References to FlyEx in publications

--------------------------------------------------

  1. Aegerter-Wilmsena, T., Aegerterb, C.M., Bisselinga, T. (2005) Model for the robust establishment of precise proportions in the early Drosophila embryo. J. Theor.Biol., 234,13-19.
  2. Aegerter, A. Aegerter_Wi;msen, T. (2006) Comment on precise domain specification in the developing Drosophila embryo. Phys. Rev. E 74, 023901.
  3. Ahmet Ay, Walid D. Fakhouri, Chichia Chiu, David N. Arnosti. (2008) Image processing and analysis for quantifying gene expression from early Drosophila embryos. Tissue Engineering Part A, 14(9): 1517-1526. doi:10.1089/ten.tea.2008.0202.
  4. Filipa Alves and Rui Dil?o (2006) Modeling segmental patterning in Drosophila: Maternal and gap genes. J. Theor. Biol., 241, 2, 342-359.
  5. Alexandrov, T., Golyandina, N., Spirov, A. (2008) Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns. Research Letters in Signal Processing, Article ID 825758, doi:10.1155/2008/825758.
  6. Ashyraliyev, M., Jaeger, J. and Blom, J.G. (2008) Parameter estimation and determinability analysis applied to Drosophila gap gene circuits. BMC Systems Biology, 2: 83, doi:10.1186/1752-0509-2-83.
  7. Bergmann, S., Sandler, O., Sberro, H., Shnider, S., Schejter, E., Shilo, B. Z., and Barkai, N. (2007). Pre-steady-state decoding of the bicoid morphogen gradient. PLoS Biol, 5(2):e46.
  8. Diambra, L. & da F. Costa, L. (2005) Complex networks approach to gene expression driven phenotype imaging Bioinformatics,21,3846-3851.
  9. Rui Dil?o, Daniele Muraro, Miguel Nicolau and Marc Schoenauer (2009) Validation of a Morphogenesis Model of Drosophila Early Development by a Multi-objective Evolutionary Optimization Algorithm. Lecture Notes in Computer Science, v. 5483,176-190.
  10. Yves Fomekong-Nanfack, Jaap A. Kaandorp, and Joke Blom (2007) Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster Bioinformatics, 23: 3356 - 3363.
  11. Fritsch, C., Ploeger, G. and Arndt-Jovin, D.J. (2006) Drosophila under the lens: imaging from chromosomes to whole embryos. Chromosome Research, 14, 4, 451-464.
  12. Hecht, I., Rappel, W.-J. and Levine, H. (2009) Determining the scale of the Bicoid morphogen gradient. PNAS, 106, 6, 1710-1715, doi: 10.1073/pnas.0807655106.
  13. Holloway, D. M.; Harrison, L. G.; Spirov, A. V. (2003) Noise in the segmentation gene network of Drosophila with implications for mechanisms of body axis specification In: "Fuctuations and Noise in Biological, Biophysical, and Biomedical Systems." Bezrukov, Sergey M., Frauenfelder, H., Moss,F. Proceedings of the SPIE, 5110, 180-191.
  14. Holloway, D. M., Harrison, L. G., Kosman, D., Vanario-Alonso, C. E., Spirov, A. V. (2006) Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Dev Dyn, 235(11), 2949-60.
  15. Isalan, M., Lemerle, C., Serrano L.(2005) Engineering Gene Networks to Emulate Drosophila Embryonic Pattern Formation. PLoS Biology, 3, 0489-0496.
  16. Krishna, S., Banerjee, B., Ramakrishnan, T. V. and Shivashankar, G. V. (2005) Stochastic simulations of the origins and implications of long-tailed distributions in gene expression PNAS, 102, 4771-4776.
  17. Francisco J.P. Lopes, Carlos E. Vanario-Alonso, Paulo M. Bisch and Fernando M.C. Vieira (2005) A kinetic mechanism for Drosophila bicoid cooperative binding. J Theor. Biol.,235,2,185-198.
  18. Lott, S.E., Kreitman, M., Palsson, A., Alekseeva,E., Ludwig, M.Z. (2007) Canalization of segmentation and its evolution in Drosophila. PNAS, 104, 26, 10926-10931.
  19. Ludwig, M.Z., Palsson, A., Alekseeva, E., Bergman, C.M., Nathan, J., Kreitman, M. (2005) Functional Evolution of a cis-Regulatory Module. PLoS Biology, 3, 4, 0588-0598.
  20. Matthews, K.A., Kaufman, T.C. & Gelbart, W.M. (2005) Research resources for Drosophila: the expanding universe. Nature Reviews Genetics 6, 179-193.
  21. Megason, S.G. & Fraser, S.E. (2007) Imaging in Systems Biology . Cell 130: 784 - 795.
  22. Yoshihiro Morishita and Yoh Iwasa (2009) Accuracy of positional information provided by multiple morphogen gradients with correlated noise. Phys. Rev. E 79, 061905.
  23. Ochoa-Espinosa, A., Yucel, G., Kaplan, L., Pare, A., Pura, N., Oberstein, A.,Papatsenko, D., and Small, S. (2005). The role of binding site cluster strength in bicoid-dependent patterning in drosophila. Proc Natl Acad Sci U S A, 102(14):4960-5.
  24. Papatsenko, D. and Levine, M. (2008) Dual regulation by the Hunchback gradient in the Drosophila embryo. PNAS, 105, 2901-2906.
  25. Dmitri Papatsenko, Yury Goltsev and Michael Levine (2009) Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Research, doi:10.1093/nar/gkp619.
  26. Perkins, T. J., Jaeger, J., Reinitz, J., and Glass, L. (2006). Reverse engineering the gap gene network of drosophila melanogaster. PLoS Comput Biol, 2(5):e51.
  27. Pereanu, W., Hartenstein, V. Digital three-dimensional models of Drosophila development. Curr Opin Genet Dev. 2004 Aug;14(4):382-91.
  28. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. (2008). Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature, 451, 7178: 535-40.
  29. Siggia, E.D. (2008) Developmental regulatory bits. Mol. Systems Biol., 4, 226, doi:10.1038/msb.2008.64.
  30. Alexander V. Spirov and David M. Holloway (2008) The Effects of Gene Recruitment on the Evolvability and Robustness of Pattern-Forming Gene Networks. Lecture Notes in Electrical Engeneering, 14, 29-49.
  31. Denis Thieffry and Lucas Sanchez (2003) Dynamical modelling of pattern formation during embryonic development. Curr. Opinion in Genet. & Dev., 13, 4, 326-330.
  32. Reiner A. Veitia and Isaac Salazar-Ciudad (2007) Commonalities in fly embryogenesis and mammalian pituitary patterning. Trends in Endocrinology & Metabolism, 18, 7. 261-265.
  33. Katrin Weigmann, Robert Klapper, Thomas Strasser, Christof Rickert, Gerd Technau, Herbert J?ckle, Wilfried Janning and Christian Kl?mbt (2003) FlyMove - a new way to look at development of Drosophila . Trends Genet., 19,6,310-311.
  34. Yucel, G. and Small, S. (2006). Morphogens: precise outputs from a variable gradient. Curr Biol, 16(1):R29-31.
  35. Zinzen, R. P. and Papatsenko, D. (2007). Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput Biol, 3(5):e84.
  36. Zamparo L, Perkins T. (2009) Statistical lower bounds on protein copy number from fluorescence expression images. Bioinformatics. 2009 Jul 2
FlyEx is also cited in our publications.

--------------------------------------------------

Back to FlyEx homepage