Simplifying biochemical models with intermediate species

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Simplifying biochemical models with intermediate species. / Feliu, Elisenda; Wiuf, Carsten.

I: Journal of the Royal Society. Interface, Bind 10, Nr. 87, 2013, s. 20130484.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Feliu, E & Wiuf, C 2013, 'Simplifying biochemical models with intermediate species', Journal of the Royal Society. Interface, bind 10, nr. 87, s. 20130484. https://doi.org/10.1098/rsif.2013.0484

APA

Feliu, E., & Wiuf, C. (2013). Simplifying biochemical models with intermediate species. Journal of the Royal Society. Interface, 10(87), 20130484. https://doi.org/10.1098/rsif.2013.0484

Vancouver

Feliu E, Wiuf C. Simplifying biochemical models with intermediate species. Journal of the Royal Society. Interface. 2013;10(87):20130484. https://doi.org/10.1098/rsif.2013.0484

Author

Feliu, Elisenda ; Wiuf, Carsten. / Simplifying biochemical models with intermediate species. I: Journal of the Royal Society. Interface. 2013 ; Bind 10, Nr. 87. s. 20130484.

Bibtex

@article{5d04b8db1cf243bb92092577354491b2,
title = "Simplifying biochemical models with intermediate species",
abstract = "Mathematical models are increasingly being used to understand complex biochemical systems, to analyse experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to the choice and uncertainties of the model. Using algebraic techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady-state concentrations of the species in the core model, after suitable matching of parameters. Importantly, our results provide guidelines to the modeller in choosing between models and in distinguishing their properties. Further, our work provides a formal way of comparing models that share a common skeleton.",
author = "Elisenda Feliu and Carsten Wiuf",
year = "2013",
doi = "10.1098/rsif.2013.0484",
language = "English",
volume = "10",
pages = "20130484",
journal = "Journal of the Royal Society. Interface",
issn = "1742-5689",
publisher = "The/Royal Society",
number = "87",

}

RIS

TY - JOUR

T1 - Simplifying biochemical models with intermediate species

AU - Feliu, Elisenda

AU - Wiuf, Carsten

PY - 2013

Y1 - 2013

N2 - Mathematical models are increasingly being used to understand complex biochemical systems, to analyse experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to the choice and uncertainties of the model. Using algebraic techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady-state concentrations of the species in the core model, after suitable matching of parameters. Importantly, our results provide guidelines to the modeller in choosing between models and in distinguishing their properties. Further, our work provides a formal way of comparing models that share a common skeleton.

AB - Mathematical models are increasingly being used to understand complex biochemical systems, to analyse experimental data and make predictions about unobserved quantities. However, we rarely know how robust our conclusions are with respect to the choice and uncertainties of the model. Using algebraic techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady-state concentrations of the species in the core model, after suitable matching of parameters. Importantly, our results provide guidelines to the modeller in choosing between models and in distinguishing their properties. Further, our work provides a formal way of comparing models that share a common skeleton.

U2 - 10.1098/rsif.2013.0484

DO - 10.1098/rsif.2013.0484

M3 - Journal article

VL - 10

SP - 20130484

JO - Journal of the Royal Society. Interface

T2 - Journal of the Royal Society. Interface

JF - Journal of the Royal Society. Interface

SN - 1742-5689

IS - 87

ER -

ID: 47847046