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Author: Jessica Galloway-Peña
Publisher: Frontiers Media SA
ISBN: 2889456536
Category :
Languages : en
Pages : 186
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Book Description
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.
Author: Jessica Galloway-Peña
Publisher: Frontiers Media SA
ISBN: 2889456536
Category :
Languages : en
Pages : 186
Get Book
Book Description
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.
Author: Yinglin Xia
Publisher: Springer
ISBN: 9811315345
Category : Computers
Languages : en
Pages : 505
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Book Description
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.
Author: Setubal
Publisher: Frontiers Media SA
ISBN: 2832506402
Category : Science
Languages : en
Pages : 223
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Book Description
Author: Megan Pirrung
Publisher:
ISBN:
Category :
Languages : en
Pages : 135
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Book Description
Sequencing technologies become cheaper and produce vast amounts of data in many biomedical domains, including in the field of microbial ecology. However, the software and analytical tools available to microbial ecologists are struggling to meet the need demanded by these complex datasets. Scientists use visualization to both support data analysis and to communicate results to scientific and public audiences. Biological data analysis software is often written by scientists who have limited background and experience in software engineering and design of interactive tools, which often results in unstable and ineffective products. To address this problem in the domain of microbial ecology we have developed TopiaryExplorer and EMPeror through a user-centered design process and utilized proper software development practices. Both tools provide an intuitive user interface and use informed visual data representations. We demonstrate the effectiveness of these tools through case studies of real analysis workflows. The tools have proven useful for scientific data analysis and communication. To communicate results scientists often rely on complex graphics for static publication, rather than dynamic data exploration tools. It is unclear how effective these types of visualizations are for communicating microbial ecology data to different audiences. To examine this question we designed an experiment for determining efficacy of different visualizations. We surveyed three different microbial ecology data types: abundance, phylogeny and multidimensional. The results from the experiment show that visualization choice has the most significant effect on understanding of microbial ecology data, but microbial ecology experience as well as previous experience with visualization also have significant effects. These results can be used to better inform scientific communication through visualization. The experiment itself provides a framework for conducting similar experiments with different types of underlying data and visual representations.
Author: Somnath Datta
Publisher: Springer Nature
ISBN: 3030733513
Category : Medical
Languages : en
Pages : 349
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Book Description
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.
Author: Lingjing Jiang
Publisher:
ISBN:
Category :
Languages : en
Pages : 101
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Book Description
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.
Author: Guangchuang Yu
Publisher: Frontiers Media SA
ISBN: 2889761908
Category : Science
Languages : en
Pages : 146
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Book Description
Author: Robert G. Beiko
Publisher:
ISBN: 9781493987283
Category : Microbiology
Languages : en
Pages : 324
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Book Description
Author: Russ B Altman
Publisher: World Scientific
ISBN: 9813207825
Category : Science
Languages : en
Pages : 668
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Book Description
The Pacific Symposium on Biocomputing (PSB) 2017 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2017 will be held on January 4 - 8, 2017 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2017 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Author: Pallaval Veera Bramhachari
Publisher: Springer Nature
ISBN: 9811631565
Category : Medical
Languages : en
Pages : 306
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Book Description
The book provides an overview on how the microbiome contributes to human health and disease. The microbiome has also become a burgeoning field of research in medicine, agriculture & environment. The readers will obtain profound knowledge on the connection between intestinal microbiota and immune defense systems, medicine, agriculture & environment. The book may address several researchers, clinicians and scholars working in biomedicine, microbiology and immunology. The application of new technologies has no doubt revolutionized the research initiatives providing new insights into the dynamics of these complex microbial communities and their role in medicine, agriculture & environment shall be more emphasized. Drawing on broad range concepts of disciplines and model systems, this book primarily provides a conceptual framework for understanding these human-microbe, animal-microbe & plant-microbe, interactions while shedding critical light on the scientific challenges that lie ahead. Furthermore this book explains why microbiome research demands a creative and interdisciplinary thinking—the capacity to combine microbiology with human, animal and plant physiology, ecological theory with immunology, and evolutionary perspectives with metabolic science.This book provides an accessible and authoritative guide to the fundamental principles of microbiome science, an exciting and fast-emerging new discipline that is reshaping many aspects of the life sciences. These microbial partners can also drive ecologically important traits, from thermal tolerance to diet in a typical immune system, and have contributed to animal and plant diversification over long evolutionary timescales. Also this book explains why microbiome research presents a more complete picture of the biology of humans and other animals, and how it can deliver novel therapies for human health and new strategies.
