Microbiome Metagenomics And High Dimensional Compositional Data Analysis

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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.

Compositional Data Analysis

Author : Vera Pawlowsky-Glahn
Publisher : John Wiley & Sons
ISBN 13 : 0470711353
Total Pages : 405 pages
Book Rating : 4.4/5 (77 download)

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Book Synopsis Compositional Data Analysis by : Vera Pawlowsky-Glahn

Download or read book Compositional Data Analysis written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2011-09-19 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is difficult to imagine that the statistical analysis of compositional data has been a major issue of concern for more than 100 years. It is even more difficult to realize that so many statisticians and users of statistics are unaware of the particular problems affecting compositional data, as well as their solutions. The issue of ``spurious correlation'', as the situation was phrased by Karl Pearson back in 1897, affects all data that measures parts of some whole, such as percentages, proportions, ppm and ppb. Such measurements are present in all fields of science, ranging from geology, biology, environmental sciences, forensic sciences, medicine and hydrology. This book presents the history and development of compositional data analysis along with Aitchison's log-ratio approach. Compositional Data Analysis describes the state of the art both in theoretical fields as well as applications in the different fields of science. Key Features: Reflects the state-of-the-art in compositional data analysis. Gives an overview of the historical development of compositional data analysis, as well as basic concepts and procedures. Looks at advances in algebra and calculus on the simplex. Presents applications in different fields of science, including, genomics, ecology, biology, geochemistry, planetology, chemistry and economics. Explores connections to correspondence analysis and the Dirichlet distribution. Presents a summary of three available software packages for compositional data analysis. Supported by an accompanying website featuring R code. Applied scientists working on compositional data analysis in any field of science, both in academia and professionals will benefit from this book, along with graduate students in any field of science working with compositional data.

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.

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.

Statistical and Computational Methods for Microbiome Multi-Omics Data

Author : Himel Mallick
Publisher : Frontiers Media SA
ISBN 13 : 2889660915
Total Pages : 170 pages
Book Rating : 4.8/5 (896 download)

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Book Synopsis Statistical and Computational Methods for Microbiome Multi-Omics Data by : Himel Mallick

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.

The Statistical Analysis of Compositional Data

Author : John Aitchison
Publisher :
ISBN 13 : 9781930665781
Total Pages : 416 pages
Book Rating : 4.6/5 (657 download)

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Book Synopsis The Statistical Analysis of Compositional Data by : John Aitchison

Download or read book The Statistical Analysis of Compositional Data written by John Aitchison and published by . This book was released on 2003 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Originally published in 1986, this text contains a new Foreword, extensive postscript detailing developments in the field since its first publication, and a selection of more recent literature references. The work provides a clear and systematic account of statistical methods designed to meet the special needs of the compositional data analyst. (Mathematics)

Modeling and Analysis of Compositional Data

Author : Vera Pawlowsky-Glahn
Publisher : John Wiley & Sons
ISBN 13 : 111900313X
Total Pages : 274 pages
Book Rating : 4.1/5 (19 download)

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Book Synopsis Modeling and Analysis of Compositional Data by : Vera Pawlowsky-Glahn

Download or read book Modeling and Analysis of Compositional Data written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2015-02-17 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling and Analysis of Compositional Data presents a practical and comprehensive introduction to the analysis of compositional data along with numerous examples to illustrate both theory and application of each method. Based upon short courses delivered by the authors, it provides a complete and current compendium of fundamental to advanced methodologies along with exercises at the end of each chapter to improve understanding, as well as data and a solutions manual which is available on an accompanying website. Complementing Pawlowsky-Glahn’s earlier collective text that provides an overview of the state-of-the-art in this field, Modeling and Analysis of Compositional Data fills a gap in the literature for a much-needed manual for teaching, self learning or consulting.

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.

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:

Microbiome and Machine Learning, Volume II

Author : Erik Bongcam-Rudloff
Publisher : Frontiers Media SA
ISBN 13 : 2832556035
Total Pages : 209 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Microbiome and Machine Learning, Volume II by : Erik Bongcam-Rudloff

Download or read book Microbiome and Machine Learning, Volume II written by Erik Bongcam-Rudloff and published by Frontiers Media SA. This book was released on 2024-10-24 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the success of Microbiome and Machine Learning, which collected research results and perspectives of researchers working in the field of machine learning (ML) applied to the analysis of microbiome data, we are launching the second volume to collate any new findings in the field to further our understanding and encourage the participation of experts worldwide in the discussion. The success of ML algorithms in the field is substantially due to their capacity to process high-dimensional data and deal with uncertainty and noise. However, to maximize the combinatory potential of these emerging fields (microbiome and ML), researchers have to deal with some aspects that are complex and inherently related to microbiome data. Microbiome data are convoluted, noisy and highly variable, and non-standard analytical methodologies are required to unlock their clinical and scientific potential. Therefore, although a wide range of statistical modelling and ML methods are available, their application is only sometimes optimal when dealing with microbiome data.

