Computational Approaches For Metagenomic Analysis Of High Throughput Sequencing Data
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Computational Approaches For Metagenomic Analysis Of High Throughput Sequencing Data
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Author : David Ainsworth
language : en
Publisher:
Release Date : 2016
Computational Approaches For Metagenomic Analysis Of High Throughput Sequencing Data written by David Ainsworth and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Metagenomics For Microbiology
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Author : Jacques Izard
language : en
Publisher: Academic Press
Release Date : 2014-11-07
Metagenomics For Microbiology written by Jacques Izard and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-11-07 with Science categories.
Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.
Introduction To Computational Metagenomics
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Author : Zhong Wang
language : en
Publisher: World Scientific
Release Date : 2022-04-11
Introduction To Computational Metagenomics written by Zhong Wang and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-11 with Science categories.
Breakthroughs in high-throughput genome sequencing and high-performance computing technologies have empowered scientists to decode many genomes including our own. Now they have a bigger ambition: to fully understand the vast diversity of microbial communities within us and around us, and to exploit their potential for the improvement of our health and environment. In this new field called metagenomics, microbial genomes are sequenced directly from the habitats without lab cultivation. Computational metagenomics, however, faces both a data challenge that deals with tens of tera-bases of sequences and an algorithmic one that deals with the complexity of thousands of species and their interactions.This interdisciplinary book is essential reading for those who are interested in beginning their own journey in computational metagenomics. It is a prism to look through various intricate computational metagenomics problems and unravel their three distinctive aspects: metagenomics, data engineering, and algorithms. Graduate students and advanced undergraduates from genomics science or computer science fields will find that the concepts explained in this book can serve as stepping stones for more advanced topics, while metagenomics practitioners and researchers from similar disciplines may use it to broaden their knowledge or identify new research targets.
Computational Methods For Next Generation Sequencing Data Analysis
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Author : Ion Mandoiu
language : en
Publisher: John Wiley & Sons
Release Date : 2016-09-12
Computational Methods For Next Generation Sequencing Data Analysis written by Ion Mandoiu and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-09-12 with Computers categories.
Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols. Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis. Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.
Metagenomics
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Author : Muniyandi Nagarajan
language : en
Publisher: Academic Press
Release Date : 2017-11-06
Metagenomics written by Muniyandi Nagarajan and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-11-06 with Medical categories.
Metagenomics: Perspectives, Methods, and Applications provides thorough coverage of the growing field of metagenomics. A diverse range of chapters from international experts offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools, and recent metagenomic studies in various environments. The emphasis on application makes this text particularly useful for applied researchers, practitioners, clinicians and students seeking to employ metagenomic approaches to advance knowledge in the biomedical and life sciences. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. Additionally, perspectives on future potential at the end of each chapter provoke new thought and motivations for continued study in this exciting and fruitful research area. Provides thorough coverage of the rapidly growing field of metagenomics, with an emphasis on applications of relevance to translational researchers, practitioners, clinicians and students Features a diverse range of chapters from international experts that offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools and research pipelines Highlights perspectives on future potential at the end of each chapter to provoke new thought and motivations for continued study in this exciting and fruitful research area
Bioinformatics For High Throughput Sequencing
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Author : Naiara Rodríguez-Ezpeleta
language : en
Publisher: Springer Science & Business Media
Release Date : 2011-10-26
Bioinformatics For High Throughput Sequencing written by Naiara Rodríguez-Ezpeleta and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-10-26 with Science categories.
Next generation sequencing is revolutionizing molecular biology. Owing to this new technology it is now possible to carry out a panoply of experiments at an unprecedented low cost and high speed. These go from sequencing whole genomes, transcriptomes and small non-coding RNAs to description of methylated regions, identification protein – DNA interaction sites and detection of structural variation. The generation of gigabases of sequence information for each of this huge bandwidth of applications in just a few days makes the development of bioinformatics applications for next generation sequencing data analysis as urgent as challenging.
