Publications by SystemsX.ch (overview)

PUBLICATIONS by WINGX:

2010

  1. Aegerter-Wilmsen T, Smith AC, Christen AJ, Aegerter CM, Hafen E, Basler K.: Exploring the effects of mechanical feedback on epithelial topology. Development. 2010 Feb;137(3):499-506. Abstract
  2. Ivo M. Vellekoop and Christof M. Aegerter.: Focusing light through living tissue. SPIE proceedings vol. 7554, p. 755430 (2010). PDF
  3. Thomas Schluck and Christof M. Aegerter.: Photo-elastic properties of the wing imaginal disc of Drosophila. Europ. Phys. J. E (2010). PDF

  4. de Lachapelle AM, Bergmann S.: Precision and scaling in morphogen gradient read-out., Mol Syst Biol. 2010;6:351. Epub 2010 Mar 9. Abstract

  5. Schwank G, Basler K.: Regulation of organ growth by morphogen gradients. Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a001669. Abstract
  6. 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. Epub 2010 Mar 22. Abstract
  7. Vellekoop, I; and Aegerter, C.: Scattered light fluorescence microscopy: imaging through turbid layers. Opt. Lett. 35, 1245-1247 (2010)   Abstract

2009

  1. Bayati, B., Chatelain, P., Koumoutsakos P.D-leaping: Accelerating stochastic simulation algorithms for reactions with delays, Journal of Computational Physics, 228, 5909-5918, 2009
  2. 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. Abstract
  3. 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.
  4. Mjolsness E, Orendorff D, Chatelain P, Koumoutsakos P. J: An exact accelerated stochastic simulation algorithm. Chem Phys. 2009 Apr 14;130(14):144110.
  5. 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. Abstract
  6. 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. Abstract
  7. 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. Abstract
  8. Gebäck T., Schulz M.M.P., Koumoutsakos P., Detmar M.: TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays; Bio Techniques, 46, 265-274, 2009; Abstract
  9. Mjolsness E., Orendorff D., Chatelain P., Koumoutsakos P.: An exact accelerated stochastic simulation algorithm, Journal of Chemical Physics, 130, 14, 2009; Abstract;
  10. Gebäck T., Koumoutsakos P.: Edge detection in microscopy images using curvelets, BMC Bioinformatics, 10,75, 2009; Abstract;
  11. Marbach D, Schaffter T, Mattiussi C, Floreano D. J: Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Comput Biol. 2009 Feb;16(2):229-39.
  12. Helmuth JA, Burckhardt CJ, Greber UF, Sbalzarini IF. J: Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. Struct Biol. 2009 Jul;167(1):1-10. Epub 2009 Apr 7.

2008

  1. Bayati B., Chatelain P., Koumoutsakos P.: Multiresolution stochastic simulations of reaction-diffusion processes, Physical Chemistry Chemical Physics, 10, 39, 5963-5966, 2008; Abstract;
  2. Hieber S.E., Koumoutsakos P.: A Lagrangian particle method for the simulation of linear and nonlinear elastic model of soft tissue, J. Computational Physics, 227, 9195-9215, 2008; Abstract;
  3. Milde F., Bergdorf M., Koumoutsakos P.: A Hybrid Model for 3D Simulations of Sprouting Angiogenesis, Biophysical J., 95, 7, 3146–3160, 2008; Abstract;
  4. Rossinelli D., Bayati B., Koumoutsakos P.: Accelerated Stochastic and Hybrid Methods for Spatial Simulations of Reaction-Diffusion Systems, Chemical Physics Letters, 451, 1-3, 136-140, 2008; Abstract;


X-LETTER

WingX article in X-Letter 20, from March 2010 (English, Deutsch, Français)

For an overview of RTD projects featured in X-Letters, please visit X-Letters/RTD.