Next generation microarray bioinformatics : methods and protocols

Contributor(s): Wang, Junbai | Tan, Aik Choon | Tian, TianhaiMaterial type: TextTextSeries: Publication details: New York : Humana Press ; Springer, c2012Description: xvi, 401 p. : ill. (some col.)ISBN: 9781617793998; 161779399X; 9781617794001; 1617794007 Subject(s): DNA microarrays | Bioinformatics | Computational Biology | Microarray AnalysisDDC classification: 572.8636 Online resources: Click here to access online | Click here to access online | Click here to access online
Contents:
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 -- Modeling gene regulation networks using ordinary differential equations -- Nonhomogeneous dynamic bayesian networks in systems biology -- Inference of regulatory networks from microarray data with R and the bioconductor package qpgraph -- Effective non-linear 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 expression data -- 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.
Summary: This book opens up new research avenues for the investigation of a wide range of biological and medical questions across the entire genome at single base resolution. It provides step-by-step detail essential for reproducible results
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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 --
Modeling gene regulation networks using ordinary differential equations --
Nonhomogeneous dynamic bayesian networks in systems biology --
Inference of regulatory networks from microarray data with R and the bioconductor package qpgraph --
Effective non-linear 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 expression data --
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.

This book opens up new research avenues for the investigation of a wide range of biological and medical questions across the entire genome at single base resolution. It provides step-by-step detail essential for reproducible results

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