Statistical Analysis of Microbiome Data with R Book PDF

Statistical Analysis of Microbiome Data with R

  • Author : Yinglin Xia
  • Publisher : Springer
  • Release Date : 2018-10-06
  • Genre : Computers
  • Pages : 505
  • ISBN : 9789811315343

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Statistical Analysis of Microbiome Data with R 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.

Statistical Analysis of Microbiome Data Book PDF

Statistical Analysis of Microbiome Data

  • Author : Somnath Datta
  • Publisher : Springer
  • Release Date : 2021-10-11
  • Genre : Medical
  • Pages : 346
  • ISBN : 3030733505

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Statistical Analysis of Microbiome Data 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.

Statistical Issues in Microbiome Data Analysis Book PDF

Statistical Issues in Microbiome Data Analysis

  • Author : Weijia Fu
  • Publisher : Unknown
  • Release Date : 2019
  • Genre : Uncategorized
  • Pages : 39
  • ISBN : OCLC:1117509333

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Statistical Issues in Microbiome Data Analysis Book Description :

Progress in high throughput sequencing has facilitated the conduct of large scale microbiome profiling studies which have already begun to elucidate the role of microbes in many disorders and clinical outcomes. Despite the many successes, statistical analysis of data from these studies continues to pose a challenge. In the thesis, we proposed methods to study two specific challenges: batch effects and integrative analysis of microbiome and other omics data. Both issues are increasingly relevant problems. As studies get larger, batching becomes inevitable and integrative analysis is imperative for gaining clues as to the mechanisms underlying discovered associations. The thesis is composed of two projects. In the first project, we compared six existing batch correction methods for microarray data when applied to microbiome data. Two real microbiome data sets were used to evaluate the performance using data visualization and several evaluation metrics. Our results suggest that an empirical bayes approach (ComBat), when applied appropriately, can outperform other methods. In the second project, we proposed a robust microbiome regression-based kernel association test (MiRKAT-R) to screen a large number of genomic markers for association with microbiome profiles. This approach utilizes a recently developed robust kernel machine test. We further propose to incorporate an omnibus test that simultaneously considers different models so as to allow for different relationships between the individual markers and microbiome composition. Systematic simulations and applications to real data show that the MiRKAT-R improves both type I error control and power.

Inflammation  Infection  and Microbiome in Cancers Book PDF

Inflammation Infection and Microbiome in Cancers

  • Author : Jun Sun
  • Publisher : Springer Nature
  • Release Date : 2021-04-20
  • Genre : Medical
  • Pages : 509
  • ISBN : 9783030679514

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Inflammation Infection and Microbiome in Cancers Book Description :

This book offers a summary and discussion of the advances of inflammation and infection in various cancers. The authors cover the classically known virus infections in cancer, novel roles of other pathogens (e.g. bacteria and fungi), as well as biomarkers for diagnosis and therapy. Further, the chapters highlight the progress of immune therapy, stem cells and the role of the microbiome in the pathophysiology of cancers. Readers will gain insights into complex microbial communities, that inhabit most external human surfaces and play a key role in health and disease. Perturbations of host-microbe interactions often lead to altered host responses that can promote cancer development. Thus, this book highlights emerging roles of the microbiome in pathogenesis of cancers and outcome of therapy. The focus is on mechanistic concepts that underlie the complex relationships between host and microbes. Approaches that can inhibit infection, suppress chronic inflammation and reverse the dysbiosis are discussed, as a means for restoring the balance between host and microbes. This comprehensive work will be beneficial to researchers and students interested in infectious diseases, microbiome, and cancer as well as clinicians and general physiologists.

