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PREFACE ix ACKNOWLEDGMENTS xiii I PRELIMINARIES 1 A Brief Introduction to Evolutionary and other Nature-Inspired Algorithms 3 Nasimul Noman and Hitoshi Iba 2 Mathematical Models and Computational Methods for Inference of Genetic Networks 30 Tatsuya Akutsu 3 Gene Regulatory Networks: Real Data Sources and Their Analysis 49 Yuji Zhang II EAs FOR GENE EXPRESSION DATA ANALYSIS AND GRN RECONSTRUCTION 4 Biclustering Analysis of Gene Expression Data Using Evolutionary Algorithms 69 Alan Wee-Chung Liew 5 Inference of Vohradsk y’s Models of Genetic Networks Using a Real-Coded Genetic Algorithm 96 Shuhei Kimura 6 GPU-Powered Evolutionary Design of Mass-Action-Based Models of Gene Regulation 118 Marco S. Nobile, Davide Cipolla, Paolo Cazzaniga and Daniela Besozzi 7 Modeling Dynamic Gene Expression in Streptomyces Coelicolor: Comparing Single and Multi-Objective Setups 151 Spencer Angus Thomas, Yaochu Jin, Emma Laing and Colin Smith 8 Reconstruction of Large-Scale Gene Regulatory Network Using S-system Model 185 Ahsan Raja Chowdhury and Madhu Chetty III EAs FOR EVOLVING GRNs AND REACTION NETWORKS 9 Design Automation of Nucleic Acid Reaction System Simulated by Chemical Kinetics Based on Graph Rewriting Model 213 Ibuki Kawamata and Masami Hagiya 10 Using Evolutionary Algorithms to Study the Evolution of Gene Regulatory Networks Controlling Biological Development 240 Alexander Spirov and David Holloway 11 Evolving GRN-inspired In Vitro Oscillatory Systems 269 Quang Huy Dinh, Nathanael Aubert, Nasimul Noman, Hitoshi Iba and Yannic Rondelez IV APPLICATION OF GRN WITH EAs 12 Artificial Gene Regulatory Networks for Agent Control 301 Sylvain Cussat-Blanc, Jean Disset, Stephane Sanchez and Yves Duthen 13 Evolving H-GRNs for Morphogenetic Adaptive Pattern Formation of Swarm Robots 327 Hyondong Oh and Yaochu Jin 14 Regulatory Representations in Architectural Design 362 Daniel Richards and Martyn Amos 15 Computing with Artificial Gene Regulatory Networks 398 Michael A. Lones INDEX 000
