Microarray image analysis : an algorithmic approach / Karl Fraser, Zidong Wang, Xiaohui Liu. — London : Chapman & Hall/CRC, 2010. – (58.174252/F841)

Contents

    CONTENTS
    
    List of Figures
    List of Algorithms
    Preface and Acknowledgments
    Biographies
    1 Introduction
    1.1 Overview 2
    1.2 Current state of art 3
    1.3 Experimental approach 5
    1.4 Key issues 7
    1.5 Contribution to knowledge 10
    1.6 Structure of the book 13
    2 Background
    2.1 Introduction 17
    2.2 Molecular biology 18
    2.3 Microarray technology 22
    2.4 Microarray analysis 30
    2.5 Copasetic microarray analysis framework overview
    2.6 Summary
    3 Data Services
    3.1 Introduction
    3.2 Image transformation engine
    3.3 Evaluation
    3.4 Summary
    4 Structure Extrapolation I
    4.1 Introduction
    4.2 Pyramidic contextual clustering
    4.3 Evaluation
    4.4 Summary
    5 Structure Extrapolation II
    5.1 Introduction
    5.2 Image layout - master blocks
    5.3 Image structure meta-blocks
    5.4 Summary
    6 Feature Identification I
    6.1 Introduction
    6.2 Spatial binding
    6.3 Evaluation of feature identification
    6.4 Evaluation of copasetic microarray analysis framework
    6.5 Summary
    7 Feature Identification II
    7.1 Background
    7.2 Proposed approach - subgrid detection
    7.3 Experimental results
    7.4 Conclusions
    8 Chained Fourier Background Reconstruction
    8.1 Introduction
    8.2 Existing techniques
    8.3 A new technique
    8.4 Experiments and results
    8.5 Conclusions
    9 Graph-Cutting for Improving Microarray Gene Expression Reconstructions
    9.1 Introduction
    9.2 Existing techniques
    9.3 Proposed technique
    9.4 Experiments and results
    9.5 Conclusions
    10 Stochastic Dynamic Modeling of Short Gene Series Data Expression Time
    10.1 Introduction
    10.2 Stochastic dynamic model for gene expression data
    10.3 An EM algorithm for parameter identification
    10.4 Simulation Results
    10.5 Discussions 235
    10.6 Conclusions and Future Work 242
    11 Conclusions
    11.1 Introduction
    11.2 Achievements
    11.3 Contributions to microarray biology domain
    11.4 Contributions to computer science domain
    11.5 Future research topics
    12 Appendices
    12.1 Appendix A: Microarray variants
    12.2 Appendix B: Basic transformations
    12.3 Appendix C: Clustering
    12.4 Appendix D: A glance on mining gene expression data
    12.5 Appendix E: Autocorrelation and GHT
    References
    Index