Parameter sensitivity analysis for biochemical reaction networks.
Math Biosci Eng. 2019.
PMID: 31499645
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SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks.
Bioinformatics. 2013.
PMID: 23104889
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Parameter sensitivity analysis for biochemical reaction networks.
Math Biosci Eng. 2019 May 6;16(5):3965-3987. doi: 10.3934/mbe.2019196.
Math Biosci Eng. 2019.
PMID: 31499645
Free article.
Parameter sensitivity analysis that studies the effects of parameter changes to the behaviour of biochemical networks can be a powerful tool in unravelling their key parameters and interactions. It can also be very useful in design …
Parameter sensitivity analysis that studies the effects of parameter changes to the behaviour of biochemical …
Sensitivity Analysis for Multiscale Stochastic Reaction Networks Using Hybrid Approximations.
Bull Math Biol. 2019 Aug;81(8):3121-3158. doi: 10.1007/s11538-018-0521-4. Epub 2018 Oct 9.
Bull Math Biol. 2019.
PMID: 30302636
We consider the problem of estimating parameter sensitivities for stochastic models of multiscale reaction networks. These sensitivity values are important for model analysis, and the methods that currently exist for sensitivity es …
We consider the problem of estimating parameter sensitivities for stochastic models of multiscale reaction networks …
Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory.
BMC Bioinformatics. 2013 Oct 22;14:311. doi: 10.1186/1471-2105-14-311.
BMC Bioinformatics. 2013.
PMID: 24148216
Free PMC article.
In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical and computational tool, yielding information regarding the robustness and the identifiability of model parameters. ...RESULTS: We deve …
In this direction, the parameter sensitivity analysis of reaction networks is an essential mathematical a …
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
PLoS Comput Biol. 2017 Jan 23;13(1):e1005331. doi: 10.1371/journal.pcbi.1005331. eCollection 2017 Jan.
PLoS Comput Biol. 2017.
PMID: 28114351
Free PMC article.
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. ...In this manuscript, we evaluate adjoint sensitivity …
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models ha …
Sensitivity analysis of biochemical systems using bond graphs.
J R Soc Interface. 2023 Jul;20(204):20230192. doi: 10.1098/rsif.2023.0192. Epub 2023 Jul 19.
J R Soc Interface. 2023.
PMID: 37464805
Free PMC article.
The sensitivity of systems biology models to parameter variation can give insights into which parameters are most important for physiological function, and also direct efforts to estimate parameters. ...To address this issue, we analyse the sensitiv …
The sensitivity of systems biology models to parameter variation can give insights into which parameters are most impor …
Vertex results for the robust analysis of uncertain biochemical systems.
J Math Biol. 2022 Sep 19;85(4):35. doi: 10.1007/s00285-022-01799-z.
J Math Biol. 2022.
PMID: 36123409
Free PMC article.
In particular, we propose approaches for the robust sensitivity analysis of systems with uncertain parameters assumed to take values in a hyper-rectangle. ...We consider different problems: robust non-singularity; robust stability of the steady-state; robust …
In particular, we propose approaches for the robust sensitivity analysis of systems with uncertain parameters assumed t …
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks.
Bioinformatics. 2013 Jan 1;29(1):140-2. doi: 10.1093/bioinformatics/bts642. Epub 2012 Oct 25.
Bioinformatics. 2013.
PMID: 23104889
SUMMARY: SPSens is a software package for the efficient computation of stochastic parameter sensitivities of biochemical reaction networks. Parameter sensitivity analysis is a valuable tool that can be used to study robustne …
SUMMARY: SPSens is a software package for the efficient computation of stochastic parameter sensitivities of biochemical …
Comprehensive Review of Models and Methods for Inferences in Bio-Chemical Reaction Networks.
Front Genet. 2019 Jun 14;10:549. doi: 10.3389/fgene.2019.00549. eCollection 2019.
Front Genet. 2019.
PMID: 31258548
Free PMC article.
Review.
The key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their non-linear dyn …
The key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology t …
Robustness and period sensitivity analysis of minimal models for biochemical oscillators.
Sci Rep. 2015 Aug 12;5:13161. doi: 10.1038/srep13161.
Sci Rep. 2015.
PMID: 26267886
Free PMC article.
Furthermore, our parameter sensitivity analysis and stochastic simulations reveal different rankings of hierarchy of period robustness that are determined by the number of sensitive parameters or network topology. ...We demonstrate that r …
Furthermore, our parameter sensitivity analysis and stochastic simulations reveal different rankings of hierarchy of pe …
Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks.
J R Soc Interface. 2015 Jul 6;12(108):20150233. doi: 10.1098/rsif.2015.0233.
J R Soc Interface. 2015.
PMID: 26063822
Free PMC article.
A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another difficulty is to study how the behaviour of a stochastic model depends on its parameters, i.e. whether a change in model parameters …
A common challenge of stochastic models is to calibrate a large number of model parameters against the experimental data. Another dif …
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