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Canalizing structure of genetic network dynamics: modelling and identification via mixed-integer programming


Cinquemani, Eugenio; Porreca, Riccardo; Lygeros, John; Ferrari-Trecate, Giancarlo (2009). Canalizing structure of genetic network dynamics: modelling and identification via mixed-integer programming. In: Combined 48th IEEE Conference on Decision and Control and 28th Chinese Control Conference, Shanghai, 15 December 2009 - 18 December 2009, 5618-23.

Abstract

We discuss the identification of genetic networks based on a class of boolean gene activation rules known as hierarchically canalizing functions. We introduce a class of kinetic models for the concentration of the proteins in the network built on a family of canalizing functions that has been shown to capture the vast majority of the known interaction networks. The simultaneous identification of the structure and of the parameters of the model from experimental data is addressed based on a mixed integer parametrization of the model class. The resulting regression problem is solved numerically via standard branch-and-bound techniques. The performance of the method is tested on simulated data generated by a simple model of Escherichia coli nutrient stress response.

Abstract

We discuss the identification of genetic networks based on a class of boolean gene activation rules known as hierarchically canalizing functions. We introduce a class of kinetic models for the concentration of the proteins in the network built on a family of canalizing functions that has been shown to capture the vast majority of the known interaction networks. The simultaneous identification of the structure and of the parameters of the model from experimental data is addressed based on a mixed integer parametrization of the model class. The resulting regression problem is solved numerically via standard branch-and-bound techniques. The performance of the method is tested on simulated data generated by a simple model of Escherichia coli nutrient stress response.

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Additional indexing

Item Type:Conference or Workshop Item (Paper), refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > YeastX
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Event End Date:18 December 2009
Deposited On:04 Jul 2013 09:28
Last Modified:07 Dec 2017 21:36
Publisher DOI:https://doi.org/10.1109/CDC.2009.5400670

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