Preface
Duccio Medini, Hervé Tettelin
Section 1. Genomic diversity and the pan-genome concept
1.1 -The pan-genome: a data-drivendiscovery in biology
Duccio Medini, Claudio Donati, Rino Rappuoli, Hervé Tettelin1.2 -The prokaryotic species concept and challenges
Louis-Marie Bobay1.3 -Bacterial guide on how to design a diversified gene portfolio
Katherine A. Innamorati, Joshua P. Earl, Surya D. Aggarwal, Garth D. Ehrlich, N. Luisa Hiller
1.4 -A review of pan-genome tools and recent studies
George Vernikos
Section2. Evolutionary biology of pan-genomes
2.1 -Structure and dynamics of bacterial populations: pan-genome ecology
Taj Azarian, I-Ting Huang, William P. Hanage
2.2 -Bacterial microevolution and the pan-genome
Florent Lasalle, Xavier Didelot
2.3 -Pan-genomes and selection: the public goods hypothesis
James O. McInerney, Fiona J. Whelan, Maria Rosa Domingo-Sananes, Alan McNally, Mary J. O'Connell
2.4 -A pan-genomic perspective on the emergence, maintenance and predictability of antibiotic resistance
Stephen Wood, Karen Zhu, DefneSurujon, Federico Rosconi, Juan C. Ortiz-Marquez, Tim van Opijnen
Section 3. Pan-genomics: an open, evolving discipline
3.1 -Metapangenome: at the crossroad of pangenomics and metagenomics
Bing Ma, Michael France, Jacques Ravel
3.2 -Pan-genome flux balance analysis towards pan-phenomes
Charles J. Norsigian, Xin Fang, Bernhard O. Palsson, Jonathan M. Monk
3.3 -Bacterial epigenomics: epigenetics in the age of population genomics
Poyin Chen, D.J. Darwin Bandoy, Bart C. Weimer
3.4 -Eukaryotic pan-genomes
Guy-Franck Richard
3.5 -Computational strategies for eukaryotic pan-genome analyses
Zhiqiang Hu, Chaochun Wei, Zhikang Li
About the Author: 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(R) (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.
