Preface -- Contributors -- Part One Gene Expression Analysis and Systems Biology -- 1. Hybrid of Neural Classifi er and Swarm Intelligence in Multiclass Cancer Diagnosis with Gene Expression Signatures (Rui Xu, Georgios C. Anagnostopoulos, and Donald C. Wunsch II) -- 1.1 Introduction -- 1.2 Methods and Systems -- 1.3 Experimental Results -- 1.4 Conclusions -- 2. Classifying Gene Expression Profi les with Evolutionary Computation (Jin-Hyuk Hong and Sung-Bae Cho) -- 2.1 DNA Microarray Data Classifi cation -- 2.2 Evolutionary Approach to the Problem -- 2.3 Gene Selection with Speciated Genetic Algorithm -- 2.4 Cancer Classifi ction Based on Ensemble Genetic Programming -- 2.5 Conclusion -- 3. Finding Clusters in Gene Expression Data Using EvoCluster (Patrick C. H. Ma, Keith C. C. Chan, and Xin Yao) -- 3.1 Introduction -- 3.2 Related Work -- 3.3 Evolutionary Clustering Algorithm -- 3.4 Experimental Results -- 3.5 Conclusions -- 4. Gene Networks and Evolutionary Computation (Jennifer Hallinan) -- 4.1 Introduction -- 4.2 Evolutionary Optimization -- 4.3 Computational Network Modeling -- 4.4 Extending Reach of Gene Networks -- 4.5 Network Topology Analysis -- 4.6 Summary -- Part Two Sequence Analysis and Feature Detection -- 5. Fuzzy-Granular Methods for Identifying Marker Genes from Microarray Expression Data (Yuanchen He, Yuchun Tang, Yan-Qing Zhang, and Rajshekhar Sunderraman) -- 5.1 Introduction -- 5.2 Traditional Algorithms for Gene Selection -- 5.3 New Fuzzy-Granular-Based Algorithm for Gene Selection -- 5.4 Simulation -- 5.5 Conclusions -- 6. Evolutionary Feature Selection for Bioinformatics (Laetitia Jourdan, Clarisse Dhaenens, and El-Ghazali Talbi) -- 6.1 Introduction -- 6.2 Evolutionary Algorithms for Feature Selection -- 6.3 Feature Selection for Clustering in Bioinformatics -- 6.4 Feature Selection for Classifi cation in Bioinformatics -- 6.5 Frameworks and Data Sets -- 6.6 Conclusion -- 7. Fuzzy Approaches for the Analysis CpG Island Methylation Patterns (Ozy Sjahputera, Mihail Popescu, James M. Keller, and Charles W. Caldwell).

7.1 Introduction -- 7.2 Methods -- 7.3 Biological Signifi cance -- 7.4 Conclusions -- Part Three Molecular Structure and Phylogenetics -- 8. Protein¿́¿Ligand Docking with Evolutionary Algorithms(Ren¿̐ư Thomsen) -- 8.1 Introduction -- 8.2 Biochemical Background -- 8.3 The Docking Problem -- 8.4 Protein¿́¿Ligand Docking Algorithms -- 8.5 Evolutionary Algorithms -- 8.6 Effect of Variation Operators -- 8.7 Differential Evolution -- 8.8 Evaluating Docking Methods -- 8.9 Comparison between Docking Methods -- 8.10 Summary -- 8.11 Future Research Topics -- 9. RNA Secondary Structure Prediction Employing Evolutionary Algorithms (Kay C. Wiese, Alain A. Desch¿̐ưnes, and Andrew G. Hendriks) -- 9.1 Introduction -- 9.2 Thermodynamic Models -- 9.3 Methods -- 9.4 Results -- 9.5 Conclusion -- 10. Machine Learning Approach for Prediction of Human Mitochondrial Proteins (Zhong Huang, Xuheng Xu, and Xiaohua Hu) -- 10.1 Introduction -- 10.2 Methods and Systems -- 10.3 Results and Discussion -- 10.4 Conclusions -- 11. Phylogenetic Inference Using Evolutionary Algorithms(Clare Bates Congdon) -- 11.1 Introduction -- 11.2 Background in Phylogenetics -- 11.3 Challenges and Opportunities for Evolutionary Computation -- 11.4 One Contribution of Evolutionary Computation: Graphyl -- 11.5 Some Other Contributions of Evolutionary computation -- 11.6 Open Questions and Opportunities -- Part Four Medicine -- 12. Evolutionary Algorithms for Cancer Chemotherapy Optimization (John McCall, Andrei Petrovski, and Siddhartha Shakya) -- 12.1 Introduction -- 12.2 Nature of Cancer -- 12.3 Nature of Chemotherapy -- 12.4 Models of Tumor Growth and Response -- 12.5 Constraints on Chemotherapy -- 12.6 Optimal Control Formulations of Cancer Chemotherapy -- 12.7 Evolutionary Algorithms for Cancer Chemotherapy Optimization -- 12.8 Encoding and Evaluation -- 12.9 Applications of EAs to Chemotherapy Optimization Problems -- 12.10 Related Work -- 12.11 Oncology Workbench -- 12.12 Conclusion -- 13. Fuzzy Ontology-Based Text Mining System for Knowledge Acquisition, Ontology Enhancement, and Query Answering from Biomedical Texts (Lipika Dey and Muhammad Abulaish).

13.1 Introduction -- 13.2 Brief Introduction to Ontologies -- 13.3 Information Retrieval form Biological Text Documents: Related Work -- 13.4 Ontology-Based IE and Knowledge Enhancement System -- 13.5 Document Processor -- 13.6 Biological Relation Extractor -- 13.7 Relation-Based Query Answering -- 13.8 Evaluation of the Biological Relation Extraction Process -- 13.9 Biological Relation Characterizer -- 13.10 Determining Strengths of Generic Biological Relations -- 13.11 Enhancing GENIA to Fuzzy Relational Ontology -- 13.12 Conclusions and Future Work -- References -- Appendix Feasible Biological Relations -- Index.