This book compiles progress on gene regulatory network (GRN) research, focusing particularly on different domains that apply evolutionary algorithms (EAs) as the computational methodology. These areas are the analysis of gene expression data to discover knowledge; the reconstruction of GRN from expression profiles; and the evolution of GRN for target behavior. The book also presents uses of GRN with EAs in applications such as architectural design, agent control and robotics. The first part of the book introduces GRN to readers with a computer science background, and EAs to readers with a life science background. The authors present the EA approaches for analysis of gene expression data. Next, readers are guided step–by–step through the reverse engineering and evolution of GRN using EAs. Topics covered include deterministic and stochastic modelling of GRN, time series data analysis, single and multi–objective genetic algorithms, and swarm intelligence. The last part of the book focuses on future applications of GRN with use of EAs, in the fields of agent control, robotics, and design. The fifteen chapters are authored by well–known researchers and experienced practitioners in their respective fields.
Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary algorithms (EAs)
Covers all sub–domains of GRN research using EAs, such as expression profile analysis, reverse engineering, GRN evolution, applications
Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology
Delivers state–of–the–art research in genetic algorithms, genetic programming, and swarm intelligenceEvolutionary Computation in Gene Regulatory Network Research is a great resource for students, researchers, and professionals in computer science, systems biology, and bioinformatics.
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. 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. He is an Editor of the BioMed Research International Journal. His research interests include computational biology, synthetic biology, and bioinformatics.
1 A Brief Introduction to Evolutionary and other Nature–Inspired Algorithms 3Nasimul Noman and Hitoshi Iba
2 Mathematical Models and Computational Methods for Inference of Genetic Networks 30Tatsuya Akutsu
3 Gene Regulatory Networks: Real Data Sources and Their Analysis 49Yuji Zhang
II EAs FOR GENE EXPRESSION DATA ANALYSIS AND GRN RECONSTRUCTION
4 Biclustering Analysis of Gene Expression Data Using Evolutionary Algorithms 69Alan Wee–Chung Liew
5 Inference of Vohradsk´ y s Models of Genetic Networks Using a Real–Coded Genetic Algorithm 96Shuhei Kimura
6 GPU–Powered Evolutionary Design of Mass–Action–Based Models of Gene Regulation 118Marco S. Nobile, Davide Cipolla, Paolo Cazzaniga and Daniela Besozzi
7 Modeling Dynamic Gene Expression in Streptomyces Coelicolor: Comparing Single and Multi–Objective Setups 151Spencer Angus Thomas, Yaochu Jin, Emma Laing and Colin Smith
8 Reconstruction of Large–Scale Gene Regulatory Network Using S–system Model 185Ahsan 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 213Ibuki Kawamata and Masami Hagiya
10 Using Evolutionary Algorithms to Study the Evolution of Gene Regulatory Networks Controlling Biological Development 240Alexander Spirov and David Holloway
11 Evolving GRN–inspired In Vitro Oscillatory Systems 269Quang 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 301Sylvain Cussat–Blanc, Jean Disset, St´ephane Sanchez and Yves Duthen
13 Evolving H–GRNs for Morphogenetic Adaptive Pattern Formation of Swarm Robots 327Hyondong Oh and Yaochu Jin
14 Regulatory Representations in Architectural Design 362Daniel Richards and Martyn Amos
15 Computing with Artificial Gene Regulatory Networks 398Michael A. Lones