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| Preface | |
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| Contributors | |
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| Qualitative Knowledge Models in Functional Genomics and Proteomics | |
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| Introduction | |
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| Methods and Tools | |
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| Modeling Approach and Results | |
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| Discussion | |
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| Conclusion | |
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| References | |
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| Interpreting Microarray Data and Related Applications Using Nonlinear System Identification | |
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| Introduction | |
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| Background | |
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| Parallel Cascade Identification | |
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| Constructing Class Predictors | |
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| Prediction Based on Gene Expression Profiling | |
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| Comparing Different Predictors Over the Same Data Set | |
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| Concluding Remarks | |
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| References | |
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| Gene Regulation Bioinformatics of Microarray Data | |
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| Introduction | |
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| Introduction to Transcriptional Regulation | |
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| Measuring Gene Expression Profiles | |
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| Preprocessing of Data | |
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| Clustering of Gene Expression Profiles | |
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| Cluster Validation | |
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| Searching for Common Binding Sites of Coregulated Genes | |
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| Inclusive: Online Integrated Analysis of Microarray Data | |
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| Further Integrative Steps | |
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| Conclusion | |
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| References | |
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| Robust Methods for Microarray Analysis | |
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| Introduction | |
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| Microarray Experiments and Analysis Methods | |
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| Unsupervised Methods | |
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| Supervised Methods | |
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| Conclusion | |
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| References | |
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| In Silico Radiation Oncology: A Platform for Understanding Cancer Behavior and Optimizing Radiation Therapy Treatment | |
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| Philosophiae Tumoralis Principia Algorithmica: Algorithmic Principles of Simulating Cancer on Computer | |
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| Brief Literature Review | |
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| Paradigm of Four-Dimensional Simulation of Tumor Growth and Response to Radiation Therapy In Vivo | |
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| Discussion | |
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| Future Trends | |
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| References | |
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| Genomewide Motif Identification Using a Dictionary Model | |
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| Introduction | |
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| Unified Model | |
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| Algorithms for Likelihood Evaluation | |
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| Parameter Estimation via Minorization-Maximization Algorithm | |
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| Examples | |
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| Discussion and Conclusion | |
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| References | |
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| Error Control Codes and the Genome | |
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| Error Control and Communication: A Review | |
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| Reverse Engineering the Genetic Error Control System | |
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| Applications of Biological Coding Theory | |
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| References | |
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| Complex Life Science Multidatabase Queries | |
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| Introduction | |
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| Architecture | |
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| Query Execution Plans | |
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| Related Work | |
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| Future Trends | |
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| References | |
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| Computational Analysis of Proteins | |
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| Introduction: Definitions | |
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| Databases | |
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| Sequence Motifs and Domains | |
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| Sequence Alignment | |
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| Modeling | |
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| Classification and Prediction | |
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| Natural Language Processing | |
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| Future Trends | |
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| References | |
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| Computational Analysis of Interactions Between Tumor and Tumor Suppressor Proteins | |
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| Introduction | |
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| Methodology: Resonant Recognition Model | |
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| Results and Discussions | |
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| Conclusion | |
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| References | |
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| Index | |
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| About the Editor | |