Next Generation Microarray Bioinformatics

Chapter 1 A Primer on the Current State of Microarray Technologies

Chapter 2 The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals.

Chapter 3 Next Generation Microarray Bioinformatics

Chapter 4 Analyzing Cancer Samples with SNP Arrays

Chapter 5 Classification Approaches for Microarray Gene Expression Data Analysis

Chapter 6 Biclustering of time series microarray data.

Chapter 7 Using the Bioconductor GeneAnswers Package to Interpret Gene Lists

Chapter 8 Analysis of Isoform Expression from Splicing Array Using Multiple Comparisons

Chapter 9 Functional Comparison of Microarray Data Across Multiple Platforms Using the Method of Percentage of Overlapping Functions

Chapter 10 Performance Comparison of Multiple Microarray Platforms for Gene Expression Profiling

Chapter 11 Integrative Approaches for Microarray Data Analysis

Chapter 12 Modeling Gene Regulation Networks Using Ordinary Differential Equations

Chapter 13 Nonhomogeneous Dynamic Bayesian Networks in Systems Biology

Chapter 14 Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraph

Chapter 15 Effective Non-linear Methods for Inferring Genetic Regulation from Time-Series Microarray Gene Expression Data

Chapter 16 An overview of the analysis of next generation sequencing data.

Chapter 17 How to Analyze Gene Expression Using RNA-Sequencing Data

Chapter 18 Analyzing ChIP-seq Data: Preprocessing, Normalization, Differential Identification, and Binding Pattern Characterization.

Chapter 19 Identifying Differential Histone Modification Sites from ChIP‐seq Data

Chapter 20 ChIP-Seq Data Analysis: Identification of Protein–DNA Binding Sites with SISSRs Peak-Finder

Chapter 21 Using ChIPMotifs for De Novo Motif Discovery of OCT4 and ZNF263 Based on ChIP-Based High-Throughput Experiments.

Chapter 22 Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis

Chapter 23 Employing Gene Set Top Scoring Pairs to Identify Deregulated Pathway-Signatures in Dilated Cardiomyopathy from Integrated Microarray Gene Expression Data

Chapter 24 JAMIE: A Software Tool for Jointly Analyzing Multiple ChIP-chip Experiments

Chapter 25 Epigenetic Analysis: ChIP-chip and ChIP-seq

Chapter 26 BiNGS!SL-seq: A Bioinformatics Pipeline for the Analysis and Interpretation of Deep Sequencing Genome-Wide Synthetic Lethal Screen.