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Author: Wontack Han
Publisher:
ISBN:
Category : Bioinformatics
Languages : en
Pages : 0
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Book Description
Microbial organisms play key roles in the human hosts' health and diseases. Recent advancements in genome sequencing have resulted in a large collection of sequencing data of microbial species and have expanded the research of microbiome from the characterization of microbiomes' community associated with different environments/hosts to the applications related with human health and diseases. Computational methods have been developed to identify microbial markers from microbiome datasets derived from cohorts of patients with different diseases. Predictive models based on these markers (features) have been built for discriminating host phenotypes such as disease vs healthy and cancer immunotherapy responder vs non-responder. In this dissertation, I developed computational methods for comparative analysis of metagenomes from raw sequencing data and developed Machine Learning (ML) approaches to build predictive models for host phenotype prediction based on identified microbial markers. First, I implemented the subtractive assembly method(called CoSA) for comparative metagenomics that directly detects differential reads between two groups of metagenomes, from which microbial marker genes could be assembled and characterized. Secondly, I reported the curation of a repository of microbial marker genes and predictive models built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline(named Mi2P) for using the repository. Lastly, I exploited locality sensitive hashing(LSH) as clustering algorithm to group billions of k-mers having similar abundance profiles across multiple samples into k-mers co-abundance groups (kCAGs) to improve the characterization of differential microbial markers. The overall goal of my research is to develop fast and efficient approaches for identifying microbial marker genes, and make them available for building predictive models for microbiome-based host phenotype predictions.
Author: Wontack Han
Publisher:
ISBN:
Category : Bioinformatics
Languages : en
Pages : 0
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Book Description
Microbial organisms play key roles in the human hosts' health and diseases. Recent advancements in genome sequencing have resulted in a large collection of sequencing data of microbial species and have expanded the research of microbiome from the characterization of microbiomes' community associated with different environments/hosts to the applications related with human health and diseases. Computational methods have been developed to identify microbial markers from microbiome datasets derived from cohorts of patients with different diseases. Predictive models based on these markers (features) have been built for discriminating host phenotypes such as disease vs healthy and cancer immunotherapy responder vs non-responder. In this dissertation, I developed computational methods for comparative analysis of metagenomes from raw sequencing data and developed Machine Learning (ML) approaches to build predictive models for host phenotype prediction based on identified microbial markers. First, I implemented the subtractive assembly method(called CoSA) for comparative metagenomics that directly detects differential reads between two groups of metagenomes, from which microbial marker genes could be assembled and characterized. Secondly, I reported the curation of a repository of microbial marker genes and predictive models built from these markers for microbiome-based prediction of host phenotype, and a computational pipeline(named Mi2P) for using the repository. Lastly, I exploited locality sensitive hashing(LSH) as clustering algorithm to group billions of k-mers having similar abundance profiles across multiple samples into k-mers co-abundance groups (kCAGs) to improve the characterization of differential microbial markers. The overall goal of my research is to develop fast and efficient approaches for identifying microbial marker genes, and make them available for building predictive models for microbiome-based host phenotype predictions.
Author: Joao Carlos Setubal
Publisher: Frontiers Media SA
ISBN: 2889664376
Category : Science
Languages : en
Pages : 170
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Book Description
Author: Himel Mallick
Publisher: Frontiers Media SA
ISBN: 2889660915
Category : Science
Languages : en
Pages : 170
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Book Description
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.
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309468698
Category : Science
Languages : en
Pages : 123
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Book Description
A great number of diverse microorganisms inhabit the human body and are collectively referred to as the human microbiome. Until recently, the role of the human microbiome in maintaining human health was not fully appreciated. Today, however, research is beginning to elucidate associations between perturbations in the human microbiome and human disease and the factors that might be responsible for the perturbations. Studies have indicated that the human microbiome could be affected by environmental chemicals or could modulate exposure to environmental chemicals. Environmental Chemicals, the Human Microbiome, and Health Risk presents a research strategy to improve our understanding of the interactions between environmental chemicals and the human microbiome and the implications of those interactions for human health risk. This report identifies barriers to such research and opportunities for collaboration, highlights key aspects of the human microbiome and its relation to health, describes potential interactions between environmental chemicals and the human microbiome, reviews the risk-assessment framework and reasons for incorporating chemicalâ€"microbiome interactions.
Author: Robert G. Beiko
Publisher:
ISBN: 9781493987283
Category : Microbiology
Languages : en
Pages : 324
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Book Description
Author: Food Forum
Publisher: National Academies Press
ISBN: 030926586X
Category : Medical
Languages : en
Pages : 197
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Book Description
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.
Author: David J. Balding
Publisher: John Wiley & Sons
ISBN: 1119429250
Category : Science
Languages : en
Pages : 1828
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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, 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.
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
ISBN: 0309458390
Category : Science
Languages : en
Pages : 133
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Book Description
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.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
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.