The Microbiome in Health and Disease Book PDF

The Microbiome in Health and Disease

  • Author : Anonim
  • Publisher : Academic Press
  • Release Date : 2020-05-29
  • Genre : Science
  • Pages : 520
  • ISBN : 9780128200018

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The Microbiome in Health and Disease Book Description :

The Microbiome in Health and Disease, Volume 171 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Microbiome in health and disease, CNS development and microbiome in infants, A gut feeling in ALS, Microbiome (Virome) and virus infection, Bugs and Drugs: microbiome in medicine metabolism, Immunity, T cells, and microbiome, Salmonella (Bacterial) infection and cancer: of mice and men, and many other highly researched topics. Provides a novel theme and multiple disciplinary topics of microbiome research in basic and translational studies Presents an updated collection on bacteria, virus, fungi and their interactions in microbiome Includes a timely discussion on the tools and methods used for modeling and analysis of microbiome data

Intestinal Dysbiosis in Inflammatory Diseases Book PDF

Intestinal Dysbiosis in Inflammatory Diseases

  • Author : Gislane Lelis Vilela de Oliveira
  • Publisher : Frontiers Media SA
  • Release Date : 2021-09-29
  • Genre : Medical
  • Pages : 231
  • ISBN : 9782889714056

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Intestinal Dysbiosis in Inflammatory Diseases Book Description :

Dr. Fasano holds stocks in Alba Therapeutics and receives financial support from Takeda Pharmaceuticals. Dr. Taneja receives financial support from Elysium Health and Evelo Biosciences. The other Topic Editors declare no competing interests with regards to the Research Topic subject.

Mechanisms Underlying Host Microbiome Interactions in Pathophysiology of Human Diseases Book PDF

Mechanisms Underlying Host Microbiome Interactions in Pathophysiology of Human Diseases

  • Author : Jun Sun
  • Publisher : Springer
  • Release Date : 2018-01-26
  • Genre : Medical
  • Pages : 381
  • ISBN : 9781493975341

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Mechanisms Underlying Host Microbiome Interactions in Pathophysiology of Human Diseases Book Description :

Only recently have we begun to appreciate the role of microbiome in health and disease. Environmental factors and change of life style including diet significantly shape human microbiome that in turn appears to modify gut barrier function affecting nutrient & electrolyte absorption and inflammation. Approaches that can reverse the gut dysbiosis represent as reasonable and novel strategies for restoring the balance between host and microbes. In the book, we offer summary and discussion on the advances in understanding of pathophysiological mechanisms of microbial host interactions in human diseases. We will not only discuss intestinal bacterial community, but also viruses, fungi and oral microbiome. Microbiome studies will facilitate diagnosis, functional studies, drug development and personalized medicine. Thus, this book will further highlight the microbiome in the context of health and disease, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.

Biocomputing 2016 Book PDF

Biocomputing 2016

  • Author : Russ B Altman
  • Publisher : World Scientific Publishing Company
  • Release Date : 2015-11-19
  • Genre : Science
  • Pages : 604
  • ISBN : 9789814749411

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Biocomputing 2016 Book Description :

The Pacific Symposium on Biocomputing (PSB) 2016 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 2016 will be held on January 4 – 8, 2016 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference. PSB 2016 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.

Biocomputing 2016   Proceedings Of The Pacific Symposium Book PDF

Biocomputing 2016 Proceedings Of The Pacific Symposium

  • Author : Russ B Altman
  • Publisher : World Scientific
  • Release Date : 2015-11-19
  • Genre : Science
  • Pages : 604
  • ISBN : 9789814749428

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Biocomputing 2016 Proceedings Of The Pacific Symposium Book Description :

The Pacific Symposium on Biocomputing (PSB) 2016 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 2016 will be held on January 4 - 8, 2016 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2016 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.

Pathogens  Pathobionts and Autoimmunity Book PDF

Pathogens Pathobionts and Autoimmunity

  • Author : Linda Ann Spatz
  • Publisher : Frontiers Media SA
  • Release Date : 2021-10-22
  • Genre : Medical
  • Pages : 231
  • ISBN : 9782889715466

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Pathogens Pathobionts and Autoimmunity Book Description :

Modern Soil Microbiology  Third Edition Book PDF

Modern Soil Microbiology Third Edition

  • Author : Jan Dirk van Elsas
  • Publisher : CRC Press
  • Release Date : 2019-04-05
  • Genre : Technology & Engineering
  • Pages : 472
  • ISBN : 9780429602405

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Modern Soil Microbiology Third Edition Book Description :

