Computational methodologies for modelling, analysis and simulation of signalling networks

David Gilbert, H. Fuss, Xu Gu, Richard Orton, S. Robinson, Vladislav Vyshemirsky, M. J. Kurth, C. S. Downes, W. Dubitzky

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

his article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.
LanguageEnglish
Pages339-353
Number of pages15
JournalBriefings in Bioinformatics
DOIs
Publication statusPublished - 2006

Fingerprint

Aptitude
Cell Communication
Wound Healing
Noise
Signal Transduction
Cell Cycle
Phosphotransferases
Signal transduction
Proteins
Ordinary differential equations
Cells
Communication
Behavior Observation Techniques

Keywords

  • systems biology
  • computational biology
  • modelling

Cite this

Gilbert, D., Fuss, H., Gu, X., Orton, R., Robinson, S., Vyshemirsky, V., ... Dubitzky, W. (2006). Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 339-353. https://doi.org/10.1093/bib/bbl043
Gilbert, David ; Fuss, H. ; Gu, Xu ; Orton, Richard ; Robinson, S. ; Vyshemirsky, Vladislav ; Kurth, M. J. ; Downes, C. S. ; Dubitzky, W. / Computational methodologies for modelling, analysis and simulation of signalling networks. In: Briefings in Bioinformatics. 2006 ; pp. 339-353.
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Gilbert, D, Fuss, H, Gu, X, Orton, R, Robinson, S, Vyshemirsky, V, Kurth, MJ, Downes, CS & Dubitzky, W 2006, 'Computational methodologies for modelling, analysis and simulation of signalling networks' Briefings in Bioinformatics, pp. 339-353. https://doi.org/10.1093/bib/bbl043

Computational methodologies for modelling, analysis and simulation of signalling networks. / Gilbert, David; Fuss, H.; Gu, Xu; Orton, Richard; Robinson, S.; Vyshemirsky, Vladislav; Kurth, M. J.; Downes, C. S.; Dubitzky, W.

In: Briefings in Bioinformatics, 2006, p. 339-353.

Research output: Contribution to journalArticle

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