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Author: Somnath Datta Publisher: Springer Nature ISBN: 3030733513 Category : Medical Languages : en Pages : 349
Book Description
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: Somnath Datta Publisher: Springer Nature ISBN: 3030733513 Category : Medical Languages : en Pages : 349
Book Description
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 Publisher: Springer ISBN: 9811315345 Category : Computers Languages : en Pages : 518
Book Description
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: Yinglin Xia Publisher: Springer Nature ISBN: 3031213912 Category : Science Languages : en Pages : 717
Book Description
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: Jacques Izard Publisher: Academic Press ISBN: 0124105084 Category : Science Languages : en Pages : 188
Book Description
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: Food Forum Publisher: National Academies Press ISBN: 030926586X Category : Medical Languages : en Pages : 197
Book Description
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: Karen E. Nelson Publisher: Springer ISBN: 9781461446743 Category : Science Languages : en Pages : 1528
Book Description
Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.
Author: Yinglin Xia Publisher: CRC Press ISBN: 1040045669 Category : Mathematics Languages : en Pages : 457
Book Description
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: Richard A. Levine Publisher: John Wiley & Sons ISBN: 1119561086 Category : Mathematics Languages : de Pages : 672
Book Description
Ein unverzichtbarer Leitfaden bei der Anwendung computergestützter Statistik in der modernen Datenwissenschaft In Computational Statistics in Data Science präsentiert ein Team aus bekannten Mathematikern und Statistikern eine fundierte Zusammenstellung von Konzepten, Theorien, Techniken und Praktiken der computergestützten Statistik für ein Publikum, das auf der Suche nach einem einzigen, umfassenden Referenzwerk für Statistik in der modernen Datenwissenschaft ist. Das Buch enthält etliche Kapitel zu den wesentlichen konkreten Bereichen der computergestützten Statistik, in denen modernste Techniken zeitgemäß und verständlich dargestellt werden. Darüber hinaus bietet Computational Statistics in Data Science einen kostenlosen Zugang zu den fertigen Einträgen im Online-Nachschlagewerk Wiley StatsRef: Statistics Reference Online. Außerdem erhalten die Leserinnen und Leser: * Eine gründliche Einführung in die computergestützte Statistik mit relevanten und verständlichen Informationen für Anwender und Forscher in verschiedenen datenintensiven Bereichen * Umfassende Erläuterungen zu aktuellen Themen in der Statistik, darunter Big Data, Datenstromverarbeitung, quantitative Visualisierung und Deep Learning Das Werk eignet sich perfekt für Forscher und Wissenschaftler sämtlicher Fachbereiche, die Techniken der computergestützten Statistik auf einem gehobenen oder fortgeschrittenen Niveau anwenden müssen. Zudem gehört Computational Statistics in Data Science in das Bücherregal von Wissenschaftlern, die sich mit der Erforschung und Entwicklung von Techniken der computergestützten Statistik und statistischen Grafiken beschäftigen.
Author: Otso Ovaskainen Publisher: Cambridge University Press ISBN: 1108492460 Category : Nature Languages : en Pages : 389
Book Description
A comprehensive account of joint species distribution modelling, covering statistical analyses in light of modern community ecology theory.
Author: Somnath Datta
Author: Somnath Datta
Author: Yinglin Xia
Author: Robert G. Beiko
Author: Yinglin Xia
Author: Jacques Izard
Author: Food Forum
Author: Karen E. Nelson
Author: Yinglin Xia
Author: Richard A. Levine
Author: Otso Ovaskainen