The Pan Genome

Author : Hervé Tettelin,Duccio Medini
Publisher : Springer Nature
Page : 311 pages
File Size : 53,9 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 : Debmalya Barh,Siomar C. Soares,Sandeep Tiwari,Vasco Ariston De Car Azevedo
Publisher : Academic Press
Page : 476 pages
File Size : 42,8 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 : Unknown
Page : 310 pages
File Size : 48,8 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 : Nils Stein,Gary J. Muehlbauer
Publisher : Springer
Page : 394 pages
File Size : 51,8 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 : 51,8 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 : Alessio Mengoni,Marco Galardini,Marco Fondi
Publisher : Unknown
Page : 298 pages
File Size : 41,9 Mb
Release : 2015
Category : Bacterial genetics
ISBN : 149391720X

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

Author : Jeffrey Bennetzen,Sherry Flint-Garcia,Candice Hirsch,Roberto Tuberosa
Publisher : Springer
Page : 390 pages
File Size : 44,6 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 : Penghao Wang,Washington Gapare,Jian Ma
Publisher : Frontiers Media SA
Page : 187 pages
File Size : 41,9 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 : Henry T. Nguyen,Madan Kumar Bhattacharyya
Publisher : Springer
Page : 211 pages
File Size : 42,7 Mb
Release : 2017-09-20
Category : Science
ISBN : 9783319641980

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The Soybean Genome by Henry T. Nguyen,Madan Kumar Bhattacharyya Pdf

This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.

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 : 52,8 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.

Author : Joao Carlos Setubal,Peter F. Stadler,Jens Stoye
Publisher : Humana
Page : 0 pages
File Size : 45,7 Mb
Release : 2024-06-22
Category : Science
ISBN : 1071638378

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Comparative Genomics by Joao Carlos Setubal,Peter F. Stadler,Jens Stoye Pdf

This second edition provides new and updated chapters covering computational and mathematical techniques and concepts related to the field of comparative genomics. The topics covered in the chapters range from those that address general techniques and concepts that apply to all organisms to others that are specialized and apply to specific biological systems such as viruses, bacteria, nematodes, and insects. Well-known comparative genomics web-based platforms are also covered in specific chapters. Written in the highly successful Methods in Molecular Biology series format, many chapters include introductions to their respective topics and step-by-step comparison procedures, demonstrated on actual sets of genome sequences. Authoritative and cutting-edge, Comparative Genomics: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

Author : Veli Mäkinen,Djamal Belazzougui,Fabio Cunial,Alexandru I. Tomescu
Publisher : Cambridge University Press
Page : 470 pages
File Size : 53,8 Mb
Release : 2023-10-12
Category : Computers
ISBN : 9781009341219

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Genome-Scale Algorithm Design by Veli Mäkinen,Djamal Belazzougui,Fabio Cunial,Alexandru I. Tomescu Pdf

Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.

Author : Dinesh Adhikary,Michael K. Deyholos,John P. Délano-Frier
Publisher : Springer Nature
Page : 181 pages
File Size : 51,7 Mb
Release : 2021-06-01
Category : Science
ISBN : 9783030723651

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The Amaranth Genome by Dinesh Adhikary,Michael K. Deyholos,John P. Délano-Frier Pdf

This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

Author : Richard C. Deonier,Simon Tavaré,Michael S. Waterman
Publisher : Springer Science & Business Media
Page : 543 pages
File Size : 47,7 Mb
Release : 2005-12-27
Category : Computers
ISBN : 9780387288079

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Computational Genome Analysis by Richard C. Deonier,Simon Tavaré,Michael S. Waterman Pdf

This book presents the foundations of key problems in computational molecular biology and bioinformatics. It focuses on computational and statistical principles applied to genomes, and introduces the mathematics and statistics that are crucial for understanding these applications. The book features a free download of the R software statistics package and the text provides great crossover material that is interesting and accessible to students in biology, mathematics, statistics and computer science. More than 100 illustrations and diagrams reinforce concepts and present key results from the primary literature. Exercises are given at the end of chapters.

Author : Rajeev K. Varshney,Mahendar Thudi,Fred Muehlbauer
Publisher : Springer
Page : 142 pages
File Size : 44,8 Mb
Release : 2018-01-02
Category : Science
ISBN : 9783319661179

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The Chickpea Genome by Rajeev K. Varshney,Mahendar Thudi,Fred Muehlbauer Pdf

This book sheds new light on the chickpea genome sequencing and resequencing of chickpea germplasm lines and provides insights into classical genetics, cytogenetics, and trait mapping. It also offers an overview of the latest advances in genome sequencing and analysis. The growing human population, rapid climate changes and limited amounts of arable land are creating substantial challenges in connection with the availability and affordability of nutritious food for smallholder farmers in developing countries. In this context, climate smart crops are essential to alleviating the hunger of the millions of poor and undernourished people living in developing countries. In addition to cereals, grain legumes are an integral part of the human diet and provide sustainable income for smallholder farmers in the arid and semi-arid regions of the world. Among grain legumes, the chickpea (Cicer arietinum) is the second most important in terms of production and productivity. Besides being a rich source of proteins, it can fix atmospheric nitrogen through symbiosis with rhizobia and increase the input of combined nitrogen. Several abiotic stresses like drought, heat, salinity, together with biotic stresses like Fusarium wilt, Ascochyta blight, and Botrytis grey mould have led to production losses, as the chickpeas is typically grown in the harsh climates of our planet’s semi-arid regions.