Bioinformatics For Microbiome Analysis

Author : Somnath Datta,Subharup Guha
Publisher : Springer Nature
Page : 349 pages
File Size : 55,5 Mb
Release : 2021-10-27
Category : Medical
ISBN : 9783030733513

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Statistical Analysis of Microbiome Data by Somnath Datta,Subharup Guha Pdf

Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.

Author : Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh
Publisher : Frontiers Media SA
Page : 170 pages
File Size : 41,9 Mb
Release : 2021-02-02
Category : Science
ISBN : 9782889664375

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Computational Methods for Microbiome Analysis by Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh Pdf

Author : Robert G. Beiko,Will Hsiao,John Parkinson
Publisher : Unknown
Page : 324 pages
File Size : 43,5 Mb
Release : 2018
Category : Microbiology
ISBN : 1493987283

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Microbiome Analysis by Robert G. Beiko,Will Hsiao,John Parkinson Pdf

Author : Yinglin Xia,Jun Sun
Publisher : Springer Nature
Page : 717 pages
File Size : 47,9 Mb
Release : 2023-06-16
Category : Science
ISBN : 9783031213915

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Bioinformatic and Statistical Analysis of Microbiome Data by Yinglin Xia,Jun Sun Pdf

This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 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. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.

Author : Xing Chen,Hongsheng Liu,Qi Zhao
Publisher : Frontiers Media SA
Page : 423 pages
File Size : 51,5 Mb
Release : 2020-06-22
Category : Electronic
ISBN : 9782889635634

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Bioinformatics in Microbiota by Xing Chen,Hongsheng Liu,Qi Zhao Pdf

Author : Luis Fernando Delgado
Publisher : Unknown
Page : 0 pages
File Size : 44,8 Mb
Release : 2024
Category : Electronic
ISBN : 9180409563

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Bioinformatics for Microbiome Analysis by Luis Fernando Delgado Pdf

Author : Yinglin Xia,Jun Sun,Ding-Geng Chen
Publisher : Springer
Page : 505 pages
File Size : 45,8 Mb
Release : 2018-10-06
Category : Computers
ISBN : 9789811315343

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Statistical Analysis of Microbiome Data with R by Yinglin Xia,Jun Sun,Ding-Geng Chen Pdf

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.

Author : Rama Kant Dubey,Vishal Tripathi,Ratna Prabha,Rajan Chaurasia,Dhananjaya Pratap Singh,Ch. Srinivasa Rao,Ali El-Keblawy,Purushothaman Chirakkuzhyil Abhilash
Publisher : Springer
Page : 118 pages
File Size : 43,8 Mb
Release : 2019-05-24
Category : Nature
ISBN : 9783030155162

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Unravelling the Soil Microbiome by Rama Kant Dubey,Vishal Tripathi,Ratna Prabha,Rajan Chaurasia,Dhananjaya Pratap Singh,Ch. Srinivasa Rao,Ali El-Keblawy,Purushothaman Chirakkuzhyil Abhilash Pdf

This book explores the significance of soil microbial diversity to understand its utility in soil functions, ecosystem services, environmental sustainability, and achieving the sustainable development goals. With a focus on agriculture and environment, the book highlights the importance of the microbial world by providing state-of-the-art technologies for examining the structural and functional attributes of soil microbial diversity for applications in healthcare, industrial biotechnology, and bioremediation studies. In seven chapters, the book will act as a primer for students, environmental biotechnologists, microbial ecologists, plant scientists, and agricultural microbiologists. Chapter 1 introduces readers to the soil microbiome, and chapter 2 discusses the below ground microbial world. Chapter 3 addresses various methods for exploring microbial diversity, chapter 4 discusses the genomics methods, chapter 5 provides the metaproteomics and metatranscriptomics approaches and chapter 6 details the bioinformatics tools for soil microbial community analysis, and chapter 7 concludes the text with future perspectives on further soil microbial uses and applications.

Author : Robert G. Beiko,Will Hsiao,John Parkinson
Publisher : Humana
Page : 324 pages
File Size : 41,6 Mb
Release : 2019-10-23
Category : Science
ISBN : 1493993763

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Microbiome Analysis by Robert G. Beiko,Will Hsiao,John Parkinson Pdf

This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of microbiome research, and the protocols described in this book are complemented with short perspectives about the history, current state, and future directions of protocols in microbiomics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbiome Analysis: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Author : Setubal,Nikos Kyrpides
Publisher : Frontiers Media SA
Page : 223 pages
File Size : 45,9 Mb
Release : 2023-01-04
Category : Science
ISBN : 9782832506400

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Computational methods for microbiome analysis, volume 2 by Setubal,Nikos Kyrpides Pdf

Author : Jacques Izard,Maria Rivera
Publisher : Academic Press
Page : 188 pages
File Size : 48,6 Mb
Release : 2014-11-07
Category : Science
ISBN : 9780124105089

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Metagenomics for Microbiology by Jacques Izard,Maria Rivera Pdf

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.

