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| Preface | |
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| Introduction to Bioinformatics | |
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| Introduction | |
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| Needs of Bioinformatics Technologies | |
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| An Overview of Bioinformatics Technologies | |
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| A Brief Discussion on the Chapters | |
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| References | |
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| Overview of Structural Bioinformatics 15 | |
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| Introduction | |
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| Organization of Structural Bioinformatics | |
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| Primary Resource: Protein Data Bank | |
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| Data Format | |
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| Growth of Data | |
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| Data Processing and Quality Control | |
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| The Future of the PDB | |
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| Visualization | |
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| Secondary Resources and Applications | |
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| Structural Classification | |
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| Structure Prediction | |
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| Functional Assignments in Structural Genomics | |
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| Protein-Protein Interactions | |
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| Protein-Ligand Interactions | |
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| Using Structural Bioinformatics Approaches in Drug Design | |
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| The Future | |
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| Integration over Multiple Resources | |
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| The Impact of Structural Genomics | |
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| The Role of Structural Bioinformatics in Systems Biology | |
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| References | |
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| Database Warehousing in Bioinformatics | |
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| Introduction | |
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| Bioinformatics Data | |
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| Transforming Data to Knowledge | |
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| Data Warehousing | |
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| Data Warehouse Architecture | |
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| Data Quality | |
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| Concluding Remarks | |
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| References | |
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| Data Mining for Bioinformatics | |
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| Introduction | |
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| Biomedical Data Analysis | |
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| Major Nucleotide Sequence Database, Protein Sequence Database, and Gene Expression Database | |
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| Software Tools for Bioinformatics Research | |
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| DNA Data Analysis | |
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| DNA Sequence | |
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| DNA Data Analysis | |
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| Protein Data Analysis | |
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| Protein and Amino Acid Sequence | |
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| Protein Data Analysis | |
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| References | |
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| Machine Learning in Bioinformatics | |
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| Introduction | |
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| Artificial Neural Network | |
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| Neural Network Architectures and Applications | |
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| Neural Network Architecture | |
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| Neural Network Learning Algorithms | |
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| Neural Network Applications in Bioinformatics | |
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| Genetic Algorithm | |
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| Fuzzy System | |
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| References | |
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| Systems Biotechnology: a New Paradigm in Biotechnology Development | |
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| Introduction | |
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| Why Systems Biotechnology? | |
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| Tools for Systems Biotechnology | |
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| Genome Analyses | |
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| Transcriptome Analyses | |
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| Proteome Analyses | |
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| Metabolome/Fluxome Analyses | |
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| Integrative Approaches | |
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| In Silico Modeling and Simulation of Cellular Processes | |
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| Statistical Modeling | |
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| Dynamic Modeling | |
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| Conclusion | |
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| References | |
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| Computational Modeling of Biological Processes with Petri Net-Based Architecture | |
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| Introduction | |
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| Hybrid Petri Net and Hybrid Dynamic Net | |
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| Hybrid Functional Petri Net | |
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| Hybrid Functional Petri Net with Extension | |
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| Definitions | |
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| Relationships with Other Petri Nets | |
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| Implementation of HFPNe in Genomic Object Net | |
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| Modeling of Biological Processes with HFPNe | |
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| From DNA to mRNA in Eucaryotes - Alternative Splicing | |
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| Translation of mRNA - Frameshift | |
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| Huntington's Disease | |
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| Protein Modification - p53 | |
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| Related Works with HFPNe | |
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| Genomic Object Net: GON | |
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| GON Features That Derived from HFPNe Features | |
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| GON GUI and Other Features | |
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| GONML and Related Works with GONML | |
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| Related Works with GON | |
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| Visualizer | |
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| Bio-processes on Visualizer | |
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| Related Works with Visualizer | |
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| BPE | |
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| Conclusion | |
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| References | |
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| Biological Sequence Assembly and Alignment | |
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| Introduction | |
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| Large-Scale Sequence Assembly | |
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| Related Research | |
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| Euler Sequence Assembly | |
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| PESA Sequence Assembly Algorithm | |
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| Large-Scale Pairwise Sequence Alignment | |
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| Pairwise Sequence Alignment | |
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| Large Smith-Waterman Pairwise Sequence Alignment | |
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| Large-Scale Multiple Sequence Alignment | |
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| Multiple Sequence Alignment | |
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| Large-Scale Clustal W Multiple Sequence Alignment | |
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| Load Balancing and Communication Overhead | |
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| Conclusion | |
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| References | |
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| Modeling for Bioinformatics 263 | |
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| Introduction | |
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| Hidden Markov Modeling for Biological Data Analysis | |
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| Hidden Markov Modeling for Sequence Identification | |
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| Hidden Markov Modeling for Sequence Classification | |
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| Hidden Markov Modeling for Multiple Alignment Generation | |
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| Conclusion | |
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| Comparative Modeling | |
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| Protein Comparative Modeling | |
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| Comparative Genomic Modeling | |
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| Probabilistic Modeling | |
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| Bayesian Networks | |
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| Stochastic Context-Free Grammars | |
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| Probabilistic Boolean Networks | |
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| Molecular Modeling | |
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| Molecular and Related Visualization Applications | |
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| Molecular Mechanics | |
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| Modern Computer Programs for Molecular Modeling | |
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| References | |
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| Pattern Matching for Motifs | |
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| Introduction | |
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| Gene Regulation | |
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| Promoter Organization | |
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| Motif Recognition | |
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| Motif Detection Strategies | |
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| Multi-genes, Single Species Approach | |
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| Single Gene, Multi-species Approach | |
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| Multi-genes, Multi-species Approach | |
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| Summary | |
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| References | |
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| Visualization and Fractal Analysis of Biological Sequences | |
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| Introduction | |
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| Fractal Analysis | |
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| What Is a Fractal? | |
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| Recurrent Iterated Function System Model | |
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| Moment Method to Estimate the Parameters of the IFS (RIFS) Model | |
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| Multifractal Analysis | |
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| DNA Walk Models | |
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| One-Dimensional DNA Walk | |
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| Two-Dimensional DNA Walk | |
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| Higher-Dimensional DNA Walk | |
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| Chaos Game Representation of Biological Sequences | |
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| Chaos Game Representation of DNA Sequences | |
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| Chaos Game Representation of Protein Sequences | |
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| Chaos Game Representation of Protein Structures | |
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| Chaos Game Representation of Amino Acid Sequences Based on the Detailed HP Model | |
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| Two-Dimensional Portrait Representation of DNA Sequences | |
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| Graphical Representation of Counters | |
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| Fractal Dimension of the Fractal Set for a Given Tag | |
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| One-Dimensional Measure Representation of Biological Sequences | |
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| Measure Representation of Complete Genomes | |
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| Measure Representation of Linked Protein Sequences | |
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| Measure Representation of Protein Sequences Based on Detailed HP Model | |
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| References | |
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| Microarray Data Analysis | |
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| Introduction | |
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| Microarray Technology for Genome Expression Study | |
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| Image Analysis for Data Extraction | |
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| Image Preprocessing | |
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| Block Segmentation | |
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| Automatic Gridding | |
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| Spot Extraction | |
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| Background Correction, Data Normalization and Filtering, and Missing Value Estimation | |
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| Data Analysis for Pattern Discovery | |
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| Cluster Analysis | |
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| Temporal Expression Profile Analysis and Gene Regulation | |
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| Gene Regulatory Network Analysis | |
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| References | |
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| Index | |