Statistical Data Analysis Of Microbiomes And Metabolomics

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Statistical Data Analysis of Microbiomes and Metabolomics

Author : Yinglin Xia
Publisher : American Chemical Society
ISBN 13 : 0841299161
Total Pages : 229 pages
Book Rating : 4.8/5 (412 download)

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Book Synopsis Statistical Data Analysis of Microbiomes and Metabolomics by : Yinglin Xia

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.

An Integrated Analysis of Microbiomes and Metabolomics

Author : Yinglin Xia
Publisher : American Chemical Society
ISBN 13 : 0841299544
Total Pages : 205 pages
Book Rating : 4.8/5 (412 download)

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Book Synopsis An Integrated Analysis of Microbiomes and Metabolomics by : Yinglin Xia

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.

Bioinformatic and Statistical Analysis of Microbiome Data

Author : Yinglin Xia
Publisher : Springer Nature
ISBN 13 : 3031213912
Total Pages : 717 pages
Book Rating : 4.0/5 (312 download)

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Book Synopsis Bioinformatic and Statistical Analysis of Microbiome Data by : Yinglin Xia

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.

Applied Microbiome Statistics

Author : Yinglin Xia
Publisher : CRC Press
ISBN 13 : 1040045669
Total Pages : 457 pages
Book Rating : 4.0/5 (4 download)

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Book Synopsis Applied Microbiome Statistics by : Yinglin Xia

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.

Statistical Analysis of Microbiome Data with R

Author : Yinglin Xia
Publisher : Springer
ISBN 13 : 9811315345
Total Pages : 518 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Statistical Analysis of Microbiome Data with R by : Yinglin Xia

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 518 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.

Microbiomes of Soils, Plants and Animals

Author : Rachael E. Antwis
Publisher :
ISBN 13 : 9781108654418
Total Pages : pages
Book Rating : 4.6/5 (544 download)

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Book Synopsis Microbiomes of Soils, Plants and Animals by : Rachael E. Antwis

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.

The Human Microbiome, Diet, and Health

Author : Food Forum
Publisher : National Academies Press
ISBN 13 : 030926586X
Total Pages : 197 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis The Human Microbiome, Diet, and Health by : Food Forum

Download or read book The Human Microbiome, Diet, and Health written by Food Forum and published by National Academies Press. This book was released on 2013-02-27 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Metagenomic Systems Biology

Author : Shailza Singh
Publisher : Springer Nature
ISBN 13 : 9811585628
Total Pages : 207 pages
Book Rating : 4.8/5 (115 download)

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Book Synopsis Metagenomic Systems Biology by : Shailza Singh

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.

Microbiome and the Eye

Author : Anat Galor
Publisher : Elsevier
ISBN 13 : 0323985378
Total Pages : 242 pages
Book Rating : 4.3/5 (239 download)

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Book Synopsis Microbiome and the Eye by : Anat Galor

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

The Chemistry of Microbiomes

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309458390
Total Pages : 133 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis The Chemistry of Microbiomes by : National Academies of Sciences, Engineering, and Medicine

Download or read book The Chemistry of Microbiomes written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-07-19 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1740 pages
Book Rating : 4.1/5 (194 download)

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Book Synopsis Handbook of Statistical Genomics by : David J. Balding

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1740 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.

Statistical Analysis of Microbiome Data

Author : Somnath Datta
Publisher : Springer Nature
ISBN 13 : 3030733513
Total Pages : 349 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis Statistical Analysis of Microbiome Data by : Somnath Datta

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.

Computational Methods and Data Analysis for Metabolomics

Author :
Publisher :
ISBN 13 : 9781071602393
Total Pages : pages
Book Rating : 4.6/5 (23 download)

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Book Synopsis Computational Methods and Data Analysis for Metabolomics by :

Download or read book Computational Methods and Data Analysis for Metabolomics written by and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Microbiome Analysis

Author : Robert G. Beiko
Publisher :
ISBN 13 : 9781493987283
Total Pages : 324 pages
Book Rating : 4.9/5 (872 download)

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Book Synopsis Microbiome Analysis by : Robert G. Beiko

Download or read book Microbiome Analysis written by Robert G. Beiko and published by . This book was released on 2018 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Microbiomes of the Built Environment

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309449839
Total Pages : 318 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Microbiomes of the Built Environment by : National Academies of Sciences, Engineering, and Medicine

Download or read book Microbiomes of the Built Environment written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-10-06 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Metabolomics

Author : Vijay Soni
Publisher : Springer Nature
ISBN 13 : 3031390946
Total Pages : 527 pages
Book Rating : 4.0/5 (313 download)

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Book Synopsis Metabolomics by : Vijay Soni

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.

Plant Adaptation to Abiotic Stress: From Signaling Pathways and Microbiomes to Molecular Mechanisms

Author : Radhouane Chaffai
Publisher : Springer Nature
ISBN 13 : 9819706726
Total Pages : 540 pages
Book Rating : 4.8/5 (197 download)

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Book Synopsis Plant Adaptation to Abiotic Stress: From Signaling Pathways and Microbiomes to Molecular Mechanisms by : Radhouane Chaffai

Download or read book Plant Adaptation to Abiotic Stress: From Signaling Pathways and Microbiomes to Molecular Mechanisms written by Radhouane Chaffai and published by Springer Nature. This book was released on 2024 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt: Zusammenfassung: The book "Plant Adaptation to Abiotic Stress: From Signaling Pathways and Microbiomes to Molecular Mechanisms" comprehensively examines abiotic stressors--cold, heat, light, salinity, and water scarcity--across its 18 chapters. Focusing particularly on Arabidopsis thaliana, it investigates abiotic stresses, adaptation strategies, and molecular pathways. Furthermore, it addresses broader issues, including climate challenges, food security, water scarcity, and agricultural concerns such as soil acidity and aluminum stress. It proposes adaptive measures for cultivating stress-resistant crops and sheds light on genetic modification methods such as CRISPR-Cas9, integrating nanotechnology in plant breeding. Emphasizing transcription factors, post-translational protein modifications, and diverse noncoding RNAs (long noncoding RNAs, circular RNAs, microRNAs, and small interfering RNAs), the book highlights their role in regulating gene expression during stress responses. It specifically underscores secondary messengers, plant hormones, and MAPK cascades within intracellular signaling pathways. Additionally, it discusses the roles of endophytic bacteria and microbial interactions in bolstering stress resilience. The book explores state-of-the-art research methodologies in plant breeding, omics approaches, and nanotechnology integration for developing stress-resistant crop varieties, advocating for agricultural sustainability. Tailored for plant physiology scientists, academics, and postgraduate students, it amalgamates diverse research findings, serving as a pivotal resource to comprehend intricate plant responses to environmental challenges