Download or read book Statistical Visual and Functional Analysis of Microbiome Data written by Achal Dhariwal and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "The advancements in next-generation sequencing technologies have revolutionized microbiome research by allowing culture-independent high-throughput profiling of the genetic contents of microbial communities. Nowadays, 16S rRNA based marker gene sequencing is widely used to characterize the taxonomic composition and phylogenetic diversity of complex microbial communities. However, statistical, visual and functional analysis of such data possess great challenges. In addition, many aspects of the current approaches can be improved to get a better understanding of communities. The proper analysis of the resulting large and complicated datasets remains a key bottleneck in current microbiome studies. Over the last decade, powerful computational pipelines and standard protocols have been developed to support efficient raw data processing and annotation of microbiome data. The focus has now shifted towards downstream statistical analysis and functional interpretation. To address this bottleneck, we have developed MicrobiomeAnalyst, a user-friendly web-based tool that incorporates recent progresses in statistics and interactive visualization techniques, coupled with novel knowledge bases, to facilitate comprehensive analysis of common data sets generated from microbiome studies. MicrobiomeAnalyst contains four major components, including i) a module for community diversity profiling, comparative analysis and functional prediction of 16S rRNA marker gene data; ii) a module for exploratory data analysis, functional profiling and metabolic network visualization for shotgun metagenomics or metatranscriptomics data; iii) a module to help users to interpret their taxa of interest via enrichment analysis against ~300 taxon sets manually collected from recent literature and public databases; and iv) a module to allow users to visually explore their data sets within the context of compatible public data (meta-analysis) for pattern discovery and biological insights. The tool is freely accessible at http://www.microbiomeanalyst.ca. " --
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 Statistical Methods for Longitudinal Data Analysis and Reproducible Feature Selection in Human Microbiome Studies written by Lingjing Jiang and published by . This book was released on 2020 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt: The microbiome is inherently dynamic, driven by interactions among microbes, with the host, and with the environment. At any point in life, human microbiome can be dramatically altered, either transiently or long term, by diseases, medical interventions or even daily routines. Since the human microbiome is highly dynamic and personalized, longitudinal microbiome studies that sample human-associated microbial communities repeatedly over time provide valuable information for researchers to observe both inter- and intra-individual variability, or to measure changes in response to an intervention in real time. Despite this increasing need in longitudinal data analysis, statistical methods for analyzing sparse longitudinal microbiome data and longitudinal multi-omics data still lag behind. In this dissertation, we describe our efforts in developing two novel statistical methods, Bayesian functional principal components analysis (SFPCA) for sparse longitudinal data analysis, and multivariate sparse functional principal components analysis (mSFPCA) for longitudinal microbiome multi-omics data analysis. Beyond longitudinal data analysis, we are also interested in utilizing statistical techniques for addressing the "reproducibility crisis" in microbiome research, especially in the indispensable task of feature selection. Instead of developing "the best" feature selection method, we focus on discovering a reproducible criterion called Stability for evaluating feature selection methods in order to yield reproducible results in microbiome analysis. To set an appropriate motivation and context for our work, Chapter 1 reviews the importance of longitudinal studies in human microbiome research, and presents the crucial need of developing novel statistical methods to meet the new challenges in longitudinal microbiome data analysis, and of producing reproducible results in microbiome feature selection. Chapter 2 introduces Bayesian SFPCA, a flexible Bayesian approach to SFPCA that enables efficient model selection and graphical model diagnostics for valid longitudinal microbiome applications. Chapter 3 presents mSFPCA, an extension of Bayesian SFPCA from modeling a univariate temporal outcome to simultaneously characterizing multiple temporal measurements, and inferring their temporal associations based on mutual information estimation. Chapter 4 proposes to use reproducibility criterion such as Stability instead of popular model prediction metric such as mean squared error (MSE) to quantify the reproducibility of identified microbial features.
