Applied Microbiome Statistics

Author : Yinglin Xia,Jun Sun
Publisher : CRC Press
Page : 457 pages
File Size : 40,7 Mb
Release : 2024-07-22
Category : Mathematics
ISBN : 9781040045664

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Applied Microbiome Statistics by Yinglin Xia,Jun Sun Pdf

This unique book officially defines microbiome statistics as a specific new field of statistics and addresses the statistical analysis of correlation, association, interaction, and composition in microbiome research. It also defines the study of the microbiome as a hypothesis-driven experimental science and describes two microbiome research themes and six unique characteristics of microbiome data, as well as investigating challenges for statistical analysis of microbiome data using the standard statistical methods. This book is useful for researchers of biostatistics, ecology, and data analysts. Presents a thorough overview of statistical methods in microbiome statistics of parametric and nonparametric correlation, association, interaction, and composition adopted from classical statistics and ecology and specifically designed for microbiome research. Performs step-by-step statistical analysis of correlation, association, interaction, and composition in microbiome data. Discusses the issues of statistical analysis of microbiome data: high dimensionality, compositionality, sparsity, overdispersion, zero-inflation, and heterogeneity. Investigates statistical methods on multiple comparisons and multiple hypothesis testing and applications to microbiome data. Introduces a series of exploratory tools to visualize composition and correlation of microbial taxa by barplot, heatmap, and correlation plot. Employs the Kruskal–Wallis rank-sum test to perform model selection for further multi-omics data integration. Offers R code and the datasets from the authors’ real microbiome research and publicly available data for the analysis used. Remarks on the advantages and disadvantages of each of the methods used.

Author : Yinglin Xia,Jun Sun,Ding-Geng Chen
Publisher : Springer
Page : 505 pages
File Size : 42,6 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 : Somnath Datta,Subharup Guha
Publisher : Springer Nature
Page : 349 pages
File Size : 51,7 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 : Yinglin Xia,Jun Sun
Publisher : Springer Nature
Page : 717 pages
File Size : 51,8 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 : Himel Mallick,Vanni Bucci,Lingling An
Publisher : Frontiers Media SA
Page : 170 pages
File Size : 47,5 Mb
Release : 2020-11-19
Category : Science
ISBN : 9782889660919

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Statistical and Computational Methods for Microbiome Multi-Omics Data by Himel Mallick,Vanni Bucci,Lingling An Pdf

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

Author : Food Forum,Food and Nutrition Board,Institute of Medicine
Publisher : National Academies Press
Page : 197 pages
File Size : 47,6 Mb
Release : 2013-02-27
Category : Medical
ISBN : 9780309265867

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The Human Microbiome, Diet, and Health by Food Forum,Food and Nutrition Board,Institute of Medicine Pdf

The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge of the human microbiome, its role in human health, its interaction with the diet, and the translation of new research findings into tools and products that improve the nutritional quality of the food supply. The Human Microbiome, Diet, and Health: Workshop Summary summarizes the presentations and discussions that took place during the workshop. Over the two day workshop, several themes covered included: The microbiome is integral to human physiology, health, and disease. The microbiome is arguably the most intimate connection that humans have with their external environment, mostly through diet. Given the emerging nature of research on the microbiome, some important methodology issues might still have to be resolved with respect to undersampling and a lack of causal and mechanistic studies. Dietary interventions intended to have an impact on host biology via their impact on the microbiome are being developed, and the market for these products is seeing tremendous success. However, the current regulatory framework poses challenges to industry interest and investment.

Author : Yinglin Xia,Jun Sun
Publisher : American Chemical Society
Page : 229 pages
File Size : 47,6 Mb
Release : 2022-02-03
Category : Science
ISBN : 9780841299160

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Statistical Data Analysis of Microbiomes and Metabolomics by Yinglin Xia,Jun Sun Pdf

Compared with other research fields, both microbiome and metabolomics data are complicated and have some unique characteristics, respectively. Thus, choosing an appropriate statistical test or method is a very important step in the analysis of microbiome and metabolomics data. However, this is still a difficult task for those biomedical researchers without a statistical background and for those biostatisticians who do not have research experiences in these fields. Graduate students studying microbiome and metabolomics; statisticians, working on microbiome and metabolomics projects, either for their own research, or for their collaborative research for experimental design, grant application, and data analysis; and researchers who investigate biomedical and biochemical projects with the microbiome, metabolome, and multi-omics data analysis will benefit from reading this work.