Author : Jessica Galloway-Peña,Michele Guindani
Publisher : Frontiers Media SA
Page : 186 pages
File Size : 45,7 Mb
Release : 2019-02-06
Category : Electronic
ISBN : 9782889456536

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Novel Approaches in Microbiome Analyses and Data Visualization by Jessica Galloway-Peña,Michele Guindani Pdf

High-throughput sequencing technologies are widely used to study microbial ecology across species and habitats in order to understand the impacts of microbial communities on host health, metabolism, and the environment. Due to the dynamic nature of microbial communities, longitudinal microbiome analyses play an essential role in these types of investigations. Key questions in microbiome studies aim at identifying specific microbial taxa, enterotypes, genes, or metabolites associated with specific outcomes, as well as potential factors that influence microbial communities. However, the characteristics of microbiome data, such as sparsity and skewedness, combined with the nature of data collection, reflected often as uneven sampling or missing data, make commonly employed statistical approaches to handle repeated measures in longitudinal studies inadequate. Therefore, many researchers have begun to investigate methods that could improve incorporating these features when studying clinical, host, metabolic, or environmental associations with longitudinal microbiome data. In addition to the inferential aspect, it is also becoming apparent that visualization of high dimensional data in a way which is both intelligible and comprehensive is another difficult challenge that microbiome researchers face. Visualization is crucial in both the analysis and understanding of metagenomic data. Researchers must create clear graphic representations that give biological insight without being overly complicated. Thus, this Research Topic seeks to both review and provide novels approaches that are being developed to integrate microbiome data and complex metadata into meaningful mathematical, statistical and computational models. We believe this topic is fundamental to understanding the importance of microbial communities and provides a useful reference for other investigators approaching the field.

Author : Pallaval Veera Bramhachari
Publisher : Springer Nature
Page : 306 pages
File Size : 41,7 Mb
Release : 2021-10-18
Category : Medical
ISBN : 9789811631566

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Microbiome in Human Health and Disease by Pallaval Veera Bramhachari Pdf

The book provides an overview on how the microbiome contributes to human health and disease. The microbiome has also become a burgeoning field of research in medicine, agriculture & environment. The readers will obtain profound knowledge on the connection between intestinal microbiota and immune defense systems, medicine, agriculture & environment. The book may address several researchers, clinicians and scholars working in biomedicine, microbiology and immunology. The application of new technologies has no doubt revolutionized the research initiatives providing new insights into the dynamics of these complex microbial communities and their role in medicine, agriculture & environment shall be more emphasized. Drawing on broad range concepts of disciplines and model systems, this book primarily provides a conceptual framework for understanding these human-microbe, animal-microbe & plant-microbe, interactions while shedding critical light on the scientific challenges that lie ahead. Furthermore this book explains why microbiome research demands a creative and interdisciplinary thinking—the capacity to combine microbiology with human, animal and plant physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet in a typical immune system, and have contributed to animal and plant diversification over long evolutionary timescales. Also this book explains why microbiome research presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for human health and new strategies.

Author : Suparna Mitra
Publisher : Springer Nature
Page : 443 pages
File Size : 48,9 Mb
Release : 2023-05-31
Category : Science
ISBN : 9781071630723

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Metagenomic Data Analysis by Suparna Mitra Pdf

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.

Author : Shailza Singh
Publisher : Springer Nature
Page : 207 pages
File Size : 55,7 Mb
Release : 2020-12-07
Category : Science
ISBN : 9789811585623

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Metagenomic Systems Biology by Shailza Singh Pdf

The book serves as an amalgamation of knowledge and principles used in the area of systems and synthetic biology, and targets inter-disciplinary research groups. The readers from diversified areas would be benefited by the valuable resources and information available in one book. Microbiome projects with efficient data handling can fuel progress in the area of microbial synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. The different chapters of the book reviews a broad range of topics, including food microbiome in ecology, use of microbiome in personalized medicine, machine learning in biomedicine. The book also describes ways to harness and exploit the incredible amounts of genomic data. The book is not only limited to medicine but also caters to the needs of environmentalists, biochemical engineers etc. It will be of interest to advanced students and researchers in life sciences, computational biology, microbiology and other inter-disciplinary areas.