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 Computational Methods for Microbiome Analysis written by Joao Carlos Setubal and published by Frontiers Media SA. This book was released on 2021-02-02 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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:
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 Statistical Tools for the Multi omics Analysis of Microbiome Data written by Angela Zhang and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The human microbiome consists of trillions of bacteria, archaea, and viruses that exist on virtually every organ in the body. The microbiome plays a fundamental role in human health and has been implicated in several different diseases and conditions such as cardiovascular disease and certain cancers. Understanding the functional role of the microbiome can lead to increased understanding of these complex diseases and result in the development of more effective treatments. Although advances in technology have allowed for the inexpensive processing and analysis of high-throughput data, several statistical challenges exist in the analysis of microbiome data. In my dissertation, I will present three projects that address the statistical challenges of high-dimensionality, multi-omics data integration, batch effects/other covariate adjustment, and the visualization of microbiome data. In Project 1, We address the issues of high-dimensionality and data integration by proposing a new procedure for testing the cumulative metabolic effect of the microbiome using a weighted variance component test framework. In this setup, we focus on metabolic pathways and recognize that metabolism can be represented by metagenomics (metabolic potential) and metabolomics (metabolic output). In Project 2, we address the issue of batch effects and high-dimensionality by outlining a two-step adjustment of the principal coordinates (PCs) of the microbial taxa data. In the first step, we project the mean effect of the unwanted covariates out of the PCs. In the second step, we adjust out the second moment of the same covariates from the PCs by assuming a linear relationship between the covariates and the variance of the PCs. Finally, in Project 3, we propose an effect modification testing procedure for evaluating interactions between microbial taxa and environmental factors on an outcome of interest. We address concerns of data integration and high-dimensionality by using a variance component test framework with LASSO-selected variables to assess the effect modification of the microbiome on environmental variables.
Download or read book The Plant Holobiont Volume I Microbiota as Part of the Holobiont Challenges for Agriculture written by Patrizia Cesaro and published by Frontiers Media SA. This book was released on 2022-02-02 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Metagenomic Data Analysis written by Suparna Mitra and published by Springer Nature. This book was released on 2023-05-31 with total page 443 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control of raw sequence data, metagenomics databases for bacterial annotations such Greengenes, SILVA, RDP and GTDB, guide to 16S rRNA microbiome analysis and pipelines such as mothur, DADA2, QIIME2 , whole genome shotgun metagenomics data analyses pipeline using MEGAN and DIAMOND, web service such as PATRIC, RDP, mothur, Kaiju, PhyloPythiaS, MG-RAST, WebMGA, MicrobiomeAnalyst, WHAM!, METAGENassist and MGnify: EBI-Metagenomics, MG-RAST Metagenomics Analysis. Then the chapters inform the readers regarding Third-generation sequencing (TGS) approaches as MinION sequencing and teaches use of Ubuntu Linux Virtual Machine configuration, clinical and environmental resistomes, use of FISH techniques and designing FISH probes, protocols for viral metagenomics, and comprehensive guideline for microbiome analysis using most used R packages. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Metagenomic Data Analysis: Methods and Protocols aims to be comprehensive guide for researchers to specialize in the metagenomics field.
Download or read book 11th international meeting on visualizing biological data VIZBI 2021 written by Sean O’Donoghue and published by Frontiers Media SA. This book was released on 2022-12-16 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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.
Download or read book Microbiome Host Interactions written by D. Dhanasekaran and published by CRC Press. This book was released on 2021-03-31 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Summarize the recent insight in the Microbiome and host interactions in distinct habitat including antarctic, hydrothermal vents water, speleothems, oral, skin, gut, feces, reproductive tract, soil, root, root nodules, forest and mangroves. Illustrates the high-throughput amplicon sequencing, computational techniques involved in the microbiota analysis, downstream analysis and visualization, multivariate analysis commonly used for microbiome analysis. Describe the probiotics and prebiotics in the composition of the gut microbiota, skin microbiome impact in dermatologic disease prevention, microbial communities in the reproductive tract of human and animals. Information presented in a reachable way for valuable to students, teachers, researchers, microbiologists, computational biologist and other professionals who interested to strengthen and enlarge their knowledge about microbiome analysis by with Next-Generation DNA Sequencing in different branches of sciences.
Download or read book Bioinformatics in Microbiota written by Xing Chen and published by Frontiers Media SA. This book was released on 2020-06-22 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt:
