CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013 vol.10 Issue No.02 - March-April

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Issue No.02 - March-April (2013 vol.10)

pp: 337-351

Qian Gao , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK

David Gilbert , Sch. of Inf. Syst., Comput., & Math., Brunel Univ., Uxbridge, UK

Monika Heiner , Fac. of Math., Natural Sci. & Comput. Sci., Brandenburg Univ. of Technol. Cottbus, Cottbus, Germany

Fei Liu , Control & Simulation Center, Harbin Inst. of Technol. Sci. Park, Harbin, China

Daniele Maccagnola , Dept. of Comput. Sci. (DISCo), Univ. of Milano-Bicocca, Milano, Italy

David Tree , Sch. of Health Sci. & Social Care, Brunel Univ., Uxbridge, UK

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.101

ABSTRACT

Modeling across multiple scales is a current challenge in Systems Biology, especially when applied to multicellular organisms. In this paper, we present an approach to model at different spatial scales, using the new concept of Hierarchically Colored Petri Nets (HCPN). We apply HCPN to model a tissue comprising multiple cells hexagonally packed in a honeycomb formation in order to describe the phenomenon of Planar Cell Polarity (PCP) signaling in Drosophila wing. We have constructed a family of related models, permitting different hypotheses to be explored regarding the mechanisms underlying PCP. In addition our models include the effect of well-studied genetic mutations. We have applied a set of analytical techniques including clustering and model checking over time series of primary and secondary data. Our models support the interpretation of biological observations reported in the literature.

INDEX TERMS

Biological system modeling, Color, Petri nets, Proteins, Mathematical model, Image color analysis, Analytical models,model checking, Biological system modeling, Color, Petri nets, Proteins, Mathematical model, Image color analysis, Analytical models, planar cell polarity, Hierarchically colored Petri nets, continuous Petri nets, ordinary differential equations, multiscale modeling, continuous simulation, cluster analysis

CITATION

Qian Gao, David Gilbert, Monika Heiner, Fei Liu, Daniele Maccagnola, David Tree, "Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing",

*IEEE/ACM Transactions on Computational Biology and Bioinformatics*, vol.10, no. 2, pp. 337-351, March-April 2013, doi:10.1109/TCBB.2012.101REFERENCES