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.
1. Phylogenomics - p. Page i 2. Cover - p. Page i 3. Title page - p. Page ii 4. Table of Contents - p. Page iii 5. Copyright - p. Page iii 6. Contents - p. Page vi 7. List of contributors - p. Page vii 8. Preface - p. Page vii 9. List of Illustrations - p. Page x 10. List of Tables - p. Page xi 11. Chapter 1 : Phylogenomic analysis and the origin and early evolution of viruses - p. Page xi 12. Chapter 2 : Application of next-generation sequencing for genetic and phenotypic studies of bacteria - p. Page 31 13. Chapter 3 : Genomic insights into deciphering bacterial outbreaks - p. Page 57 14. Chapter 4 : Drug resistance in bacteria, molecular mechanisms, and evolution - p. Page 74 15. Chapter 5 : Virulence evolution of bacterial species - p. Page 98 16. Chapter 6 : Modeling evolutionary changes of k-mer patterns of bacterial genomes - p. Page 124 17. Chapter 7 : Clock rates and Bayesian evaluation of temporal signal - p. Page 151 18. Chapter 8 : Microbial evolutionary reconstruction in the presence of mosaic sequences - p. Page 172 19. Chapter 9 : Tools for short variant calling and the way to deal with big datasets - p. Page 205 20. Chapter 10 : Phylogenomics of Yersinia pestis - p. Page 243 21. Chapter 11 : Salmonella phylogenomics - p. Page 263 22. Chapter 12 : The phylogenomics of Shigella spp. - p. Page 278 23. Chapter 13 : Phylogenomic diversity within Corynebacterium diphtheriae, a reemerging threat to global public health - p. Page 299 24. Chapter 14 : Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis - p. Page 316 25. Chapter 15 : Population genomics of Mycobacterium kansasii - p. Page 338 26. Chapter 16 : Taxonomy and phylogenomics of Leptospira - p. Page 356 27. Chapter 17 : Phylogenomics and evolution of measles virus - p. Page 385 28. Chapter 18 : Phylogenomics of human immunodeficiency virus type 1 (HIV-1) - p. Page 407 29. Chapter 19 : Respiratory syncytial viruses - p. Page 433 30. Chapter 20 : The phylogenomics of flaviviruses - p. Page 455 31. Chapter 21 : How clonal is Staphylococcus aureus? - p. Page 498 32. Chapter 22 : Genomic research of ancient pathogens in Central Asia - p. Page 519 33. Chapter 23 : Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution model - p. Page 539 34. Chapter 24 : Phylogenomics of Mycobacterium leprae - p. Page 550 35. Index - p. Page 573
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.
1. Phylogenomics - p. Page i 2. Cover - p. Page i 3. Title page - p. Page ii 4. Table of Contents - p. Page iii 5. Copyright - p. Page iii 6. Contents - p. Page vi 7. List of contributors - p. Page vii 8. Preface - p. Page vii 9. List of Illustrations - p. Page x 10. List of Tables - p. Page xi 11. Chapter 1 : Phylogenomic analysis and the origin and early evolution of viruses - p. Page xi 12. Chapter 2 : Application of next-generation sequencing for genetic and phenotypic studies of bacteria - p. Page 31 13. Chapter 3 : Genomic insights into deciphering bacterial outbreaks - p. Page 57 14. Chapter 4 : Drug resistance in bacteria, molecular mechanisms, and evolution - p. Page 74 15. Chapter 5 : Virulence evolution of bacterial species - p. Page 98 16. Chapter 6 : Modeling evolutionary changes of k-mer patterns of bacterial genomes - p. Page 124 17. Chapter 7 : Clock rates and Bayesian evaluation of temporal signal - p. Page 151 18. Chapter 8 : Microbial evolutionary reconstruction in the presence of mosaic sequences - p. Page 172 19. Chapter 9 : Tools for short variant calling and the way to deal with big datasets - p. Page 205 20. Chapter 10 : Phylogenomics of Yersinia pestis - p. Page 243 21. Chapter 11 : Salmonella phylogenomics - p. Page 263 22. Chapter 12 : The phylogenomics of Shigella spp. - p. Page 278 23. Chapter 13 : Phylogenomic diversity within Corynebacterium diphtheriae, a reemerging threat to global public health - p. Page 299 24. Chapter 14 : Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis - p. Page 316 25. Chapter 15 : Population genomics of Mycobacterium kansasii - p. Page 338 26. Chapter 16 : Taxonomy and phylogenomics of Leptospira - p. Page 356 27. Chapter 17 : Phylogenomics and evolution of measles virus - p. Page 385 28. Chapter 18 : Phylogenomics of human immunodeficiency virus type 1 (HIV-1) - p. Page 407 29. Chapter 19 : Respiratory syncytial viruses - p. Page 433 30. Chapter 20 : The phylogenomics of flaviviruses - p. Page 455 31. Chapter 21 : How clonal is Staphylococcus aureus? - p. Page 498 32. Chapter 22 : Genomic research of ancient pathogens in Central Asia - p. Page 519 33. Chapter 23 : Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution model - p. Page 539 34. Chapter 24 : Phylogenomics of Mycobacterium leprae - p. Page 550 35. Index - p. Page 573
