Genome Analysis : Current Procedures and Applications.

Intro -- Contributors -- Contents -- Preface -- 1 Identification of Structural Variation -- Introduction -- Defining structural variants -- Causes of structural variation -- Early methods for SV identification -- Identification of structural variation from sequencing data -- Discussion -- Future trends -- 2 Methods for RNA Isolation, Characterization and Sequencing (RNA-Seq) -- A brief history of RNA -- Principles of RNA isolation -- Methods of RNA sequencing -- Using RNA sequencing to define transcriptional landscapes -- RNA sequencing to discover RNA modifications -- RNA base modifications and epitranscriptomics -- Conclusions -- 3 Transcriptome Reconstruction and Quantification from RNA Sequencing Data -- Introduction -- Transcriptome reconstruction -- Transcriptome quantification -- Future trends -- Conclusions -- 4 Identification of Small Interfering RNA from Next-generation Sequencing Data -- Introduction -- Applying sequencing technologies to siRNAs -- Experimental designs -- Available tools for analysis of siRNA-seq data -- Processing of siRNA-seq data -- Locus finding -- Association of siRNA loci with genomic features -- Differential expression in siRNAs -- Phased siRNAs -- Post-analysis visualization -- Target finding and small RNA networks -- Discussion -- 5 Motif Discovery and Motif Finding in ChIP-Seq Data -- Introduction -- ChIP-Seq data: advantages and challenges for sequence analysis bioinformatics -- Cooking recipes for motif analysis of ChIP-Seq data -- Conclusion: the present and the future of motif analysis for the ChIP-Seq technology -- 6 Mammalian Enhancer Prediction -- Introduction -- Transcriptional enhancers -- Computational prediction of enhancers -- Discussion and conclusions -- Future trends -- 7 DNA Patterns for Nucleosome Positioning -- Nucleosome as the basic unit of chromatin.

Role of nucleosome positioning in gene regulation -- Different nucleosome sequence patterns -- Early history (pre-genomic and genomic era) -- Post-genomic era and high-throughput data -- Positive versus negative, combining and splitting the patterns -- Discussion and conclusions -- 8 Hypermethylation in Cancer -- Introduction: hypermethylation in the context of other epigenetic modifications -- Types of DNA methylation -- Hypermethylation machineries: the role of DNMTs -- Epigenetic factors contribute to tumourigenesis and cancer progression -- Biological pathways of frequently methylated genes in cancer -- The relevance of high-throughput technologies as accelerating discovery means of epigenetic events in cancer -- Translational applications of methylome analyses as a source of cancer biomarkers -- Conclusions -- Acknowledgements -- References -- 9 Identification and Analysis of Transposable Elements in Genomic Sequences -- Introduction -- Classic detection methods for TEs in genome sequences -- TEs in the next-generation sequencing data era -- What do NGS data bring to TE analyses? -- Conclusions -- Future trends -- 10 The Current State of Metagenomic Analysis -- Introduction -- Metagenome sequencing -- Metagenome sequencing protocols -- Metagenomic diversity studies -- Functional metagenomics and bioprospecting -- Metagenomics and 'meta-omics' approaches for ecosystems biology studies -- Conclusions -- Future perspectives -- 11 Metatranscriptomics -- Introduction -- Metatranscriptomic approaches -- NGS method for metatranscriptome -- Comparison of approaches -- Bioinformatics for metatranscriptome: RNA assembly -- Metagenome-based tools -- Transcriptome-based tools -- Bioinformatics for metatranscriptome -- Bioinformatics for metatranscriptome: network analysis -- Case study: metatranscriptome of marine microbiome -- Future trends -- Conclusion.

12 Inferring Viral Quasispecies Spectra from Shotgun and Amplicon Next-generation Sequencing Reads -- Introduction -- Quasispecies spectrum reconstruction -- Viral Spectrum Assembler (ViSpA) (Astrovskaya et al., 2011) -- VSEM enhancement of ViSpA (Mangul et al., 2011) -- Viral Assembler (VirA) (Mancuso et al., 2012)* -- Results and discussions -- Future trends -- Conclusions -- References -- 13 DNA Instability in Bacterial Genomes: Causes and Consequences -- Introduction -- Spontaneous DNA lesions, replication and transcription as sources of instability -- Stress-induced instability -- More stable bacterial genomes and DNA-based therapeutic molecules -- Concluding remarks -- 14 Comparative Methods for RNA Structure Prediction -- Introduction -- The RNA folding problem -- Conceptual building blocks for computational RNA structure prediction -- RNA single-sequence structure prediction -- Comparative methods for secondary structure prediction -- Genome-wide search for structured RNAs -- Discussion -- Future trends -- 15 Context-free Grammars and RNA Secondary Structure Prediction -- Introduction -- Context-free grammars -- Stochastic context-free grammars -- SCFGs for structure prediction -- SCFG-based algorithms -- Length-dependent stochastic context-free grammars -- Concluding remarks -- 16 Stochastic Context-free Grammars and RNA Secondary Structure Prediction -- Introduction -- Context-free grammars and SCFGs -- Normal forms -- Ambiguity, completeness and grammar design -- Algorithms for SCFGs, parameter estimation, structure prediction -- Comparative modelling -- Measures of SCFG variability -- Thermodynamic methods -- Discussion -- Future trends -- Index.

In this book, an impressive array of expert authors highlight and review current advances in genome analysis. This volume provides an invaluable, up-to-date and comprehensive overview of the methods currently employed for next-generation sequencing (NGS) data analysis, highlights their problems and limitations, demonstrates the applications and indicates the developing trends in various fields of genome research. The first part of the book is devoted to the methods and applications that arose from, or were significantly advanced by, NGS technologies: the identification of structural variation from DNA-seq data; whole-transcriptome analysis and discovery of small interfering RNAs (siRNAs) from RNA-seq data; motif finding in promoter regions, enhancer prediction and nucleosome sequence code discovery from ChiP-Seq data; identification of methylation patterns in cancer from MeDIP-seq data; transposon identification in NGS data; metagenomics and metatranscriptomics; NGS of viral communities; and causes and consequences of genome instabilities. The second part is devoted to the field of RNA biology with the last three chapters devoted to computational methods of RNA structure prediction including context-free grammar applications. An essential book for everyone involved in sequence data analysis, next-generation sequencing, high-throughput sequencing, RNA structure prediction, bioinformatics and genome analysis.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.