Applied Microbiome Statistics
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| Author | : Yinglin Xia |
| Publisher | : CRC Press |
| Total Pages | : 457 |
| Release | : 2024-07-22 |
| Genre | : Mathematics |
| ISBN | : 1040045669 |
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 |
| Publisher | : Springer |
| Total Pages | : 518 |
| Release | : 2018-10-06 |
| Genre | : Computers |
| ISBN | : 9811315345 |
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 | : Food Forum |
| Publisher | : National Academies Press |
| Total Pages | : 197 |
| Release | : 2013-02-27 |
| Genre | : Medical |
| ISBN | : 030926586X |
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 | : National Academies of Sciences, Engineering, and Medicine |
| Publisher | : National Academies Press |
| Total Pages | : 123 |
| Release | : 2018-03-01 |
| Genre | : Science |
| ISBN | : 0309468698 |
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 | : Somnath Datta |
| Publisher | : Springer Nature |
| Total Pages | : 349 |
| Release | : 2021-10-27 |
| Genre | : Medical |
| ISBN | : 3030733513 |
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 | : National Academies of Sciences, Engineering, and Medicine |
| Publisher | : National Academies Press |
| Total Pages | : 133 |
| Release | : 2017-07-19 |
| Genre | : Science |
| ISBN | : 0309458390 |
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 | : Robert G. Beiko |
| Publisher | : |
| Total Pages | : 324 |
| Release | : 2018 |
| Genre | : Microbiology |
| ISBN | : 9781493987283 |
| Author | : |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2022 |
| Genre | : |
| ISBN | : |
| Author | : Mingxiu Hu |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 340 |
| Release | : 2013-09-14 |
| Genre | : Medical |
| ISBN | : 1461478464 |
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 | : National Academies of Sciences, Engineering, and Medicine |
| Publisher | : National Academies Press |
| Total Pages | : 318 |
| Release | : 2017-10-06 |
| Genre | : Science |
| ISBN | : 0309449839 |
People's desire to understand the environments in which they live is a natural one. People spend most of their time in spaces and structures designed, built, and managed by humans, and it is estimated that people in developed countries now spend 90 percent of their lives indoors. As people move from homes to workplaces, traveling in cars and on transit systems, microorganisms are continually with and around them. The human-associated microbes that are shed, along with the human behaviors that affect their transport and removal, make significant contributions to the diversity of the indoor microbiome. The characteristics of "healthy" indoor environments cannot yet be defined, nor do microbial, clinical, and building researchers yet understand how to modify features of indoor environmentsâ€"such as building ventilation systems and the chemistry of building materialsâ€"in ways that would have predictable impacts on microbial communities to promote health and prevent disease. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem by engaging the fields of microbial biology and ecology, chemistry, building science, and human physiology. This report reviews what is known about the intersection of these disciplines, and how new tools may facilitate advances in understanding the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being. It offers a research agenda to generate the information needed so that stakeholders with an interest in understanding the impacts of built environments will be able to make more informed decisions.
