Metagenomic Systems Biology

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Metagenomic Systems Biology

Author : Shailza Singh
Publisher : Springer Nature
ISBN 13 : 9811585628
Total Pages : 207 pages
Book Rating : 4.8/5 (115 download)

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Book Synopsis Metagenomic Systems Biology by : Shailza Singh

Download or read book Metagenomic Systems Biology written by Shailza Singh and published by Springer Nature. This book was released on 2020-12-07 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book serves as an amalgamation of knowledge and principles used in the area of systems and synthetic biology, and targets inter-disciplinary research groups. The readers from diversified areas would be benefited by the valuable resources and information available in one book. Microbiome projects with efficient data handling can fuel progress in the area of microbial synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. The different chapters of the book reviews a broad range of topics, including food microbiome in ecology, use of microbiome in personalized medicine, machine learning in biomedicine. The book also describes ways to harness and exploit the incredible amounts of genomic data. The book is not only limited to medicine but also caters to the needs of environmentalists, biochemical engineers etc. It will be of interest to advanced students and researchers in life sciences, computational biology, microbiology and other inter-disciplinary areas.

The New Science of Metagenomics

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309106761
Total Pages : 170 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis The New Science of Metagenomics by : National Research Council

Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Introduction To Computational Metagenomics

Author : Zhong Wang
Publisher : World Scientific
ISBN 13 : 9811242488
Total Pages : 210 pages
Book Rating : 4.8/5 (112 download)

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Book Synopsis Introduction To Computational Metagenomics by : Zhong Wang

Download or read book Introduction To Computational Metagenomics written by Zhong Wang and published by World Scientific. This book was released on 2022-04-11 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Breakthroughs in high-throughput genome sequencing and high-performance computing technologies have empowered scientists to decode many genomes including our own. Now they have a bigger ambition: to fully understand the vast diversity of microbial communities within us and around us, and to exploit their potential for the improvement of our health and environment. In this new field called metagenomics, microbial genomes are sequenced directly from the habitats without lab cultivation. Computational metagenomics, however, faces both a data challenge that deals with tens of tera-bases of sequences and an algorithmic one that deals with the complexity of thousands of species and their interactions.This interdisciplinary book is essential reading for those who are interested in beginning their own journey in computational metagenomics. It is a prism to look through various intricate computational metagenomics problems and unravel their three distinctive aspects: metagenomics, data engineering, and algorithms. Graduate students and advanced undergraduates from genomics science or computer science fields will find that the concepts explained in this book can serve as stepping stones for more advanced topics, while metagenomics practitioners and researchers from similar disciplines may use it to broaden their knowledge or identify new research targets.

Metagenomics for Microbiology

Author : Jacques Izard
Publisher : Academic Press
ISBN 13 : 0124105084
Total Pages : 188 pages
Book Rating : 4.1/5 (241 download)

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Book Synopsis Metagenomics for Microbiology by : Jacques Izard

Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Functional Metagenomics: Tools and Applications

Author : Trevor C. Charles
Publisher : Springer
ISBN 13 : 3319615106
Total Pages : 253 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis Functional Metagenomics: Tools and Applications by : Trevor C. Charles

Download or read book Functional Metagenomics: Tools and Applications written by Trevor C. Charles and published by Springer. This book was released on 2017-10-09 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the latest tools available for functional metagenomics research are described.This research enables scientists to directly access the genomes from diverse microbial genomes at one time and study these “metagenomes”. Using the modern tools of genome sequencing and cloning, researchers have now been able to harness this astounding metagenomic diversity to understand and exploit the diverse functions of microorganisms. Leading scientists from around the world demonstrate how these approaches have been applied in many different settings, including aquatic and terrestrial habitats, microbiomes, and many more environments. This is a highly informative and carefully presented book, providing microbiologists with a summary of the latest functional metagenomics literature on all specific habitats.

