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TABLE OF CONTENTS PREFACE LIST OF CONTRIBUTORS I) Introduction and Resources for Microarray Bioinformatics 1. A Primer on the Current State of Microarray TechnologiesAlexander J. Trachtenberg, Robert J. Chang, Azza E. Abdalla, Andrew Fraser, Steven Y. He, Jessica N. Lacy, Chiara Rivas-Morello, Allison Truong, Gary Hardiman, Lucila Ohno-Machado, Fang Liu, Eivind Hovig and Winston Patrick Kuo2. The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals Masaaki Kotera, Mika Hirakawa, Toshiaki Tokimatsu, Susumu Goto and Minoru Kanehisa3. Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO DatabaseStephen E. Wilhite and Tanya Barrett II) Microarray Data Analysis (Top down approach) 4. Analyzing Cancer Samples with SNP Arrays Peter Van Loo, Gro Nilsen, Silje H. Nordgard, Hans Kristian Moen Vollan, Anne- Lise Børresen-Dale, Vessela N. Kristensen and Ole Christian Lingjærde5. Classification Approaches for Microarray Gene Expression Data AnalysisLeo Wang-Kit Cheung6. Biclustering of Time Series Microarray DataJia Meng and Yufei Huang7. Using the Bioconductor GeneAnswers Package to Interpret Gene ListsGang Feng, Pamela Shaw, Steven T. Rosen, Simon M. Lin and Warren A. Kibbe8. Analysis of Isoform Expression from Splicing Array using Multiple ComparisonsT. Murlidharan Nair9. Functional Comparison of Microarray Data across Multiple Platforms Using the Method of Percentage of Overlapping FunctionsZhiguang Li, Joshua C. Kwekel and Tao Chen10. Performance Comparison of Multiple Microarray Platforms for Gene Expression ProfilingFang Liu, Winston P. Kuo, Tor-Kristian Jenssen and Eivind Hovig11. Integrative Approaches for Microarray Data AnalysisLevi Waldron, Hilary A. Coller and Curtis Huttenhower III) Microarray Bioinformatics in Systems Biology (Bottom up approach) 12. Modelling Gene Regulation Networks using Ordinary Differential Equations Jiguo Cao, Xin Qi and Hongyu Zhao13. Non-homogeneous Dynamic Bayesian Networks in Systems BiologySophie Lèbre, Frank Dondelinger and Dirk Husmeier14. Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraphRobert Castelo and Alberto Roverato15. Effective Nonlinear Methods for Inferring Genetic Regulation from Time-series Microarray Gene Expression DataJunbai Wang and Tianhai Tian IV) Next Generation Sequencing Data Analysis 16. An Overview of the Analysis of Next Generation Sequencing DataAndreas Gogol-Döring and Wei Chen17. How to Analyze Gene Expression using RNA-Sequencing DataDaniel Ramsköld, Ersen Kavak and Rickard Sandberg18. Analyzing ChIP-seq Data: Preprocessing, Normalization, Differential Identification and Binding Pattern CharacterizationCenny Taslim, Kun Huang, Tim Huang and Shili Lin19. Identifying Differential Histone Modification Sites from ChIP-seq DataHan Xu and Wing-Kin Sung20. ChIP-Seq Data Analysis: Identification of Protein-DNA Binding Sites with SISSRs Peak FinderLeelavati Narlikar and Raja Jothi21. Using ChIPMotifs for de novo Motif Discovery of OCT4 and ZNF263 based on ChIP-based High-throughput ExperimentsBrian A. Kennedy, Xun Lan, Tim H-M. Huang, Peggy J. Farnham and Victor X. Jin V) Emerging Applications of Microarray and Next Generation Sequencing 22. Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association AnalysisZhi Wei23. Employing Gene Set Top Scoring Pairs to Identify Deregulated Pathway-Signatures in Dilated Cardiomyopathy from Integrated Microar
