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Control Theory and Systems Biology$
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Pablo A. Iglesias and Brian P. Ingalls

Print publication date: 2009

Print ISBN-13: 9780262013345

Published to MIT Press Scholarship Online: August 2013

DOI: 10.7551/mitpress/9780262013345.001.0001

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PRINTED FROM MIT PRESS SCHOLARSHIP ONLINE (www.mitpress.universitypressscholarship.com). (c) Copyright The MIT Press, 2022. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in MITSO for personal use.date: 02 July 2022

System-Theoretic Approaches to Network Reconstruction

System-Theoretic Approaches to Network Reconstruction

(p.265) 13 System-Theoretic Approaches to Network Reconstruction
Control Theory and Systems Biology

Jorge Gonçalves

Sean Warnick

The MIT Press

This chapter introduces the biochemical network, highlighting its role in managing the complexity of biochemical systems and its link to system dynamics. It describes network reconstruction and its fundamental difficulties and limitations and the effect of noise and nonlinearities in a biochemical system. It addresses how network reconstruction can be attained using two common types of experiments based on gene silencing and overexpression, and discusses trade-offs between steady-state and time-series data. This chapter shows that the use of dynamic structure functions revealed the dynamic properties of structurally perturbed systems, enabling convenient analysis of modified structures.

Keywords:   biochemical network, biochemical systems, system dynamics, network reconstruction, noise, nonlinearities, gene silencing, overexpression, dynamic structure functions, trade-offs

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