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Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks

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by Ilya Shmulevich and Edward R. Dougherty


2010 / xiv + 267 pages / Softcover / ISBN: 978-0-898716-92-4 / List Price $67.50 / SIAM Member Price $47.25 / Order Code OT118

Keywords: probabilistic boolean network, genetic network, computational biology, dynamical system, systems biology


This is the first comprehensive treatment of probabilistic Boolean networks (PBNs), an important model class for studying genetic regulatory networks. This book covers basic model properties, including

  • the relationships between network structure and dynamics,
  • steady-state analysis, and
  • relationships to other model classes.

It also discusses the inference of model parameters from experimental data and control strategies for driving network behavior towards desirable states.

The PBN model is well suited to serve as a mathematical framework to study basic issues dealing with systems-based genomics, specifically, the relevant aspects of stochastic, nonlinear dynamical systems. The book builds a rigorous mathematical foundation for exploring these issues, which include

  • long-run dynamical properties and how these correspond to therapeutic goals;
  • the effect of complexity on model inference and the resulting consequences of model uncertainty;
  • altering network dynamics via structural intervention, such as perturbing gene logic;
  • optimal control of regulatory networks over time;
  • limitations imposed on the ability to achieve optimal control owing to model complexity; and
  • the effects of asynchronicity.

The authors attempt to unify different strands of current research and address emerging issues such as constrained control, greedy control, and asynchronicity.

Researchers in mathematics, computer science, and engineering are exposed to important applications in systems biology and presented with ample opportunities for developing new approaches and methods. The book is also appropriate for advanced undergraduates, graduate students, and scientists working in the fields of computational biology, genomic signal processing, control and systems theory, and computer science.

About the Authors
Ilya Shmulevich is a professor at the Institute for Systems Biology, Seattle, WA.

Edward R. Dougherty is a professor and director of the Genomic Signal Processing Laboratory at Texas A&M University, College Station, TX. He is also co-director of the Computational Biology Division of the Translational Genomics Research Institute, Phoenix, AZ.

ISBN: 9780898716924

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