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.

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.

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.

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.

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.

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

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:

Metabolomics Data Processing and Data Analysis-Current Best Practices

Author : Justin Van Der Hooft
Publisher : Mdpi AG
ISBN 13 : 9783036511948
Total Pages : 276 pages
Book Rating : 4.5/5 (119 download)

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Book Synopsis Metabolomics Data Processing and Data Analysis-Current Best Practices by : Justin Van Der Hooft

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.

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429145
Total Pages : 1223 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 2019-09-10 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.

Computational Methods and Data Analysis for Metabolomics

Author : Shuzhao Li
Publisher : Humana
ISBN 13 : 9781071602386
Total Pages : 0 pages
Book Rating : 4.6/5 (23 download)

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Book Synopsis Computational Methods and Data Analysis for Metabolomics by : Shuzhao Li

Download or read book Computational Methods and Data Analysis for Metabolomics written by Shuzhao Li and published by Humana. This book was released on 2020-01-18 with total page 0 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.

Data Analysis and Chemometrics for Metabolomics

Author : Richard G. Brereton
Publisher : John Wiley & Sons
ISBN 13 : 1119639409
Total Pages : 437 pages
Book Rating : 4.1/5 (196 download)

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Book Synopsis Data Analysis and Chemometrics for Metabolomics by : Richard G. Brereton

Download or read book Data Analysis and Chemometrics for Metabolomics written by Richard G. Brereton and published by John Wiley & Sons. This book was released on 2024-07-08 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understand new modes of analysing metabolomic data Metabolomics is the study of metabolites, small molecules and chemical substrates within cells or larger structures which collectively make up the metabolome. The field of metabolomics stands to benefit enormously from chemometrics, an approach which brings advanced statistical techniques to bear on data of this kind. Data Analysis and Chemometrics for Metabolomics constitutes an accessible introduction to chemometric techniques and their applications in the field of metabolomics. Thoroughly and accessibly written by a leading expert in chemometrics, and printed in full-colour, it brings robust data analysis into conversation with the metabolomic field to the immense benefit of practitioners. Data Analysis and Chemometrics for Metabolomics readers will also find: Statistical insights into the nature of metabolomic hypothesis testing, validation, and more All metabolomics data sets from the book on a companion website Case studies from human, animal, plant and bacterial biology Data Analysis and Chemometrics for Metabolomics is ideal for practitioners in the life sciences, clinical sciences and chemistry, as well as metabolomics researchers or developers of research instruments looking to apply cutting-edge analytical techniques, and statisticians developing methods to design experiments and analyse large datasets of clinical and biological origin.

Metabolomics in Food and Nutrition

Author : Bart C Weimer
Publisher : Elsevier
ISBN 13 : 0857098810
Total Pages : 262 pages
Book Rating : 4.8/5 (57 download)

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Book Synopsis Metabolomics in Food and Nutrition by : Bart C Weimer

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