Abstract
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.
Chapter PDF
Similar content being viewed by others
Keywords
- Regulatory Network
- Biological Cell
- Regulatory Relationship
- Drosophila Embryo
- Temporal Expression Pattern
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
Akutsu, T., Miyano, S., Kuhara, S.: Inferring qualitative relations in genetic networks and metabolic pathways, Bioinformatics 16 (2000) 727–734
Brazma, A., Schlitt, T.: Reverse engineering of gene regulatory networks: a finite linear model ()
Carroll, S.B., Grenier, J.K., Weatherbee, S.D.: From DNA to diversity: molecular genetics and the evolution of animal design, (2001)
Davidson, E.H.: Genomic regulatory systems: development and evolution, Academic Press, London (2001)
Davidson, E.H. et al.: A genomic regulatory network for development Science 295 (2002) 1669–1678
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)
Glazier, J.A., Graner, F.: Simulation of the Differential Adhesion Driven Rearrangement of Biological Cells, Physical Review E 47 (1993) 2128–2154
Graner, F., Glazier, J.A.: Simulation of Biological Cell Sorting Using a Two-Dimensional Extended Potts Model, Physical Review Letters 69 (1992) 2013–2016
Jackson, E.R., Johnson, D., Nash, W.G.: Gene networks in development, Journal of Theoretical Biology 119 (1986) 379–396
Kaneko, K., Yomo, T. Isologous deversification: a theory of cell differentiation. Bull. Math. Biol. 59 (1997) 139–196
Kauffman, S.A., J. Theoretical Biology 44 (1974) 167–190
Mjolness, E., Sharp, D.H., Reinitz, J.A.: connectionist model of development. J. Theoretical Biology 152 (1991) 429–453
Murphy, K. and Mian, S., Modelling gene expression data using dynamic Bayesian networks, Technical report, Computer Science Division, University of California, Berkeley, CA. (1999)
St Johnston, D, Nüsslein-Volhard, C.: The origin of pattern and polarity in the Drosophila embryo, Cell 68 (1992) 201–209
Reinitz, J., Kosman, D., Vanario-Alonso, C.E., Sharp D.H.: Stripe forming architecture of the gap gene system. Developmental Genetics 23 (1998) 11–27
Reinitz, J., Sharp, D.H.: Mechanism of formation of eve stripes. Mechanisms of Development 49 (1995) 133–158
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) 84–94
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) 95–103
Turing, A.M., The chemical basis of morphogenesis, Transactions R. Soc. Lond B. 237 (1952) 37–72. Reprinted in Bull. Math. Biol. 52 (1991) 153–197
Wolpert, L., Beddinton R., Brooks J., Jessel, T.: Principles of development, Current Biology Ltd, Oxford University Press (1998)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Krul, T., Kaandorp, J.A., Blom, J.G. (2003). Modelling Developmental Regulatory Networks. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J.J., Zomaya, A.Y. (eds) Computational Science — ICCS 2003. ICCS 2003. Lecture Notes in Computer Science, vol 2660. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-44864-0_71
Download citation
DOI: https://doi.org/10.1007/3-540-44864-0_71
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-40197-1
Online ISBN: 978-3-540-44864-8
eBook Packages: Springer Book Archive