The living soil is crucial to photosynthesis, biogeochemical cycles, global food production, climate change, biodiversity, and plant and animal health. In the past decade, scientists have made significant advances in soil microbiology research. While the basic principles are now better understood, knowledge has been forthcoming on the best available technologies and methods applied to researching soil microorganisms, their diversity, interactions, biochemistry, survival, gene expression, and their roles in global climate change, plant disease suppression and growth stimulation, and biogeochemical cycles. This knowledge can be applied to better predict the transformation of pollutants in soil and the activities of microbes in the rhizosphere. It will also assist us in fostering crop production in an era with an increasing human population and intensification of agriculture. Following the tradition of its predecessors, Modern Soil Microbiology, Third Edition, is an indispensable source that supports graduate/undergraduate teaching for soil and environmental microbiologists in academia, as well as in government and industrial laboratories. It is a comprehensive collection of chapters on various aspects of soil microbiology, useful for all professionals working with soils. Compiled by internationally renowned educators and research scholars, this textbook contains key tables, figures, and photographs, supported by thousands of references to illustrate the depth of knowledge in soil microbiology. FEATURES Fully updated and expanded to include new key chapters on historical developments, future applications, and soil viruses and proteins Discusses molecular methods applied to soil microbiology, diverse soil microorganisms, and global climate change Emphasizes the role of terrestrial microorganisms and cycles involved in climate change Details the latest molecular methods applied to soil microbiology research User-friendly for students, and containing numerous tables, figu

Handbook of Statistical Genomics Book PDF

Handbook of Statistical Genomics

  • Author : David J. Balding
  • Publisher : John Wiley & Sons
  • Release Date : 2019-09-16
  • Genre : Science
  • Pages : 1224
  • ISBN : 9781119429142

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Handbook of Statistical Genomics Book Description :

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,

The Social Biology of Microbial Communities Book PDF

The Social Biology of Microbial Communities

  • Author : Institute of Medicine
  • Publisher : National Academies Press
  • Release Date : 2013-01-10
  • Genre : Medical
  • Pages : 632
  • ISBN : 9780309264327

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The Social Biology of Microbial Communities Book Description :

Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; the

Manual of Environmental Microbiology Book PDF

Manual of Environmental Microbiology

  • Author : Cindy H. Nakatsu
  • Publisher : John Wiley & Sons
  • Release Date : 2020-08-11
  • Genre : Science
  • Pages : 231
  • ISBN : 9781555818821

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Manual of Environmental Microbiology Book Description :

The single most comprehensive resource for environmental microbiology Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manual is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation and biotransformation. This wealth of information is divided into 18 sections each containing chapters written by acknowledged topical experts from the international community. Specifically, this new edition of the Manual Contains completely new sections covering microbial risk assessment, quality control, and microbial source tracking Incorporates a summary of the latest methodologies used to study microorganisms in various environments Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.

Dietary Plant Origin Bio Active Compounds  Intestinal Functionality and Microbiome Book PDF

Dietary Plant Origin Bio Active Compounds Intestinal Functionality and Microbiome

  • Author : Elad Tako
  • Publisher : MDPI
  • Release Date : 2020-12-17
  • Genre : Medical
  • Pages : 214
  • ISBN : 9783039438655

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Dietary Plant Origin Bio Active Compounds Intestinal Functionality and Microbiome Book Description :

Plant-based diets contain a plethora of metabolites that may impact on health and disease prevention. Most are focused on the potential bioactivity and nutritional relevance of several classes of phytochemicals, such as polyphenols, flavonoids, carotenoids, phyto-oestrogens, and frucrooligo-saccharides. These compounds are found in fruit, vegetables, and herbs. Daily intakes of some of these compounds may exceed 100 mg. Moreover, intestinal bacterial activity may transform complex compounds such as anthocyanins, procyanidins, and isoflavones into simple phenolic metabolites. The colon is thus a rich source of potentially active phenolic acids that may impact both locally and systemically on gut health. Further, nondigestible fiber (prebiotics) are dietary substrates that selectively promote proliferation and/or activity of health-promoting bacterial populations in the colon. Prebiotics, such as inulin, raffinose, and stachyose, have a proven ability to promote the abundance of intestinal bacterial populations, which may provide additional health benefits to the host. Further, various pulse seed soluble (fiber) extracts are responsible for improving gastrointestinal motility, intestinal functionality and morphology, and mineral absorption. Studies indicated that the consumption of seed origin soluble extracts can upregulate the expression of BBM proteins that contribute for digestion and absorption of nutrients.