Modelling Developmental Regulatory Networks

  • Tommy Krul
  • Jaap A. Kaandorp
  • Joke G. Blom
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2660)


This paper introduces a model for simulating regulatory networks that is capable of reproducing spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard connectionist model used for modelling genetic interactions, where the terms for the regulation of gene products and the diffusion term have been separated. This model can be coupled with biomechanical models of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems.


Regulatory Network Biological Cell Regulatory Relationship Drosophila Embryo Temporal Expression Pattern 
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  1. 1.
    Akutsu, T., Miyano, S., Kuhara, S.: Inferring qualitative relations in genetic networks and metabolic pathways, Bioinformatics 16 (2000) 727–734CrossRefGoogle Scholar
  2. 2.
    Brazma, A., Schlitt, T.: Reverse engineering of gene regulatory networks: a finite linear model ()Google Scholar
  3. 3.
    Carroll, S.B., Grenier, J.K., Weatherbee, S.D.: From DNA to diversity: molecular genetics and the evolution of animal design, (2001)Google Scholar
  4. 4.
    Davidson, E.H.: Genomic regulatory systems: development and evolution, Academic Press, London (2001)Google Scholar
  5. 5.
    Davidson, E.H. et al.: A genomic regulatory network for development Science 295 (2002) 1669–1678Google Scholar
  6. 6.
    D’haeseleer, P., X. Wen, Fuhrman, S., Somogyi, R.: Linear Modelling of mRNA expression levels during CNS development and ingury, Pacific Symposion on Biocomputing (1999)Google Scholar
  7. 7.
    Glazier, J.A., Graner, F.: Simulation of the Differential Adhesion Driven Rearrangement of Biological Cells, Physical Review E 47 (1993) 2128–2154CrossRefGoogle Scholar
  8. 8.
    Graner, F., Glazier, J.A.: Simulation of Biological Cell Sorting Using a Two-Dimensional Extended Potts Model, Physical Review Letters 69 (1992) 2013–2016CrossRefGoogle Scholar
  9. 9.
    Jackson, E.R., Johnson, D., Nash, W.G.: Gene networks in development, Journal of Theoretical Biology 119 (1986) 379–396CrossRefGoogle Scholar
  10. 10.
    Kaneko, K., Yomo, T. Isologous deversification: a theory of cell differentiation. Bull. Math. Biol. 59 (1997) 139–196zbMATHCrossRefGoogle Scholar
  11. 11.
    Kauffman, S.A., J. Theoretical Biology 44 (1974) 167–190CrossRefGoogle Scholar
  12. 12.
    Mjolness, E., Sharp, D.H., Reinitz, J.A.: connectionist model of development. J. Theoretical Biology 152 (1991) 429–453CrossRefGoogle Scholar
  13. 13.
    Murphy, K. and Mian, S., Modelling gene expression data using dynamic Bayesian networks, Technical report, Computer Science Division, University of California, Berkeley, CA. (1999)Google Scholar
  14. 14.
    St Johnston, D, Nüsslein-Volhard, C.: The origin of pattern and polarity in the Drosophila embryo, Cell 68 (1992) 201–209CrossRefGoogle Scholar
  15. 15.
    Reinitz, J., Kosman, D., Vanario-Alonso, C.E., Sharp D.H.: Stripe forming architecture of the gap gene system. Developmental Genetics 23 (1998) 11–27CrossRefGoogle Scholar
  16. 16.
    Reinitz, J., Sharp, D.H.: Mechanism of formation of eve stripes. Mechanisms of Development 49 (1995) 133–158CrossRefGoogle Scholar
  17. 17.
    Salazar-Ciudad, I, Newman, S.A., Sole, R.V.: Phenotypic and dynamical transistions in model genetic networks I. emergence of patterns and genotype-phenotype relationships, Evolution and Development 3 (2001) 84–94CrossRefGoogle Scholar
  18. 18.
    Salazar-Ciudad, I, Sole, R.V., Newman, S.A.: Phenotypic and dynamical transistions in model genetic networks II. application to the evolution of segmentation mechanisms, Evolution and Development 3 (2001) 95–103CrossRefGoogle Scholar
  19. 19.
    Turing, A.M., The chemical basis of morphogenesis, Transactions R. Soc. Lond B. 237 (1952) 37–72. Reprinted in Bull. Math. Biol. 52 (1991) 153–197CrossRefGoogle Scholar
  20. 20.
    Wolpert, L., Beddinton R., Brooks J., Jessel, T.: Principles of development, Current Biology Ltd, Oxford University Press (1998)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Tommy Krul
    • 1
  • Jaap A. Kaandorp
    • 1
  • Joke G. Blom
    • 2
  1. 1.Section Computational Science, Faculty of ScienceUniversity of AmsterdamAmsterdamThe Netherlands
  2. 2.CWI (Center for Mathematics and Informatics)AmsterdamThe Netherlands

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