Computational methods for microbiome analysis, volume 2

Author : Setubal
Publisher : Frontiers Media SA
ISBN 13 : 2832506402
Total Pages : 223 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Computational methods for microbiome analysis, volume 2 by : Setubal

Download or read book Computational methods for microbiome analysis, volume 2 written by Setubal and published by Frontiers Media SA. This book was released on 2023-01-04 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Novel Approaches in Microbiome Analyses and Data Visualization

Author : Jessica Galloway-Peña
Publisher : Frontiers Media SA
ISBN 13 : 2889456536
Total Pages : 186 pages
Book Rating : 4.8/5 (894 download)

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Book Synopsis Novel Approaches in Microbiome Analyses and Data Visualization by : Jessica Galloway-Peña

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.

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.

Imbalanced Learning

Author : Haibo He
Publisher : John Wiley & Sons
ISBN 13 : 1118646339
Total Pages : 222 pages
Book Rating : 4.1/5 (186 download)

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Book Synopsis Imbalanced Learning by : Haibo He

Download or read book Imbalanced Learning written by Haibo He and published by John Wiley & Sons. This book was released on 2013-06-07 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first book of its kind to review the current status and future direction of the exciting new branch of machine learning/data mining called imbalanced learning Imbalanced learning focuses on how an intelligent system can learn when it is provided with imbalanced data. Solving imbalanced learning problems is critical in numerous data-intensive networked systems, including surveillance, security, Internet, finance, biomedical, defense, and more. Due to the inherent complex characteristics of imbalanced data sets, learning from such data requires new understandings, principles, algorithms, and tools to transform vast amounts of raw data efficiently into information and knowledge representation. The first comprehensive look at this new branch of machine learning, this book offers a critical review of the problem of imbalanced learning, covering the state of the art in techniques, principles, and real-world applications. Featuring contributions from experts in both academia and industry, Imbalanced Learning: Foundations, Algorithms, and Applications provides chapter coverage on: Foundations of Imbalanced Learning Imbalanced Datasets: From Sampling to Classifiers Ensemble Methods for Class Imbalance Learning Class Imbalance Learning Methods for Support Vector Machines Class Imbalance and Active Learning Nonstationary Stream Data Learning with Imbalanced Class Distribution Assessment Metrics for Imbalanced Learning Imbalanced Learning: Foundations, Algorithms, and Applications will help scientists and engineers learn how to tackle the problem of learning from imbalanced datasets, and gain insight into current developments in the field as well as future research directions.

Microbiome-Host Interactions

Author : D. Dhanasekaran
Publisher : CRC Press
ISBN 13 : 1000353141
Total Pages : 863 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis Microbiome-Host Interactions by : D. Dhanasekaran

Download or read book Microbiome-Host Interactions written by D. Dhanasekaran and published by CRC Press. This book was released on 2021-04-01 with total page 863 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiota are a promising and fascinating subject in biology because they integrate the microbial communities in humans, animals, plants, and the environment. In humans, microbiota are associated with the gut, skin, and genital, oral, and respiratory organs. The plant microbial community is referred to as "holobiont," and it is influential in the maintenance and health of plants, which themselves play a role in animal health and the environment. The contents of Microbiome-Host Interactions cover all areas as well as new research trends in the fields of plant, animal, human, and environmental microbiome interactions. The book covers microbiota in polar soil environments, in health and disease, in Caenorhabditis elegans, and in agroecosystems, as well as in rice root and actinorhizal root nodules, speleothems, and marine shallow-water hydrothermal vents. Moreover, this book provides comprehensive accounts of advanced next-generation DNA sequencing, metagenomic techniques, high-throughput 16S rRNA sequencing, and understanding nucleic acid sequence data from fungal, algal, viral, bacterial, cyanobacterial, actinobacterial, and archaeal communities using QIIME software (Quantitative Insights into Microbial Ecology). FEATURES Summarizes recent insight in microbiota and host interactions in distinct habitats, including Antarctic, hydrothermal vents, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forests, and mangroves Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, and multivariate analysis commonly used for microbiome analysis Describes probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, and microbial communities in the reproductive tract of humans and animals Presents information in a reachable way for students, teachers, researchers, microbiologists, computational biologists, and other professionals who are interested in strengthening or enlarging their knowledge about microbiome analysis with next-generation DNA sequencing in the different branches of the sciences

Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research

Author : Lixin Cheng
Publisher : Frontiers Media SA
ISBN 13 : 2889716635
Total Pages : 574 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research by : Lixin Cheng

Download or read book Bioinformatics Analysis of Omics Data for Biomarker Identification in Clinical Research written by Lixin Cheng and published by Frontiers Media SA. This book was released on 2022-01-10 with total page 574 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Healthcare and Big Data Management

Author : Bairong Shen
Publisher : Springer
ISBN 13 : 981106041X
Total Pages : 165 pages
Book Rating : 4.8/5 (11 download)

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Book Synopsis Healthcare and Big Data Management by : Bairong Shen

Download or read book Healthcare and Big Data Management written by Bairong Shen and published by Springer. This book was released on 2017-10-20 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book addresses the interplay of healthcare and big data management. Thanks to major advances in big data technologies and precision medicine, healthcare is now becoming the new frontier for both scientific research and economic development. This volume covers a range of aspects, including: big data management for healthcare; physiological and gut microbiota – data collection and analysis; big data standardization and ontology; and personal data privacy and systems level modeling in the healthcare context. The book offers a valuable resource for biomedical informaticians, clinicians, health practitioners and researchers alike.