Computational Tools For The Analysis Of High Throughput Genome Scale Sequence Data
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Author : David Adrian Lopez
language : en
Publisher:
Release Date : 2016
Computational Tools For The Analysis Of High Throughput Genome Scale Sequence Data written by David Adrian Lopez and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
As high-throughput sequence data becomes increasingly used in a variety of fields, there is a growing need for computational tools that facilitate analyzing and interpreting the sequence data to extract biological meaning. To date, several computational tools have been developed to analyze raw and processed sequence data in a number of contexts. However, many of these tools primarily focus on well-studied, reference organisms, and in some cases, such as the visualization of molecular signatures in expression data, there is a scarcity or complete absence of tools. Furthermore, the compendium of genome-scale data in publicly accessible databases can be leveraged to inform new studies. The focus of this dissertation is the development of computational tools and methods to analyze high-throughput genome-scale sequence data, as well as applications in mammalian, algal, and bacterial systems. Chapter 1 introduces the challenges of analyzing high-throughput sequence data. Chapter 2 presents the Signature Visualization Tool (SaVanT), a framework to visualize molecular signatures in user-generated expression data on a sample-by-sample basis. This chapter demonstrates that SaVanT can use immune activation signatures to distinguish patients with different types of acute infections (influenza A and bacterial pneumonia), and determine the primary cell types underlying different leukemias (acute myeloid and acute lymphoblastic) and skin disorders. Chapter 3 describes the Algal Functional Annotation Tool, which biologically interprets large gene lists, such as those derived from differential expression experiments. This tool integrates data from several pathway, ontology, and protein domain databases and performs enrichment testing on gene lists for several algal genomes. Chapter 4 describes a survey of the Chlamydomonas reinhardtii transcriptome and methylome across various stages of its sexual life cycle. This chapter discusses the identification and function of 361 gamete-specific and 627 zygote-specific genes, the first base-resolution methylation map of C. reinhardtii, and the changes in chloroplast methylation throughout key stages of its life cycle. Chapter 5 presents a comparative genomics approach to identifying previously uncharacterized bacterial microcompartment (BMC) proteins. Based on genomic proximity of genes in 131 fully-sequenced bacterial genomes, this chapter describes new putative microcompartments and their function.
Field Guidelines For Genetic Experimental Designs In High Throughput Sequencing
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Author : Ana M. Aransay
language : en
Publisher: Springer
Release Date : 2016-06-02
Field Guidelines For Genetic Experimental Designs In High Throughput Sequencing written by Ana M. Aransay and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-06-02 with Medical categories.
High throughput sequencing (HTS) technologies have conquered the genomics and epigenomics worlds. The applications of HTS methods are wide, and can be used to sequence everything from whole or partial genomes, transcriptomes, non-coding RNAs, ribosome profiling, to single-cell sequencing. Having such diversity of alternatives, there is a demand for information by research scientists without experience in HTS that need to choose the most suitable methodology or combination of platforms and to define their experimental designs to achieve their specific objectives. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing aims to collect in a single volume all aspects that should be taken into account when HTS technologies are being incorporated into a research project and the reasons behind them. Moreover, examples of several successful strategies will be analyzed to make the point of the crucial features. This book will be of use to all scientist that are unfamiliar with HTS and want to incorporate such technologies to their research.
Computing For Comparative Microbial Genomics
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Author : David Wayne Ussery
language : en
Publisher: Springer Science & Business Media
Release Date : 2009-02-26
Computing For Comparative Microbial Genomics written by David Wayne Ussery and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-02-26 with Science categories.
Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.
Computational Methods For Microbiome Analysis
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Author : Joao Carlos Setubal
language : en
Publisher: Frontiers Media SA
Release Date : 2021-02-02
Computational Methods For Microbiome Analysis written by Joao Carlos Setubal and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-02-02 with Science categories.