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences,Board on Environmental Studies and Toxicology,Committee on Advancing Understanding of the Implications of Environmental-Chemical Interactions with the Human Microbiome
Publisher : National Academies Press
Page : 123 pages
File Size : 48,7 Mb
Release : 2018-03-01
Category : Science
ISBN : 9780309468695

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Environmental Chemicals, the Human Microbiome, and Health Risk by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences,Board on Environmental Studies and Toxicology,Committee on Advancing Understanding of the Implications of Environmental-Chemical Interactions with the Human Microbiome Pdf

A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.

Author : Mingxiu Hu,Yi Liu,Jianchang Lin
Publisher : Springer Science & Business Media
Page : 340 pages
File Size : 46,5 Mb
Release : 2013-09-14
Category : Medical
ISBN : 9781461478461

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Topics in Applied Statistics by Mingxiu Hu,Yi Liu,Jianchang Lin Pdf

This volume presents 27 selected papers in topics that range from statistical applications in business and finance to applications in clinical trials and biomarker analysis. All papers feature original, peer-reviewed content. The editors intentionally selected papers that cover many topics so that the volume will serve the whole statistical community and a variety of research interests. The papers represent select contributions to the 21st ICSA Applied Statistics Symposium. The International Chinese Statistical Association (ICSA) Symposium took place between the 23rd and 26th of June, 2012 in Boston, Massachusetts. It was co-sponsored by the International Society for Biopharmaceutical Statistics (ISBS) and American Statistical Association (ASA). This is the inaugural proceedings volume to share research from the ICSA Applied Statistics Symposium.

Author : Jessica Galloway-Peña,Michele Guindani
Publisher : Frontiers Media SA
Page : 186 pages
File Size : 46,9 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 : Yinglin Xia,Jun Sun
Publisher : American Chemical Society
Page : 205 pages
File Size : 43,9 Mb
Release : 2022-03-25
Category : Science
ISBN : 9780841299542

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An Integrated Analysis of Microbiomes and Metabolomics by Yinglin Xia,Jun Sun Pdf

Because the microbial community is dynamic, an individual’s microbiota at a given time is varied, and many factors, including age, host genetics, diet, and the local environment, significantly change the microbiota. Thus, microbiome researchers have naturally expanded their research to look for insights into the interaction of the microbiome with other “omics”. Metabolites (small molecules) are the intermediate or end products of metabolism. Metabolites have various functions. The microbial-derived metabolites play an important role in the function of the microbiome. Thus, the advancement in microbiome studies is becoming particularly critical for the integration of microbial DNA sequencing data with other omics data, especially microbiome-metabolomics integration.

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable
Publisher : National Academies Press
Page : 133 pages
File Size : 42,8 Mb
Release : 2017-07-19
Category : Science
ISBN : 9780309458399

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The Chemistry of Microbiomes by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Chemical Sciences and Technology,Chemical Sciences Roundtable Pdf

The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

Author : Mohsen Nady
Publisher : Unknown
Page : 0 pages
File Size : 41,7 Mb
Release : 2023-12
Category : Electronic
ISBN : 1774699028

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Statistics with R for Microbiome Analysis: From Raw Reads to Relative Abundance by Mohsen Nady Pdf

This book covers the necessary analysis steps for dealing with microbiome data. The microbial samples are sequenced into raw reads or fastq files. These raw reads should be quality checked to assure their quality per base or per read. Then, after removing the errors, we can infer their exact amplicon sequence variants (ASVs). After that, we taxonomically classify these sequences to represent the different taxonomy levels of species, genus, family, order, class, and phylum and generate a phylogenetic tree. Finally, the sequence data, the taxonomy table, phylogenetic tree, and sample data are combined in a single phyloseq object for ease of plotting, manipulation, and analysis of the different components of microbiome data. The final phyloseq object can also be cleaned for certain low prevalent sequences. All these steps are explained in R codes using a freely available microbiome data of 360 fecal samples.

Author : Joao Carlos Setubal,Jens Stoye,Bas E. Dutilh
Publisher : Frontiers Media SA
Page : 170 pages
File Size : 44,9 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 : 49,8 Mb
Release : 2018
Category : Microbiology
ISBN : 1493987283

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