Computational Systems Biology

Author : Jean-Luc Bouchot
Publisher : Elsevier Inc. Chapters
ISBN 13 : 0128070153
Total Pages : 548 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Computational Systems Biology by : Jean-Luc Bouchot

Download or read book Computational Systems Biology written by Jean-Luc Bouchot and published by Elsevier Inc. Chapters. This book was released on 2013-11-26 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in next-generation sequencing have enabled high-throughput determination of biological sequences in microbial communities, also known as microbiomes. The large volume of data now presents the challenge of how to extract knowledge—recognize patterns, find similarities, and find relationships—from complex mixtures of nucleic acid sequences currently being examined. In this chapter we review basic concepts as well as state-of-the-art techniques to analyze hundreds of samples which each contain millions of DNA and RNA sequences. We describe the general character of sequence data and describe some of the processing steps that prepare raw sequence data for inference. We then describe the process of extracting features from the data, assigning taxonomic and gene labels to the sequences. Then we review methods for cross-sample comparisons: (1) using similarity measures and ordination techniques to visualize and measure differences between samples and (2) feature selection and classification to select the most relevant features for discriminating between samples. Finally, in conclusion, we outline some open research problems and challenges left for future research.

Systems Biology

Author : Jens Nielsen
Publisher : John Wiley & Sons
ISBN 13 : 3527696172
Total Pages : 600 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Systems Biology by : Jens Nielsen

Download or read book Systems Biology written by Jens Nielsen and published by John Wiley & Sons. This book was released on 2017-03-15 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive coverage of the many different aspects of systems biology, resulting in an excellent overview of the experimental and computational approaches currently in use to study biological systems. Each chapter represents a valuable introduction to one specific branch of systems biology, while also including the current state of the art and pointers to future directions. Following different methods for the integrative analysis of omics data, the book goes on to describe techniques that allow for the direct quantification of carbon fluxes in large metabolic networks, including the use of 13C labelled substrates and genome-scale metabolic models. The latter is explained on the basis of the model organism Escherichia coli as well as the human metabolism. Subsequently, the authors deal with the application of such techniques to human health and cell factory engineering, with a focus on recent progress in building genome-scale models and regulatory networks. They highlight the importance of such information for specific biological processes, including the ageing of cells, the immune system and organogenesis. The book concludes with a summary of recent advances in genome editing, which have allowed for precise genetic modifications, even with the dynamic control of gene expression. This is part of the Advances Biotechnology series, covering all pertinent aspects of the field with each volume prepared by eminent scientists who are experts on the topic in question.

Prokaryotic Systems Biology

Author : Nevan J. Krogan, PhD
Publisher : Springer
ISBN 13 : 3319236032
Total Pages : 319 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis Prokaryotic Systems Biology by : Nevan J. Krogan, PhD

Download or read book Prokaryotic Systems Biology written by Nevan J. Krogan, PhD and published by Springer. This book was released on 2015-11-30 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on innovative experimental and computational approaches for charting interaction networks in bacterial species. The first part of the volume consists of nine chapters, focusing on biochemical and genetics and genomics approaches including yeast two hybrid, metagenomics, affinity purification in combination with mass spectrometry, chromatin-immunoprecipitation coupled with sequencing, large-scale synthetic genetic screens, and quantitative-based mass spectrometry strategies for mapping the bacterial physical, functional, substrate, and regulatory interaction networks needed for interpreting biological networks, inferring gene function, enzyme discovery, and identifying new drug targets. The second part comprises five chapters, covering the network of participants for protein folding and complex enzyme maturation. It also covers the structural approaches required to understand bacterial intramembrane proteolysis and the structure and function of bacterial proteins involved in surface polysaccharides, outer membrane, and envelope assembly. This volume concludes with a focus on computational and comparative genomics approaches, especially network-based methods for predicting physical or functional interactions, and integrative analytical approaches for generating more reliable information on bacterial gene function. This book provides foundational knowledge in the understanding of prokaryotic systems biology by illuminating how bacterial genes f unction within the framework of global cellular processes. The book will enable the microbiology community to create substantive resources for addressing many pending unanswered questions, and facilitate the development of new technologies that can be applied to other bacterial species lacking experimental data.

Metagenomic Data Analysis

Author : Suparna Mitra
Publisher : Springer Nature
ISBN 13 : 1071630725
Total Pages : 443 pages
Book Rating : 4.0/5 (716 download)

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Book Synopsis Metagenomic Data Analysis by : Suparna Mitra

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.

Metagenomics

Author : Diana Marco
Publisher :
ISBN 13 : 9781912530564
Total Pages : pages
Book Rating : 4.5/5 (35 download)

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Book Synopsis Metagenomics by : Diana Marco

Download or read book Metagenomics written by Diana Marco and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Theoretical and Applied Aspects of Systems Biology

Author : Fabricio Alves Barbosa da Silva
Publisher : Springer
ISBN 13 : 3319749749
Total Pages : 259 pages
Book Rating : 4.3/5 (197 download)

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Book Synopsis Theoretical and Applied Aspects of Systems Biology by : Fabricio Alves Barbosa da Silva

Download or read book Theoretical and Applied Aspects of Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer. This book was released on 2018-06-21 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multiresistant bacteria, systems biology of cancer, systems immunology, networks in systems biology.

