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Statistical Analysis of Microbiome Data, Datta Somnath, Guha Subharup


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Автор: Datta Somnath, Guha Subharup
Название:  Statistical Analysis of Microbiome Data
ISBN: 9783030733506
Издательство: Springer
Классификация:




ISBN-10: 3030733505
Обложка/Формат: Hardcover
Страницы: 242
Вес: 0.68 кг.
Дата издания: 30.10.2021
Серия: Frontiers in probability and the statistical sciences
Язык: English
Издание: 1st ed. 2021
Иллюстрации: 2 tables, color; 49 illustrations, color; 15 illustrations, black and white; xiv, 346 p. 64 illus., 49 illus. in color.; 2 tables, color; 49 illustrat
Размер: 23.39 x 15.60 x 2.06 cm
Читательская аудитория: Professional & vocational
Ссылка на Издательство: Link
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Поставляется из: Германии
Описание: 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.

Statistical Analysis of Microbiome Data with R

Автор: Yinglin Xia; Jun Sun; Ding-Geng Chen
Название: Statistical Analysis of Microbiome Data with R
ISBN: 9811346453 ISBN-13(EAN): 9789811346453
Издательство: Springer
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Цена: 139750.00 T
Наличие на складе: Поставка под заказ.
Описание: 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.

Statistical Analysis of Microbiome Data with R

Автор: Xia Yinglin, Sun Jun, Chen Ding-Geng
Название: Statistical Analysis of Microbiome Data with R
ISBN: 9811315337 ISBN-13(EAN): 9789811315336
Издательство: Springer
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Цена: 139750.00 T
Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: Chapter 1: Introduction to R, RStudio and ggplot2 1.1 Introduction to R 1.2 Introduction to RStudio 1.3 Introduction to ggplot2 1.4 Introduction to R Packages for Microbiome Data
Chapter 2: What are Microbiome Data?2.1 Phylogenetics--The Basics 2.2 What Microbiome Data Look Like? 2.2.1 Basic Data Structure and Format of Microbiome Data 2.2.2 OUT Table2.2 3 Response Variables and Covariates2.3 Some Specific Features of Microbiome Data
Chapter 3: Bioinformatic and Statistical Analyses of Microbiome Data 3.1 Overview of Bioinformatic Analysis 3.1.1 Taxonomic Diversity: from the 16S-based Approach 3.1.2 Taxonomic Profiling of Shotgun Metagenomes3.1.3 Introduction to Bioinformatic toolso QIIME o Mothuro 16S rRNA Gene Sequence Data Analysis using QIIME and Mothuro Other Biostatistics Tools3.2 Statistical Analysis of Microbiome Community Composition 3.2.1 Alpha Diversity Analysis and Statistical Measurements 3.2.2 Beta Diversity Analysis and Statistical Measurements3.3 Multivariate Statistical Techniques 3.3.1Data Visualization: Principal Component and Principal Coordinates Analyses 3.3.2 Classification and Clustering with Visualization 3.4 Hypothesis Testing and Statistical Modeling 3.4.1 Statistical Testing of Microbiome Community 3.4.2 Multivariate Statistical Methods and Modeling of Microbiome Community and Environmental Covariates3.4.3 Mediational and Longitudinal Microbiome Data Analysis3.4.4 Host Interactions and Interventions3.4.5 Mediation Analysis and Longitudinal Analysis 3.5 Multiple Comparisons and Testing Correlation 3.6 Correlation Analysis of Microbiome Community and Environmental Covariates
Chapter 4: Power and Sample Size Calculation in Hypothesis Testing Microbiome Data4.1 Statistical Hypothesis Testing and Power Analysis 4.1.1 Hypothesis Testing 4.1.2 Power Analysis and Sample Size Calculation4.2 Comparing Diversity or a Taxon of Interest between Two Groups 4.2.1 Hypotheses and Basic Power and Sample Size Formulas4.2.2 Diversity Data for Vitamin D and Vitamin D Receptor Study4.2.3 Theory of Power for a Test for Comparing Proportions4.2.4 Power of Fisher's Exact Test for Comparing Proportions4.2.5 R Function power.t.test4.3 Comparing Diversity across More than Two Groups 4.3.1 Hypotheses and Theory of Power for One-Way ANOVA4.3.2 Examples4.3.2 R Function pwr.avova.test4.4 Comparing the Frequency of all Taxa across Groups4.4.1 Hypotheses Testing and Power and Sample Size Calculations for Comparing all Taxa4.4.2 Dirichlet-multinomial model in Power and Sample Size Analyses4.4.3 Power and Size Calculations using HMP Package4.5 Power and Sample Size Estimation using Pairwise Distances and PERMANOVA 4.5.1 PERMANOVA and Estimation of PERMANOVA Power 4.5.2 Examples using micropower Package4.6 Power Calculations using ANOSIM Package
Chapter 5: Microbiome Data Management5.1 Data Importing and Merging datasets or components 5.1.1 Importing the Output from QIIME 5.1.2 Importing the Output from mothur&

Metagenomic Systems Biology: Integrative Analysis of the Microbiome

Автор: Singh Shailza
Название: Metagenomic Systems Biology: Integrative Analysis of the Microbiome
ISBN: 981158561X ISBN-13(EAN): 9789811585616
Издательство: Springer
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Цена: 149060.00 T
Наличие на складе: Поставка под заказ.
Описание: 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.

