Pan Genomics

Author : Debmalya Barh,Siomar C. Soares,Sandeep Tiwari,Vasco Ariston De Car Azevedo
Publisher : Academic Press
Page : 476 pages
File Size : 40,7 Mb
Release : 2020-03-06
Category : Science
ISBN : 9780128170779

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Pan-genomics: Applications, Challenges, and Future Prospects by Debmalya Barh,Siomar C. Soares,Sandeep Tiwari,Vasco Ariston De Car Azevedo Pdf

Pan-genomics: Applications, Challenges, and Future Prospects covers current approaches, challenges and future prospects of pan-genomics. The book discusses bioinformatics tools and their applications and focuses on bacterial comparative genomics in order to leverage the development of precise drugs and treatments for specific organisms. The book is divided into three sections: the first, an "overview of pan-genomics and common approaches, brings the main concepts and current approaches on pan-genomics research; the second, “case studies in pan-genomics, thoroughly discusses twelve case, and the last, “current approaches and future prospects in pan-multiomics , encompasses the developments on omics studies to be applied on bacteria related studies. This book is a valuable source for bioinformaticians, genomics researchers and several members of biomedical field interested in understanding further bacterial organisms and their relationship to human health. Covers the entire spectrum of pangenomics, highlighting the use of specific approaches, case studies and future perspectives Discusses current bioinformatics tools and strategies for exploiting pangenomics data Presents twelve case studies with different organisms in order to provide the audience with real examples of pangenomics applicability

Author : Hervé Tettelin,Duccio Medini
Publisher : Springer Nature
Page : 311 pages
File Size : 55,9 Mb
Release : 2020-04-30
Category : Science
ISBN : 9783030382810

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The Pangenome by Hervé Tettelin,Duccio Medini Pdf

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Author : Alessio Mengoni,Marco Galardini,Marco Fondi
Publisher : Unknown
Page : 298 pages
File Size : 47,6 Mb
Release : 2015
Category : Bacterial genetics
ISBN : 149391720X

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Bacterial Pangenomics by Alessio Mengoni,Marco Galardini,Marco Fondi Pdf

Author : Penghao Wang,Washington Gapare,Jian Ma
Publisher : Frontiers Media SA
Page : 187 pages
File Size : 52,7 Mb
Release : 2021-11-26
Category : Science
ISBN : 9782889717040

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Pan-Genome Level Genotype and Phenotype Prediction: Advances in Precision Agriculture by Penghao Wang,Washington Gapare,Jian Ma Pdf

Author : Nils Stein,Gary J. Muehlbauer
Publisher : Springer
Page : 394 pages
File Size : 51,7 Mb
Release : 2018-08-18
Category : Science
ISBN : 9783319925288

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The Barley Genome by Nils Stein,Gary J. Muehlbauer Pdf

This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.

Author : Hervé Tettelin,Duccio Medini
Publisher : Springer
Page : 309 pages
File Size : 49,9 Mb
Release : 2020-06-07
Category : Science
ISBN : 303038280X

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The Pan-Genome by Hervé Tettelin,Duccio Medini Pdf

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Author : Maryam Javed,Asif Nadeem, Faiz-ul Hassan
Publisher : Bentham Science Publishers
Page : 202 pages
File Size : 47,7 Mb
Release : 2021-11-02
Category : Science
ISBN : 9781681089263

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Introduction to Molecular Genomics by Maryam Javed,Asif Nadeem, Faiz-ul Hassan Pdf

Introduction to Molecular Genomics introduces the college student to the fundamental concepts of molecular biology and genomics. The text puts an emphasis on important topics in the subject that contribute to the learner’s understanding. These topics include molecular genomics, biodiversity and molecular phenomenon behind evolution of species, modern molecular methods for enhanced genomics research, DNA modifications at the molecular level for transgenic animal species, the role of cell environment on the gene expression, to name a few. The book has been designed to suit the requirements of educational courses in molecular biology, genomics and biochemistry. Key features - Covers basic concepts on key topics in molecular biology and genomics - Simple easy-to-read layout - Includes references for further reading - Includes a section on ethical aspects of scientific research Introduction to Molecular Genomics is a simple primer for students in applied or advanced life science courses at undergraduate levels

Author : Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore
Publisher : Springer Nature
Page : 285 pages
File Size : 40,8 Mb
Release : 2019-11-05
Category : Science
ISBN : 9789811387395

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Microbial Genomics in Sustainable Agroecosystems by Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore Pdf

