano D:Generating realistic in silico gene networks for performance assessment of reverse engineering methods.J Comput Biol. 2009 Feb;16(2):229-39. Pubmed
      • 2008

        • Hieber SE, Koumoutsakos P:A Langrangian particle method for the simulation of linear and nonlinear elastic model of soft tissue.Journal of Computational Physics. 2008 Nov;227(21):9195-9215. DOI Link
        • Bayati B, Chatelain P, Koumoutsakos P:Multiresolution stochastic simulations of reaction-diffusion processes.Phys Chem Chem Phys. 2008 Oct 21;10(39):5963-6. Epub 2008 Sep 1. Pubmed
        • Milde F, Bergdorf M, Koumoutsakos P:A hybrid model for three-dimensional simulations of sprouting angiogenesis.Biophys J. 2008 Oct;95(7):3146-60. Epub 2008 Jun 27. Pubmed
        • Rossinelli D, Bayati B, Koumoutsakos P:Accelerated stochastic and hybrid methods for spatial simulations of reaction–diffusion systems.Chemical Physics Letters. 2008 Jan;451(1-3):136-140 DOI Link

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