Statistical Methods For Functional Metagenomic Analysis Based On Next Generation Sequencing Data
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Statistical Methods For Functional Metagenomic Analysis Based On Next Generation Sequencing Data
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Author : Naruekamol Pookhao
language : en
Publisher:
Release Date : 2014
Statistical Methods For Functional Metagenomic Analysis Based On Next Generation Sequencing Data written by Naruekamol Pookhao and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014 with categories.
Metagenomics is the study of a collective microbial genetic content recovered directly from natural (e.g., soil, ocean, and freshwater) or host-associated (e.g., human gut, skin, and oral) environmental communities that contain microorganisms, i.e., microbiomes. The rapid technological developments in next generation sequencing (NGS) technologies, enabling to sequence tens or hundreds of millions of short DNA fragments (or reads) in a single run, facilitates the studies of multiple microorganisms lived in environmental communities. Metagenomics, a relatively new but fast growing field, allows us to understand the diversity of microbes, their functions, cooperation, and evolution in a particular ecosystem. Also, it assists us to identify significantly different metabolic potentials in different environments. Particularly, metagenomic analysis on the basis of functional features (e.g., pathways, subsystems, functional roles) enables to contribute the genomic contents of microbes to human health and leads us to understand how the microbes affect human health by analyzing a metagenomic data corresponding to two or multiple populations with different clinical phenotypes (e.g., diseased and healthy, or different treatments). Currently, metagenomic analysis has substantial impact not only on genetic and environmental areas, but also on clinical applications. In our study, we focus on the development of computational and statistical methods for functional metagnomic analysis of sequencing data that is obtained from various environmental microbial samples/communities.
Statistical Analysis Of Next Generation Sequencing Data
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Author : Somnath Datta
language : en
Publisher: Springer
Release Date : 2014-07-03
Statistical Analysis Of Next Generation Sequencing Data written by Somnath Datta and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-07-03 with Medical categories.
Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized medicine. About the editors: Somnath Datta is Professor and Vice Chair of Bioinformatics and Biostatistics at the University of Louisville. He is Fellow of the American Statistical Association, Fellow of the Institute of Mathematical Statistics and Elected Member of the International Statistical Institute. He has contributed to numerous research areas in Statistics, Biostatistics and Bioinformatics. Dan Nettleton is Professor and Laurence H. Baker Endowed Chair of Biological Statistics in the Department of Statistics at Iowa State University. He is Fellow of the American Statistical Association and has published research on a variety of topics in statistics, biology and bioinformatics.
Statistical Analysis Of Microbiome Data With R
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Author : Yinglin Xia
language : en
Publisher: Springer
Release Date : 2018-10-06
Statistical Analysis Of Microbiome Data With R written by Yinglin Xia and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-10-06 with Computers categories.
This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.
Bioinformatics
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Author : Hamid D. Ismail
language : en
Publisher: CRC Press
Release Date : 2023-06-29
Bioinformatics written by Hamid D. Ismail and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-06-29 with Computers categories.
This book contains the latest material in the subject, covering next generation sequencing (NGS) applications and meeting the requirements of a complete semester course. This book digs deep into analysis, providing both concept and practice to satisfy the exact need of researchers seeking to understand and use NGS data reprocessing, genome assembly, variant discovery, gene profiling, epigenetics, and metagenomics. The book does not introduce the analysis pipelines in a black box, but with detailed analysis steps to provide readers with the scientific and technical backgrounds required to enable them to conduct analysis with confidence and understanding. The book is primarily designed as a companion for researchers and graduate students using sequencing data analysis but will also serve as a textbook for teachers and students in biology and bioscience.
Statistical Methods For High Dimensional Count And Compositional Data With Applications To Microbiome Studies
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Author : Yuanpei Cao
language : en
Publisher:
Release Date : 2016
Statistical Methods For High Dimensional Count And Compositional Data With Applications To Microbiome Studies written by Yuanpei Cao 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.
Next generation sequencing (NGS) technologies make the studies of microbiomes in very large-scale possible without cultivation in vitro. One approach to sequencing-based microbiome studies is to sequence specific genes (often the 16S rRNA gene) to produce a profile of diversity of bacterial taxa. Alternatively, the NGS-based sequencing strategy, also called shotgun metagenomics, provides further insights at the molecular level, such as species/strain quantification, gene function analysis and association studies. Such studies generate large-scale high-dimensional count and compositional data, which are the focus of this dissertation.
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.
Metagenomic Data Analysis
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Author : Suparna Mitra
language : en
Publisher: Springer Nature
Release Date : 2023-05-31
Metagenomic Data Analysis written by Suparna Mitra and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-31 with Science categories.
This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis using most used R packages. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.
Evolutionary Genomics
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Author : Maria Anisimova
language : en
Publisher:
Release Date : 2012
Evolutionary Genomics written by Maria Anisimova and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with Evolutionary genetics categories.
Statistical Visual And Functional Analysis Of Microbiome Data
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Author : Achal Dhariwal
language : en
Publisher:
Release Date : 2018
Statistical Visual And Functional Analysis Of Microbiome Data written by Achal Dhariwal and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with categories.
"The advancements in next-generation sequencing technologies have revolutionized microbiome research by allowing culture-independent high-throughput profiling of the genetic contents of microbial communities. Nowadays, 16S rRNA based marker gene sequencing is widely used to characterize the taxonomic composition and phylogenetic diversity of complex microbial communities. However, statistical, visual and functional analysis of such data possess great challenges. In addition, many aspects of the current approaches can be improved to get a better understanding of communities. The proper analysis of the resulting large and complicated datasets remains a key bottleneck in current microbiome studies. Over the last decade, powerful computational pipelines and standard protocols have been developed to support efficient raw data processing and annotation of microbiome data. The focus has now shifted towards downstream statistical analysis and functional interpretation. To address this bottleneck, we have developed MicrobiomeAnalyst, a user-friendly web-based tool that incorporates recent progresses in statistics and interactive visualization techniques, coupled with novel knowledge bases, to facilitate comprehensive analysis of common data sets generated from microbiome studies. MicrobiomeAnalyst contains four major components, including i) a module for community diversity profiling, comparative analysis and functional prediction of 16S rRNA marker gene data; ii) a module for exploratory data analysis, functional profiling and metabolic network visualization for shotgun metagenomics or metatranscriptomics data; iii) a module to help users to interpret their taxa of interest via enrichment analysis against ~300 taxon sets manually collected from recent literature and public databases; and iv) a module to allow users to visually explore their data sets within the context of compatible public data (meta-analysis) for pattern discovery and biological insights. The tool is freely accessible at http://www.microbiomeanalyst.ca. " --
Data Production And Analysis In Population Genomics
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Author : Francois Pompanon
language : en
Publisher: Humana Press
Release Date : 2012-06-06
Data Production And Analysis In Population Genomics written by Francois Pompanon and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-06-06 with Medical categories.
Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough a priori data on the polymorphism, population genomics analyses of populations will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, Data Production and Analysis in Population Genomics purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available, Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Data Production and Analysis in Population Genomics serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose.