A global sensitivity analysis approach for morphogenesis models

@article{Boas2015AGS,
  title={A global sensitivity analysis approach for morphogenesis models},
  author={Sonja E. M. Boas and Mar{\'i}a I. Navarro Jimenez and Roeland M. H. Merks and Joke G. Blom},
  journal={BMC Systems Biology},
  year={2015},
  volume={9}
}
BackgroundMorphogenesis is a developmental process in which cells organize into shapes and patterns. Complex, non-linear and multi-factorial models with images as output are commonly used to study morphogenesis. It is difficult to understand the relation between the uncertainty in the input and the output of such ‘black-box’ models, giving rise to the need for sensitivity analysis tools. In this paper, we introduce a workflow for a global sensitivity analysis approach to study the impact of… 
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References

SHOWING 1-10 OF 68 REFERENCES
Modeling Morphogenesis in silico and in vitro: Towards Quantitative, Predictive, Cell-based Modeling
TLDR
This review discusses two cell culture models of morphogenesis that have been studied using this combined experimental-mathematical approach and discusses how to include quantitative cell descriptions into a cell-based model: the Cellular Potts model.
Simulating tissue morphogenesis and signaling.
TLDR
This chapter introduces different descriptions of tissue morphogenesi s, a process best described by agent-based models during embryonic development when tissue morphogenesis and signaling are tightly coupled.
Simulation Frameworks for Morphogenetic Problems
TLDR
Here, common tissue modelling techniques are reviewed and the principles and main applications of the spheroid, vertex, Cellular Potts, Immersed Boundary and Subcellular Element models are discussed in detail.
Modelling vascular morphogenesis: current views on blood vessels development
TLDR
This work describes the basic steps in the known mechanisms of blood vessel morphogenesis, whose structure, function and unfolding properties are examined, and provides a wide account of mathematical models used to describe and discuss particular aspects of the overall biological process considered.
Computational analysis of three-dimensional epithelial morphogenesis using vertex models.
TLDR
This model allows for the construction of complex three-dimensional shapes from simple sheets of cells and may be useful for formulating and testing hypotheses regarding the mechanical forces underlying a wide range of morphogenetic processes.
Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects
TLDR
This work applies local and global sensitivity analyses to two recent transcriptional models to determine the sensitivity of individual parameters, indicating that structural differences between the two types of transcriptional enhancers analyzed may not be as simple as altered activator cooperativity.
A cell-based model exhibiting branching and anastomosis during tumor-induced angiogenesis.
TLDR
This model provides a quantitative framework to test hypotheses on the biochemical and biomechanical mechanisms that control tumor-induced angiogenesis and shows inhomogeneities in the extravascular tissue lead to sprout branching and anastomosis, phenomena that emerge without any prescribed rules.
Cell resolved, multiparticle model of plastic tissue deformations and morphogenesis.
TLDR
The proposed stochastic simulation of cell activities yields fluctuating tissue movements which exhibit the same autocorrelation properties as empirical data from avian embryos.
Single-Cell-Based Models in Biology and Medicine
TLDR
A Hybrid Multiscale Model of Tumour Invasion: Evolution and the Microenvironment and modeling Multicellular Structures Using the Subcellular Element Model are presented.
...
1
2
3
4
5
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