The Pangenome: Diversity, Dynamics and Evolution of Genomes
Editat de Hervé Tettelin, Duccio Medinien Limba Engleză Paperback – 18 sep 2020
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.
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Specificații
ISBN-13: 9783030382834
ISBN-10: 3030382834
Pagini: 307
Ilustrații: XIV, 307 p. 47 illus., 43 illus. in color.
Dimensiuni: 155 x 235 mm
Greutate: 0.45 kg
Ediția:1st ed. 2020
Editura: Springer International Publishing
Colecția Springer
Locul publicării:Cham, Switzerland
ISBN-10: 3030382834
Pagini: 307
Ilustrații: XIV, 307 p. 47 illus., 43 illus. in color.
Dimensiuni: 155 x 235 mm
Greutate: 0.45 kg
Ediția:1st ed. 2020
Editura: Springer International Publishing
Colecția Springer
Locul publicării:Cham, Switzerland
Cuprins
Part 1: Genomic diversity and the pan-genome concept.- Chapter 1: The pan-genome: a data-drivendiscovery in biology.- Chapter 2: The prokaryotic species concept and challenges.- Chapter 3: Bacterial guide on how to design a diversified gene portfolio.- Chapter 4: A review of pan-genome tools and recent studies.- Part 2: Evolutionary biology of pan-genomes.- Chapter 5: Structure and dynamics of bacterial populations: pan-genome ecology.- Chapter 6: Bacterial microevolution and the pan-genome.- Chapter 7: Pan-genomes and selection: the public goods hypothesis.- Chapter 8: A pan-genomic perspective on the emergence, maintenance and predictability of antibiotic resistance.- Part 3: Pan-genomics: an open, evolving discipline.- Chapter 9: Metapangenome: at the crossroad of pangenomics and metagenomics.- Chapter 10: Pan-genome flux balance analysis towards pan-phenomes.- Chapter 11: Bacterial epigenomics: epigenetics in the age of population genomics.- Chapter 12: Eukaryotic pan-genomes.- Chapter 13: Computational strategies for eukaryotic pan-genome analyses.
Notă biografică
Hervé Tettelin
Dr. Tettelin is a Professor of Microbiology and Immunology at the University of Maryland School of Medicine, Institute for Genome Sciences. Over the course of his career, Dr. Tettelin developed an extensive expertise in microbial genomics, functional genomics, comparative genomics, and bioinformatics.
He led seminal genome sequencing and analysis projects for many important human bacterial pathogens and related commensals, including the initial genomes of Streptococcus agalactiae (group B Streptococcus, GBS).
In collaboration with the group of Dr. Rino Rappuoli (GlaxoSmithKline, former Chiron Vaccines and Novartis Vaccines and Diagnostics), Dr. Tettelin pioneered the fields of reverse vaccinology and pan-genome analyses. The former makes use of genomics to identify novel protein candidates for vaccine development, which was first applied to Neisseria meningitidis; this approach resulted in the recent commercialization of the Bexsero® (4CMenB) vaccine. The latter is the focus of this book.
Dr. Tettelin has conducted many studies of bacterial diversity and transcriptional profiling using DNA microarrays and RNA-seq, as well as functional genomics analyses to identify genes essential for virulence using Tn-seq. He has also supervised the development of bioinformatics tools to compare closely related bacterial genomes in the context of infectious diseases.
Duccio MediniDr. Duccio Medini is a Data Scientist and Pharma Executive, currently serving as Head of Data Science and Digital Innovation for GSK Vaccines Research and Development.
After graduating in Theoretical Physics and receiving his Ph.D. in Biophysics from the University of Perugia, Italy, and the Northeastern University in Boston, MA., Dr. Medini dedicated his activity at solving biological problems that impact human health globally, by extracting knowledge from genomic, epidemiological, preclinical and clinical data with advanced analytics and data-driven computing.
He studied the diversity of bacterial populations leading to the discovery of the pan-genome concept, solving the pan-genome structure and dynamics of several pathogens; he contributed to the development of the first universal vaccine against serogroup B meningitis, and led the Meningococcal Antigen Typing System (MATS) platform worldwide. Recently he focused on elucidating the mechanisms of action of vaccines and their impact on infectious diseases through complex systems methodologies, and initiated a radical, patient-centric re-design of the data models and infrastructure underpinning clinical vaccines research. He has published 40+ scientific articles, book chapters and patents, on the population genomics of bacteria and on mathematical modelling of vaccine effects.
Dr. Medini is Full Professor of Molecular Biology and member of international PhD school committees at the Perugia and Turin Universities in Italy, honorary member of the Cuban Immunology Society, Research Fellow of the ISI Foundation, Oversees Fellow of the Royal Society of Medicine, member of the International Society for Computational Biology.
Dr. Tettelin is a Professor of Microbiology and Immunology at the University of Maryland School of Medicine, Institute for Genome Sciences. Over the course of his career, Dr. Tettelin developed an extensive expertise in microbial genomics, functional genomics, comparative genomics, and bioinformatics.
He led seminal genome sequencing and analysis projects for many important human bacterial pathogens and related commensals, including the initial genomes of Streptococcus agalactiae (group B Streptococcus, GBS).
In collaboration with the group of Dr. Rino Rappuoli (GlaxoSmithKline, former Chiron Vaccines and Novartis Vaccines and Diagnostics), Dr. Tettelin pioneered the fields of reverse vaccinology and pan-genome analyses. The former makes use of genomics to identify novel protein candidates for vaccine development, which was first applied to Neisseria meningitidis; this approach resulted in the recent commercialization of the Bexsero® (4CMenB) vaccine. The latter is the focus of this book.
Dr. Tettelin has conducted many studies of bacterial diversity and transcriptional profiling using DNA microarrays and RNA-seq, as well as functional genomics analyses to identify genes essential for virulence using Tn-seq. He has also supervised the development of bioinformatics tools to compare closely related bacterial genomes in the context of infectious diseases.
Duccio MediniDr. Duccio Medini is a Data Scientist and Pharma Executive, currently serving as Head of Data Science and Digital Innovation for GSK Vaccines Research and Development.
After graduating in Theoretical Physics and receiving his Ph.D. in Biophysics from the University of Perugia, Italy, and the Northeastern University in Boston, MA., Dr. Medini dedicated his activity at solving biological problems that impact human health globally, by extracting knowledge from genomic, epidemiological, preclinical and clinical data with advanced analytics and data-driven computing.
He studied the diversity of bacterial populations leading to the discovery of the pan-genome concept, solving the pan-genome structure and dynamics of several pathogens; he contributed to the development of the first universal vaccine against serogroup B meningitis, and led the Meningococcal Antigen Typing System (MATS) platform worldwide. Recently he focused on elucidating the mechanisms of action of vaccines and their impact on infectious diseases through complex systems methodologies, and initiated a radical, patient-centric re-design of the data models and infrastructure underpinning clinical vaccines research. He has published 40+ scientific articles, book chapters and patents, on the population genomics of bacteria and on mathematical modelling of vaccine effects.
Dr. Medini is Full Professor of Molecular Biology and member of international PhD school committees at the Perugia and Turin Universities in Italy, honorary member of the Cuban Immunology Society, Research Fellow of the ISI Foundation, Oversees Fellow of the Royal Society of Medicine, member of the International Society for Computational Biology.
Textul de pe ultima copertă
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.
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.
Caracteristici
This open access book covers the fundamental impacts of intra-species genomic diversity Focuses on the evolutionary biology of pan-genomes Elaborates on computational strategies and mathematical models for pan-genome analysis Discusses cutting-edge concepts such as pan-phenomes and pan-epigenomes