# Prediction stability in a data-based, mechanistic model of σF regulation during sporulation in Bacillus subtilis

@article{Fengos2013PredictionSI,
title={Prediction stability in a data-based, mechanistic model of $\sigma$F regulation during sporulation in Bacillus subtilis},
author={Georgios Fengos and Dagmar Iber},
journal={Scientific Reports},
year={2013},
volume={3}
}
• Published 6 September 2013
• Biology
• Scientific Reports
Mathematical modeling of biological networks can help to integrate a large body of information into a consistent framework, which can then be used to arrive at novel mechanistic insight and predictions. We have previously developed a detailed, mechanistic model for the regulation of σ F during sporulation in Bacillus subtilis. The model was based on a wide range of quantitative data, and once fitted to the data, the model made predictions that could be confirmed in experiments. However, the…
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## References

SHOWING 1-10 OF 35 REFERENCES
Ensemble modeling for analysis of cell signaling dynamics
• Biology
Nature Biotechnology
• 2007
It is shown here that ensemble modeling, when combined with targeted experimental analysis, can unravel key operating principles in complex cellular pathways and elucidate other insufficiently characterized cellular circuits.
A quantitative study of the benefits of co-regulation using the spoIIA operon as an example
• D. Iber
• Biology
Molecular systems biology
• 2006
A previously described quantitative model of the network that controls the transcription factor σF during sporulation in Bacillus subtilis is employed to quantify the benefits arising from both organization of the sporulation genes into the spoIIA operon and from translational coupling.
The mechanism of cell differentiation in Bacillus subtilis
• Biology
Nature
• 2006
A mathematical model is developed that reproduces published in vitro experiments and explains how the activation of the key transcription factor is regulated and identifies the difference in volume between the two cell types as the primary trigger for determining cell fate.
A Computational Analysis of the Dynamic Roles of Talin, Dok1, and PIPKI for Integrin Activation
• Biology
PloS one
• 2011
By sampling model behaviors over the physiologically realistic parameter range, this study finds that the model exhibits only two different qualitative behaviors and these depend mainly on the relative protein concentrations, which offers a powerful point of control to the cell.
Rule-based modeling of biochemical systems with BioNetGen.
• Biology
Methods in molecular biology
• 2009
This work focuses on how a rule-based model is specified in the BioNetGen language (BNGL) and how a model specification is analyzed using the Bio netGen software tool.
An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa
• Biology, Chemistry
Proceedings of the National Academy of Sciences of the United States of America
• 2002
An efficient Monte Carlo method for walking through the parameter space of possible chemical reaction networks is developed and was successful in identifying a model ensemble fitting available RNA profiling data on the qa gene cluster.
A rate equation approach to elucidate the kinetics and robustness of the TGF-beta pathway.
• Biology
Biophysical journal
• 2006
Analysis in terms of parameter sensitivity reveals that this negative feedback loop in TGF-beta signaling renders the system global robustness, and sheds light upon the role of the Smad7 protein in this system.
Evolution of complexity in signaling pathways
• Biology
Proceedings of the National Academy of Sciences
• 2006
It is found that final pathway size tends to be lower when pathways evolve under stringent selection criteria, which leads to the counterintuitive conclusion that simple response requirements on a pathway would facilitate its evolution toward higher complexity.
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
• Biology
Bioinform.
• 1998
A generic approach to combine numerical optimization methods with biochemical kinetic simulations is described, suitable for use in the rational design of improved metabolic pathways with industrial significance and for solving the inverse problem of metabolic pathways.