Microbiome Analysis

Автор: Beiko
Название: Microbiome Analysis
ISBN: 1493987267 ISBN-13(EAN): 9781493987269
Издательство: Springer
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Цена: 121110.00 T
Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: 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.

Microbiome Analysis

Автор: Robert G. Beiko; Will Hsiao; John Parkinson
Название: Microbiome Analysis
ISBN: 1493993763 ISBN-13(EAN): 9781493993765
Издательство: Springer
Рейтинг:
Цена: 111790.00 T
Наличие на складе: Поставка под заказ.
Описание: 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.

The Brazilian Microbiome

Автор: Victor Pylro; Luiz Roesch
Название: The Brazilian Microbiome
ISBN: 3319867555 ISBN-13(EAN): 9783319867557
Издательство: Springer
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Цена: 93160.00 T
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Описание: Brazilian Microbiome: Current status and perspectives unites a set of distinguished investigators conducting microbiome research and builds a comprehensive reference book with up-to-date information regarding the Brazilian microbiome studies and trends.

Understanding Host-Microbiome Interactions - An Omics Approach

Автор: Ravindra Pal Singh; Ramesh Kothari; Prakash G. Kor
Название: Understanding Host-Microbiome Interactions - An Omics Approach
ISBN: 9811353042 ISBN-13(EAN): 9789811353048
Издательство: Springer
Рейтинг:
Цена: 186330.00 T
Наличие на складе: Поставка под заказ.
Описание: This book offers up-to-date information on different microbiomes, their community composition and interactive functions with the host, bringing together information from diverse research reports to provide an overview of the rapid developments in meta-omics technologies. It is a valuable resource for scientists, researchers, postgraduate and graduate students interested in understanding the impact and importance of next generation sequencing technologies on different hosts and their microbiomes.

Colorectal Neoplasia And The Colorectal Microbiome

Автор: Floch, Martin H.
Название: Colorectal Neoplasia And The Colorectal Microbiome
ISBN: 0128196726 ISBN-13(EAN): 9780128196724
Издательство: Elsevier Science
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Цена: 151590.00 T
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Описание:

Colorectal Neoplasia and the Microbiome: Dysplasia, Probiotics, and Fusobacteria provides foundational knowledge on the gut microbiome and evidence for an association with colorectal neoplasia. It covers the role of microbiota in causing adenomatous polyps and colorectal cancer as well as the modulatory effect of diet and probiotics. Chapters explain a foundational history of microbiology in the colon, the epidemiology of colon polyps and cancer, dysbiosis, the role of immunology and bacteria, and the diet. The book combines medical and scientific aspects to show mechanistic aspects between microbiota and hosts, clearly presenting the association between microbiota, colonic lesions and possible causal links.

The book is essential reading for everyone working with human microbiota including basic scientists, physiologists of the intestine, experts in intestinal microbiota, gastroenterologists, oncologists and surgeon.


Functional Importance of the Plant Microbiome

Автор: Sharon Lafferty Doty
Название: Functional Importance of the Plant Microbiome
ISBN: 3319658964 ISBN-13(EAN): 9783319658964
Издательство: Springer
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Цена: 121110.00 T
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Описание:

This book addresses all the major mechanisms by which endophytes are thought to impact plant growth and health. A unique aspect of this publication is that it is multidisciplinary, covering plant microbiology, plant physiology, fungal and bacterial endophytes, plant biochemistry, and genomics.

Just as research on the mammalian microbiome has demonstrated its importance for overall health of the host, the plant microbiota is essential for plant health in natural environments. Endophytes, the microorganisms living fully within plants, can provide a multitude of benefits to the host including N-fixation, P solubilization, increased photosynthetic efficiency and water use efficiency, stress tolerance, pathogen resistance, and overall increased growth and health. A variety of culturable endophytes have been isolated and shown to be mutualistic symbionts with a broad range of plant species. These studies point to the functional importance of the microbiota of plants and suggest the potential for tailoring plant microbiota for improved vigor and yields with reduced inputs. This review covers the major benefits of microbial endophytes to plants and discusses the implications of using symbiosis as an alternative to chemical inputs for agriculture, forestry, and bioenergy.


Microbiome Community Ecology

Автор: Muhammad Saleem
Название: Microbiome Community Ecology
ISBN: 3319116649 ISBN-13(EAN): 9783319116648
Издательство: Springer
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Цена: 51230.00 T
Наличие на складе: Есть у поставщика Поставка под заказ.
Описание: Chapter 1.

