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  • Open Access
  • © 2020

The Pangenome

Diversity, Dynamics and Evolution of Genomes

  • 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

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Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)

Table of contents (13 chapters)

  1. Front Matter

    Pages i-xiv
  2. Genomic Diversity and the Pangenome Concept

    1. Front Matter

      Pages 1-1
    2. The Pangenome: A Data-Driven Discovery in Biology

      • Duccio Medini, Claudio Donati, Rino Rappuoli, Hervé Tettelin
      Pages 3-20Open Access
    3. The Prokaryotic Species Concept and Challenges

      • Louis-Marie Bobay
      Pages 21-49Open Access
    4. The Bacterial Guide to Designing a Diversified Gene Portfolio

      • Katherine A. Innamorati, Joshua P. Earl, Surya D. Aggarwal, Garth D. Ehrlich, N. Luisa Hiller
      Pages 51-87Open Access
    5. A Review of Pangenome Tools and Recent Studies

      • G. S. Vernikos
      Pages 89-112Open Access
  3. Evolutionary Biology of Pangenomes

    1. Front Matter

      Pages 113-113
    2. Structure and Dynamics of Bacterial Populations: Pangenome Ecology

      • Taj Azarian, I-Ting Huang, William P. Hanage
      Pages 115-128Open Access
    3. Bacterial Microevolution and the Pangenome

      • Florent Lassalle, Xavier Didelot
      Pages 129-149Open Access
    4. Pangenomes and Selection: The Public Goods Hypothesis

      • James O. McInerney, Fiona J. Whelan, Maria Rosa Domingo-Sananes, Alan McNally, Mary J. O’Connell
      Pages 151-167Open Access
    5. A Pangenomic Perspective on the Emergence, Maintenance, and Predictability of Antibiotic Resistance

      • Stephen Wood, Karen Zhu, Defne Surujon, Federico Rosconi, Juan C. Ortiz-Marquez, Tim van Opijnen
      Pages 169-202Open Access
  4. Pangenomics: An Open, Evolving Discipline

    1. Front Matter

      Pages 203-203
    2. Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics

      • Bing Ma, Michael France, Jacques Ravel
      Pages 205-218Open Access
    3. Pangenome Flux Balance Analysis Toward Panphenomes

      • Charles J. Norsigian, Xin Fang, Bernhard O. Palsson, Jonathan M. Monk
      Pages 219-232Open Access
    4. Bacterial Epigenomics: Epigenetics in the Age of Population Genomics

      • Poyin Chen, D. J. Darwin Bandoy, Bart C. Weimer
      Pages 233-252Open Access
    5. Eukaryotic Pangenomes

      • Guy-Franck Richard
      Pages 253-291Open Access
    6. Computational Strategies for Eukaryotic Pangenome Analyses

      • Zhiqiang Hu, Chaochun Wei, Zhikang Li
      Pages 293-307Open Access

About this book

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.


Keywords

  • Comparative genomics
  • Metagenomics
  • Microbial Population Analysis
  • Pangenome Profile
  • Supra-Genome Analysis
  • Adaptive Evolution
  • Computational Tools
  • Bioinformatic Genomics
  • Core Dispensable Genome
  • Selection, Recombination, Composition
  • Acquired Resistance
  • Bacterial Species Concept
  • Genomic Diversity
  • Bacterial Ecology, Microevolution
  • Open Access
  • Pan-metagenomics
  • Pan-microbiomics
  • Pan-epigenome
  • Gene Transfer
  • Pan-phenomes

Editors and Affiliations

  • Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA

    Hervé Tettelin

  • GSK Vaccines R&D, Siena, Italy

    Duccio Medini

About the editors

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 Medini

Dr. 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.


Bibliographic Information

Buying options

Softcover Book USD 59.99
Price excludes VAT (USA)
Hardcover Book USD 59.99
Price excludes VAT (USA)