Download or read book Statistical Data Analysis of Microbiomes and Metabolomics written by Yinglin Xia and published by American Chemical Society. This book was released on 2022-02-03 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical Analysis of Microbiome Data written by Somnath Datta and published by Springer Nature. This book was released on 2021-10-27 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book An Integrated Analysis of Microbiomes and Metabolomics written by Yinglin Xia and published by American Chemical Society. This book was released on 2022-03-25 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Applied Microbiome Statistics written by Yinglin Xia and published by CRC Press. This book was released on 2024-07-22 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Bioinformatic and Statistical Analysis of Microbiome Data written by Yinglin Xia and published by Springer Nature. This book was released on 2023-06-16 with total page 717 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical and Computational Methods for Microbiome Multi Omics Data written by Himel Mallick and published by Frontiers Media SA. This book was released on 2020-11-19 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Statistical Analysis of Microbiome Data with R written by Yinglin Xia and published by Springer. This book was released on 2018-10-06 with total page 505 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Microbiome and the Eye written by Anat Galor and published by Elsevier. This book was released on 2023-06-20 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiome and the Eye: What’s the connection? highlights how alterations in the gut and eye microbiomes can lead to systemic immune alterations with subsequent effects on the eye. The book is divided into two sections, one highlighting how alterations in the gut microbiome impact various components of health outside the gut, with a focus on the immune system and inflammatory mediators, and the second focusing on studies on a variety of ocular diseases, including ocular surface diseases/dry eye, keratitis, uveitis, glaucoma, and retinopathy to gut dysbiosis. With its translational approach, the book is suitable for both researchers and clinicians. The book will help readers understand the mechanisms in which gut and eye microbiome composition may influence health in multiple compartments, with a focus on eye diseases. Helps researchers understand the clinical eye diseases that have been linked to gut microbiome abnormalities Helps clinicians understand the mechanisms in which gut microbiome composition may influence health in multiple compartments Provides a foundation for future studies that consider gut microbiome manipulations as a treatment for specific eye diseases
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-09-10 with total page 1223 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Download or read book Novel Approaches in Microbiome Analyses and Data Visualization written by Jessica Galloway-Peña and published by Frontiers Media SA. This book was released on 2019-02-06 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Metabolomics Data Processing and Data Analysis Current Best Practices written by Justin Van Der Hooft and published by Mdpi AG. This book was released on 2021-09-10 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics data analysis strategies are central to transforming raw metabolomics data files into meaningful biochemical interpretations that answer biological questions or generate novel hypotheses. This book contains a variety of papers from a Special Issue around the theme "Best Practices in Metabolomics Data Analysis". Reviews and strategies for the whole metabolomics pipeline are included, whereas key areas such as metabolite annotation and identification, compound and spectral databases and repositories, and statistical analysis are highlighted in various papers. Altogether, this book contains valuable information for researchers just starting in their metabolomics career as well as those that are more experienced and look for additional knowledge and best practice to complement key parts of their metabolomics workflows.
Download or read book Metagenomic Systems Biology written by Shailza Singh and published by Springer Nature. This book was released on 2020-12-07 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Microbiomes of Soils Plants and Animals written by Rachael E. Antwis and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: A comparative, holistic synthesis of microbiome research, spanning soil, plant, animal and human hosts.
Download or read book Statistical Analysis of Proteomics Metabolomics and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2018-07-07 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.
Download or read book Computational Methods and Data Analysis for Metabolomics written by Shuzhao Li and published by Humana. This book was released on 2021-02-01 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive guide to scientists, engineers, and students that employ metabolomics in their work, with an emphasis on the understanding and interpretation of the data. Chapters guide readers through common tools for data processing, using database resources, major techniques in data analysis, and integration with other data types and specific scientific domains. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, practical guidance of methods and techniques, useful web supplements, and connect the steps from experimental metabolomics to scientific discoveries. Authoritative and cutting-edge, Computational Methods and Data Analysis for Metabolomics to ensure successful results in the further study of this vital field.
Download or read book Metabolomics in Food and Nutrition written by Bart C Weimer and published by Elsevier. This book was released on 2013-10-31 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metabolomics enables valuable information about the biochemical composition of foods to be rapidly obtained. Since the biochemical profile of food largely determines key food properties such as flavour and shelf life, the information gained using metabolomics-based methods will enable greater control of food quality and also help to determine the relationship between diet and health. Metabolomics in food and nutrition provides an overview of their current and potential use in the food industry.Part one reviews equipment, methods and data interpretation in metabolomics including the use of nuclear magnetic resonance (NMR), statistical methods in metabolomics, and metabolic reconstruction databases and their application to metabolomics research. Part two explores applications of metabolomics in humans, plants and food. Chapters discuss metabolomics in nutrition, human samples for health assessments, and current methods for the analysis of human milk oligosaccharides (HMOs) and their novel applications. Further chapters highlight metabolomic analysis of plants and crops, metabolomics for the safety assessment of genetically modified (GM) crops, and applications of metabolomics in food science including food composition and quality, sensory and nutritional attributes.With its distinguished editors and team of expert contributors, Metabolomics in food and nutrition is a technical resource for industrial researchers in the food and nutrition sectors interested in the potential of metabolomics methods and academics and postgraduate students working in the area. Provides an overview of the current and potential future use of metabolomics in the food industry Chapters focus on key applications and review the analytical methods used and the bioinformatics techniques involved in processing the results Discusses metabolomics in nutrition, human samples for health assessments, and current methods for the analysis of human milk oligosaccharides (HMOs) and their novel applications
Download or read book Metabolomics written by Vijay Soni and published by Springer Nature. This book was released on 2023-10-24 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book Introduces the extensive applications of metabolomics from all possible areas of research and development so that not only an undergraduate can understand the advancement of metabolomics, but an entrepreneur can harness the knowledge to address possible problems to make a perfect tool to address their research question. Topics covered include the role of metabolomics in the development of agriculture, plant pathology, and their applications; the generalized application of the metabolomics and use of related technologies in various sectors of industries; and the future of metabolomics and upcoming related technologies that can fill the gap between different -omics and their applications for the betterment of humankind. This is an ideal book for university professors, researchers, and advanced-level scientists who are exploring different avenues in metabolomics. Availability of this concise information in one place will aid scientists by expanding their arsenal of techniques and can be helpful to bring more collaborations and to identify the expert at the global level.