In recent decades, significant advances in new methodologies like DNA sequencing and high-throughput sequencing have been used to identify microorganisms and monitor their interactions with different environments. Microbial genomics techniques are opening new approaches to microbiology by revealing how microorganisms affect human beings and the environment. This book covers four major areas: 1) Environmental microbial genomics, 2) Microbial genomics in human health, 3) Microbial genomics in crop improvement and plant health protection, and 4) Genome analysis of microbial pathogens. Within these areas, the topics addressed include: microbial genome diversity, evolution, and microbial genome sequencing; bioinformatics and microarray-based genomic technologies; functional genomics of bioremediation of soil and water from organic and inorganic pollutants and carbon management; functional genomics of microbial pathogens and relevant microorganisms; functional genomics of model microorganisms; and applied functional genomics. Given its scope, the book offers a comprehensive source of information on the latest applications of microorganisms and microbial genomics to enhance the sustainability of agriculture and the environment.

Author : Alessio Mengoni,Marco Galardini,Marco Fondi
Publisher : Humana Press
Page : 298 pages
File Size : 42,8 Mb
Release : 2014-10-24
Category : Science
ISBN : 1493917218

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Bacterial Pangenomics by Alessio Mengoni,Marco Galardini,Marco Fondi Pdf

Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science. Thanks to the large diffusion of bacterial genome analysis, Bacterial Pangenomics: Methods and Protocols is able to provide the most recent methodologies about the study of bacterial pangenomes by covering the three major areas: the experimental methods for approaching bacterial pangenomics, the bio informatic pipelines for analysis and annotation of sequence data and finally the methods for inferring functional and evolutionary features from the pangenome. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Bacterial Pangenomics: Methods and Protocols will serve as a field guide for both qualified bacterial genomics investigators who want to update their technical knowledge, for less experienced researchers who want to start working with bacterial genomics and pangenomics, as well as serving as a manual and supplemental textbook for graduate students of genomics and bioinformatics.

Author : Hervé Tettelin,Duccio Medini
Publisher : Unknown
Page : 310 pages
File Size : 51,6 Mb
Release : 2020-10-09
Category : Science
ISBN : 1013277074

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The Pangenome by Hervé Tettelin,Duccio Medini Pdf

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book's respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Author : David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini
Publisher : Springer Science & Business Media
Page : 272 pages
File Size : 51,5 Mb
Release : 2009-02-26
Category : Science
ISBN : 9781848002548

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Computing for Comparative Microbial Genomics by David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini Pdf

Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Author : Manjit S. Kang
Publisher : CABI
Page : 433 pages
File Size : 55,6 Mb
Release : 2020-04-01
Category : Science
ISBN : 9781789240214

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Quantitative Genetics, Genomics and Plant Breeding, 2nd Edition by Manjit S. Kang Pdf

This book presents state-of-the-art, authoritative chapters on contemporary issues in the broad areas of quantitative genetics, genomics and plant breeding. Section 1 (Chapters 2 to 12) emphasizes the application of genomics, and genome and epigenome editing techniques, in plant breeding; bioinformatics; quantitative trait loci mapping; and the latest approaches of examining and exploiting genotype-environment interactions. Section 2 (Chapters 13 to 20) represents the intersection of breeding, genetics and genomics. This section describes the use of cutting-edge molecular breeding and quantitative genetics techniques in wheat, rice, maize, root and tuber crops and pearl millet. Overall, the book focuses on using genomic information to help evaluate traits that can combat biotic/abiotic stresses, genome-wide association mapping, high-throughput genotyping/phenotyping, biofortification, use of big data, orphan crops, and gene editing techniques. The examples featured are taken from across crop science research and cover a wide geographical base.

Author : Jeffrey Bennetzen,Sherry Flint-Garcia,Candice Hirsch,Roberto Tuberosa
Publisher : Springer
Page : 390 pages
File Size : 47,8 Mb
Release : 2018-11-24
Category : Science
ISBN : 9783319974279

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The Maize Genome by Jeffrey Bennetzen,Sherry Flint-Garcia,Candice Hirsch,Roberto Tuberosa Pdf

This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.

Author : Alejandro Pereira-Santana,Samuel David Gamboa-Tuz,Luis Carlos Rodríguez-Zapata
Publisher : Springer Nature
Page : 293 pages
File Size : 42,5 Mb
Release : 2022-07-11
Category : Science
ISBN : 9781071624296

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Plant Comparative Genomics by Alejandro Pereira-Santana,Samuel David Gamboa-Tuz,Luis Carlos Rodríguez-Zapata Pdf

This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.

Author : National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences
Publisher : National Academies Press
Page : 201 pages
File Size : 48,8 Mb
Release : 2020-12-18
Category : Science
ISBN : 9780309676731

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Next Steps for Functional Genomics by National Academies of Sciences, Engineering, and Medicine,Division on Earth and Life Studies,Board on Life Sciences Pdf

One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.