Advances in Bioinformatics and Computational Biology

Author : Sérgio Campos
Publisher : Springer
ISBN 13 : 3319124188
Total Pages : 156 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Advances in Bioinformatics and Computational Biology by : Sérgio Campos

Download or read book Advances in Bioinformatics and Computational Biology written by Sérgio Campos and published by Springer. This book was released on 2014-10-23 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 9th Brazilian Symposium on Bioinformatics, BSB 2014, held in Belo Horizonte, Brazil, in October 2014. The 18 revised full papers presented were carefully reviewed and selected from 32 submissions. The papers cover all aspects of bioinformatics and computational biology.

Marine Metagenomics

Author : Takashi Gojobori
Publisher : Springer
ISBN 13 : 9811381348
Total Pages : 271 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Marine Metagenomics by : Takashi Gojobori

Download or read book Marine Metagenomics written by Takashi Gojobori and published by Springer. This book was released on 2019-07-24 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner. Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods.

Metagenomics

Author : Muniyandi Nagarajan
Publisher : Academic Press
ISBN 13 : 0128134038
Total Pages : 398 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Metagenomics by : Muniyandi Nagarajan

Download or read book Metagenomics written by Muniyandi Nagarajan and published by Academic Press. This book was released on 2017-11-06 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metagenomics: Perspectives, Methods, and Applications provides thorough coverage of the growing field of metagenomics. A diverse range of chapters from international experts offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools, and recent metagenomic studies in various environments. The emphasis on application makes this text particularly useful for applied researchers, practitioners, clinicians and students seeking to employ metagenomic approaches to advance knowledge in the biomedical and life sciences. Case-study based application chapters examine topics ranging from viral metagenome profiling, metagenomics in oral disease and health, metagenomic insights into the human gut microbiome and metabolic syndromes, and more. Additionally, perspectives on future potential at the end of each chapter provoke new thought and motivations for continued study in this exciting and fruitful research area. Provides thorough coverage of the rapidly growing field of metagenomics, with an emphasis on applications of relevance to translational researchers, practitioners, clinicians and students Features a diverse range of chapters from international experts that offer an introduction to the field and examine methods for metagenomic analysis of microbiota, metagenomic computational tools and research pipelines Highlights perspectives on future potential at the end of each chapter to provoke new thought and motivations for continued study in this exciting and fruitful research area

Systems-Level Modelling of Microbial Communities

Author : Aarthi Ravikrishnan
Publisher : CRC Press
ISBN 13 : 0429946066
Total Pages : 88 pages
Book Rating : 4.4/5 (299 download)

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Book Synopsis Systems-Level Modelling of Microbial Communities by : Aarthi Ravikrishnan

Download or read book Systems-Level Modelling of Microbial Communities written by Aarthi Ravikrishnan and published by CRC Press. This book was released on 2018-09-06 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.

Metagenomics of the Human Body

Author : Karen E. Nelson
Publisher : Springer Science & Business Media
ISBN 13 : 1441970894
Total Pages : 351 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Metagenomics of the Human Body by : Karen E. Nelson

Download or read book Metagenomics of the Human Body written by Karen E. Nelson and published by Springer Science & Business Media. This book was released on 2010-11-16 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book brings a completely different perspective than available books by combining the information gained from the human genome with that derived from parallel metagenomic studies, and new results from investigating the effects of these microbes on the host immune system. Although there are a number of books that focus on the human genome that are currently available, there are no books that bring to the forefront the mix of the human genome and the genomes and metagenomes of the microbial species that live within and on us.

Encyclopedia of Metagenomics

Author : Karen E. Nelson
Publisher : Springer
ISBN 13 : 9781461446743
Total Pages : 1528 pages
Book Rating : 4.4/5 (467 download)

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Book Synopsis Encyclopedia of Metagenomics by : Karen E. Nelson

Download or read book Encyclopedia of Metagenomics written by Karen E. Nelson and published by Springer. This book was released on 2015-02-18 with total page 1528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.