Evolutionary Computation in Gene Regulatory Network Research (eBook)

Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Tokyo, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the Journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a Lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012, he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

Preface ix

Acknowledgments xiii

Contributors xv

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 Vohradsky'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, Stéphane 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 425