Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approaches for conducting new research. Early chapters introduce phylogenomic taxonomies of organisms and pathogens, phylogenomic networks, phylogenomics of virus virulence, and ancient DNA analysis, with a second section offering methods, detailed descriptions and step-by-step instruction in genome assembly and annotation, horizontal gene transfer studies, Bayesian evaluation, phylogenetic tree building, microbial evolution modeling, and molecular epidemiology.
The book's final section offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Shigella, Vibrio cholera, and Mycobacterium tuberculosis, amongst others.
- Offers a full overview of phylogenetics and phylogenomics, from its foundations to methods and specialized case studies
- Presents methodologies and algorithms for phylogenomic research studies and analyzes medically significant microorganisms
- Considers examples of phylogenomic analysis across a range of medically significant pathogens
- Includes chapter contributions from leading international experts
Sprache
Verlagsort
Verlagsgruppe
Elsevier Science & Techn.
Dateigröße
ISBN-13
978-0-323-91309-6 (9780323913096)
Schweitzer Klassifikation
PART I. GENERAL TOPICS AND FOUNDATIONS1. Phylogenomic analysis and the origin and early evolution of viruses2. Application of Next Generation Sequencing for Genetic and Phenotypic Studies of Bacteria 3. Genomic insight into deciphering bacterial outbreaks 4. Drug resistance in bacteria, molecular mechanisms and evolution 5. Virulence evolution of bacterial species PART II. METHODS IN THE PHYLOGENOMICS 6. Modeling evolutionary changes of k-mer patterns of bacterial genomes 7. Clock Rates and Bayesian Evaluation of Temporal Signal 8. Microbial evolutionary reconstruction in the presence of mosaic sequences9. Tools for SNP calling and the way to deal with big datasetsPART III. PHYLOGENOMICS OF SPECIFIC PATHOGENS 10. Phylogenomics of Yersinia pestis 11. Salmonella Phylogenomics12. The phylogenomics of Shigella spp. 13. Phylogenomic diversity within Corynebacterium diphtheriae, a re-emerging threat to global public health14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis15. Mycobacterium kansasii16. Taxonomy and phylogenomics of Leptospira 17. Phylogenomics and evolution of Measles virus18. Phylogenomics of HIV-119. Respiratory syncytial virus20. Phylogenomics of Flaviviruses 21. How clonal is Staphylococcus aureus? 22. Genomic research of ancient pathogens in Central Asia23. Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution (PCE) model 24. Phylogenomics of Mycobacterium leprae
