Simulation of developmental regulatory networks
Simulation of developmental regulatory networks
Simulation of developmental regulatory networks
Genetic regulation plays a fundamental role in biological processes. Regulatory systems cannot simply be described as an assembly of genes and proteins and diagrams of their interconnections. Many analysis techniques, as for example cluster analysis, only provide `correlations' between genes and do not provide insight into causal relations between the genes in a regulatory network. An important option for the analysis of regulatory control systems are simulation models in combination with optimization algorithms.
In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems. As a case study we are planning to use the body plan formation in relatively simple multi-cellular organisms (sponges and sceleractinian corals). Genetic regulation plays a fundamental role in biological processes. Regulatory systems cannot simply be described as an assembly of genes and proteins and diagrams of their interconnections. Many analysis techniques, as for example cluster analysis, only provide `correlations' between genes and do not provide insight into causal relations between the genes in a regulatory network. An important option for the analysis of regulatory control systems are simulation models in combination with optimization algorithms.
A major issue are correct estimations of the parameter settings in the network model (the regulatory weight factors). Therefore the model will be used in combination with optimization algorithms (genetic algorithms and simulated annealing) to explore large parameter spaces of regulatory networks and to select specific spatial and temporal expression patterns. In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems. As a case study we are planning to use the body plan formation in relatively simple multi-cellular organisms (sponges and sceleractinian corals). Mathematically speaking this amounts to continuum-discrete hybrid models where discrete, moving and deformable objects in which biochemical reactions take place exchange species with the surrounding environment modelled as a continuum in which species diffuse and decay. A major issue are correct estimations of the parameter settings in the network model (the regulatory weight factors). Therefore the model will be used in combination with optimization algorithms (genetic algorithms and simulated annealing) to explore large parameter spaces of regulatory networks and to select specific spatial and temporal expression patterns. Mathematically speaking this amounts to continuum-discrete hybrid models where discrete, moving and deformable objects in which biochemical reactions take place exchange species with the surrounding environment modelled as a continuum in which species diffuse and decay.
Publications UvA/SCS
M. Ashyraliyev, Y. Fomekong Nanfack, J.A. Kaandorp, J.G. Blom Systems biology: Parameter estimation for biochemical models, FEBS journal 276:886-902, 2009
M. Ashyraliyev, Johannes Jaeger and Joke G. Blom. On Parameter Estimation and Determinability for Drosophila Gap Gene Circuits. BMC Systems Biology, 2:83 (2008)
Cui, J., Kaandorp, J.A., Ositelu, O. O., Beaudry, V., Knight, A., Nanfack, Y. F. & Cunningham, K. W. Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 45: 123-132, (2009)
Y. Fomekong Nanfack, J.A. Kaandorp and J.G. Blom Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster Bioinformatics 23:3356-3363, 2007
Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis BMC Systems Biology 3:94, 2009
Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila} gap gene regulatory network: pattern analysis of gene expression profiles and stability analysis BMC Research Notes (in press)
T. Krul, J.A. Kaandorp and J.G. Blom. Modelling Developmental Regulatory Networks. In: Proceedings of Computational Science - ICCS 2003, International Conference Saint Petersburg Russian Federation, Melbourne Australia, June 2-4, 2003. Eds: P.M.A. Sloot, D. Abramson, A. Bogdanov, J.J Dongarra, A. Zomaya, and Y. Gorbachev. upringer-Verlag, Berlin pp 688-697 (2003).
J.A. Kaandorp, J.G. Blom, J. Verhoef, M. Filatov, M. Postma and W.E.G. Müller, Modelling genetic regulation of growth and form in a branching sponge Proc. Roy. Soc. B. 275:2569-2577, 2008
In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems. As a case study we are planning to use the body plan formation in relatively simple multi-cellular organisms (sponges and sceleractinian corals). Genetic regulation plays a fundamental role in biological processes. Regulatory systems cannot simply be described as an assembly of genes and proteins and diagrams of their interconnections. Many analysis techniques, as for example cluster analysis, only provide `correlations' between genes and do not provide insight into causal relations between the genes in a regulatory network. An important option for the analysis of regulatory control systems are simulation models in combination with optimization algorithms.
A major issue are correct estimations of the parameter settings in the network model (the regulatory weight factors). Therefore the model will be used in combination with optimization algorithms (genetic algorithms and simulated annealing) to explore large parameter spaces of regulatory networks and to select specific spatial and temporal expression patterns. In this project we will develop a model for simulating regulatory networks that are capable of quantitatively reproducing spatial and temporal expression patterns in developmental processes. The model is a generalization of the standard connectionist model used for modelling genetic interactions. The model will be coupled with a biomechanical model of cell aggregates and used to study the formation of spatial and temporal expression patterns of gene products during development in cellular systems. As a case study we are planning to use the body plan formation in relatively simple multi-cellular organisms (sponges and sceleractinian corals). Mathematically speaking this amounts to continuum-discrete hybrid models where discrete, moving and deformable objects in which biochemical reactions take place exchange species with the surrounding environment modelled as a continuum in which species diffuse and decay. A major issue are correct estimations of the parameter settings in the network model (the regulatory weight factors). Therefore the model will be used in combination with optimization algorithms (genetic algorithms and simulated annealing) to explore large parameter spaces of regulatory networks and to select specific spatial and temporal expression patterns. Mathematically speaking this amounts to continuum-discrete hybrid models where discrete, moving and deformable objects in which biochemical reactions take place exchange species with the surrounding environment modelled as a continuum in which species diffuse and decay.
Publications UvA/SCS
M. Ashyraliyev, Y. Fomekong Nanfack, J.A. Kaandorp, J.G. Blom Systems biology: Parameter estimation for biochemical models, FEBS journal 276:886-902, 2009
M. Ashyraliyev, Johannes Jaeger and Joke G. Blom. On Parameter Estimation and Determinability for Drosophila Gap Gene Circuits. BMC Systems Biology, 2:83 (2008)
Cui, J., Kaandorp, J.A., Ositelu, O. O., Beaudry, V., Knight, A., Nanfack, Y. F. & Cunningham, K. W. Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 45: 123-132, (2009)
Y. Fomekong Nanfack, J.A. Kaandorp and J.G. Blom Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster Bioinformatics 23:3356-3363, 2007
Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis BMC Systems Biology 3:94, 2009
Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila} gap gene regulatory network: pattern analysis of gene expression profiles and stability analysis BMC Research Notes (in press)
T. Krul, J.A. Kaandorp and J.G. Blom. Modelling Developmental Regulatory Networks. In: Proceedings of Computational Science - ICCS 2003, International Conference Saint Petersburg Russian Federation, Melbourne Australia, June 2-4, 2003. Eds: P.M.A. Sloot, D. Abramson, A. Bogdanov, J.J Dongarra, A. Zomaya, and Y. Gorbachev. upringer-Verlag, Berlin pp 688-697 (2003).
J.A. Kaandorp, J.G. Blom, J. Verhoef, M. Filatov, M. Postma and W.E.G. Müller, Modelling genetic regulation of growth and form in a branching sponge Proc. Roy. Soc. B. 275:2569-2577, 2008
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