Next Generation Microarray Bioinformatics

A Primer on the Current State of Microarray Technologies.- The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals.- Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database.-Analyzing Cancer Samples with SNP Arrays.- Classification Approaches for Microarray Gene Expression Data Analysis.-Biclustering of Time Series Microarray Data.- Using the Bioconductor GeneAnswers Package to Interpret Gene Lists.- Analysis of Isoform Expression from Splicing Array using Multiple Comparisons.- Functional Comparison of Microarray Data across Multiple Platforms Using the Method of Percentage of Overlapping Functions.- Performance Comparison of Multiple Microarray Platforms for Gene Expression Profiling.- Integrative Approaches for Microarray Data Analysis-.Modelling Gene Regulation Networks using Ordinary Differential Equations.- Non-homogeneous Dynamic Bayesian Networks in Systems Biology.- Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraph.- Effective Nonlinear Methods for Inferring Genetic Regulation from Time-series Microarray Gene Expression Data.- An Overview of the Analysis of Next Generation Sequencing Data.- How to Analyze Gene Expression using RNA-Sequencing Data.- Analyzing ChIP-seq Data: Preprocessing, Normalization, Differential Identification and Binding Pattern Characterization.- Identifying Differential Histone Modification Sites from ChIP-seq Data.- ChIP-Seq Data Analysis: Identification of Protein-DNA Binding Sites with SISSRs Peak Finder.- Using ChIPMotifs for de novo Motif Discovery of OCT4 and ZNF263 based on ChIP-based High-throughput Experiments.- Hidden Markov Models for Controlling False Discovery Rate in Genome-Wide Association Analysis.- Employing Gene Set Top Scoring Pairs to Identify Deregulated Pathway-Signatures in Dilated Cardiomyopathy from Integrated Microarray Gene ExpressionData.-JAMIE: A Software Tool for Jointly Analyzing Multiple ChIP-chip Experiments.- Epigenetic Analysis: ChIP-chip and ChIP-seq.- BiNGS!SL-seq: A Bioinformatics Pipeline for the Analysis and Interpretation of Deep Sequencing Genome-wide Synthetic Lethal Screen.