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Large-Scale Computing Techniques for Complex System Simulations by Bernard Schott, Krzysztof Kurowski, Werner Dubitzky

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Chapter 8

A Topology-Aware Evolutionary Algorithm for Reverse-Engineering Gene Regulatory Networks

Martin Swain

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, United Kingdom

Camille Coti

LIPN, CNRS-UMR7030, Université Paris 13, Villetaneuse, France

Johannes Mandel

Roche Diagnostics GmbH, Penzberg, Germany

Werner Dubitzky

School of Biomedical Sciences, University of Ulster, Coleraine, United Kingdom

8.1 INTRODUCTION

This chapter is concerned with modeling and simulating the dynamics of gene regulatory networks (GRNs). Gene regulation refers to processes that cells use to create functional gene products, in particular proteins, from the information stored in genes. Gene regulation is essential for life as it increases the versatility and adaptability of an organism by allowing it to express or synthesize protein when needed. While aspects of gene regulation are well understood, many open research questions still remain (Davidson and Levin, 2005).

The modeling of dynamic biomedical phenomena such as gene regulation is inspired by the approach taken in physics, where models are frequently constructed to explain existing data, then predictions are made, which again are compared to new data. If a sufficient correspondence exists, it is claimed that the phenomenon has been understood. The ability to construct, analyze, and interpret qualitative and quantitative aspects of gene-regulation models is becoming increasingly important (Hasty et al., 2001). ...

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