Microbiome ecosystem ecology: unseen majority in an anthropogenic ecosystem

Authors: M. Saleem

Abstract

1. Microbiome ecosystem ecology

References

Chapter 2.

Theories, mechanisms and patterns of microbiome species coexistence in an era of climate change

Authors: M. Saleem, ZH Pervaiz, MB Traw

Abstract

2.1. Niche theory and microbial diversity

2.1.1. Temperature-metabolic theory of ecology

(i). Thermal niche specialization

(ii). Temperature as a driver of ecological divergence, evolution, speciation and thermal niche evolution trade-offs

2.1.2. Implication of habitat heterogeneity in determining ecological niche

(i). Resource heterogeneity

Factors determining resource heterogeneity

Optimal foraging theory of ecology

r/K selection theory of ecology

(ii). Role of habitat physical structure and variations in determining ecological niche

(iii). Role of habitat pH in determining ecological niche

(iv). Role of biotic factors in determining ecological niche

2.2. Island biogeography theory and microbial diversity

2.2.1. Ecology theory of species area relationship

2.2.2 Ecological theory of distance decay relationships (DDR)

(i). Elevational patterns of microbial diversity

(ii). Latitudinal pattern of microbial diversity

2.3. Species-time relationships (STRs)

2.4. Neutral theory and microbial diversity

References

Chapter 3.

Eco-evolutionary processes regulating microbiome community assembly in a changing global ecosystem

Authors: M. Saleem

Abstract

3. Processes underlying microbiome community assembly

3.1. Selection

3.1.1. Constant selection pressure

3.1.2. Frequency- or density-dependent selection

(i). Negative frequency- or density-dependent selection

(ii). Positive frequency- or density-dependent selection

(iii). Spatially- or temporally-variable selection

3.2. Drift

3.2.1. Ecological drift

3.2.2. Evolutionary or genetic drift

3.2.3. Neutral drift

3.3. Dispersal

3.3.1. Environmental factors determining dispersal

(i). Dispersal in air/atmospheric ecosystem and air mediated microbial dispersal

(ii). Water currents and movement

(iii). Nutrients-mediated microbial dispersal

(iv). Miscellaneous factors determining microbial dispersal

3.3.2. Factors liming the dispersal of microbes

3.4. Diversification, speciation and mutation

5. Dormancy

References

Chapter 4.

Loss of microbiome ecological niches and diversity by global change and trophic downgrading

Authors: M. Saleem

Abstract

4. Habitat alteration, trophic downgrading and microbiome biodiversity loss

4.1. Atmosphere ecosystem

4.2. Phyllosphere ecosystem

4.3 Rhizosphere ecosystem

4.4. Human and animal ecosystem

4.5 Aquatic ecosystems

4.6 Extreme ecosystems

4.6. Miscellaneous

References

Chapter 5.

Microbiome mediated multitrophic interactions in an age of microbial extinction

Authors: M. Saleem

Abstract

5.1. Trophic interactions

5.1.1 Trophic interactions with protists predators

5.1.2. Trophic interactions with predatory bacteria

5.1.3. Trophic interactions with viruses

5.1.4. Multi-trophic interactions

5.2 Non-trophic interactions

References

Chapter 6.

Global microbiome for agroecology, industry and human well-being: opportunities and challenges in climate change

Authors: M. Saleem


Unravelling the Soil Microbiome

Автор: Rama Kant Dubey; Vishal Tripathi; Ratna Prabha; Ra
Название: Unravelling the Soil Microbiome
ISBN: 3030155153 ISBN-13(EAN): 9783030155155
Издательство: Springer
Рейтинг:
Цена: 46570.00 T
Наличие на складе: Поставка под заказ.
Описание: 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.

Fundamentals of Microbiome Science: How Microbes Shape Animal Biology

Автор: Douglas Angela E.
Название: Fundamentals of Microbiome Science: How Microbes Shape Animal Biology
ISBN: 0691217718 ISBN-13(EAN): 9780691217710
Издательство: Wiley
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Цена: 29570.00 T
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Описание:

An essential introduction to microbiome science, a new cutting-edge discipline that is transforming the life sciences

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. Resident microbes in healthy animals--including humans-can dictate many traits of the animal host. This animal microbiome is a second immune system conferring protection against pathogens; it can structure host metabolism in animals as diverse as reef corals and hibernating mammals; and it may influence animal behavior, from social recognition to emotional states. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet, and have contributed to animal diversification over long evolutionary timescales.

Drawing on concepts and data across a broad range of disciplines and systems, Angela Douglas provides a conceptual framework for understanding these animal-microbe interactions while shedding critical light on the scientific challenges that lie ahead. Douglas explains why microbiome science demands creative and interdisciplinary thinking-the capacity to combine microbiology with animal physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.

An essential introduction to a cutting-edge field that is revolutionizing the life sciences, this book explains why microbiome science presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for many medical conditions and new strategies for pest control.



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