Phylogenomics Foundations, Methods, and Pathogen Analysis
Coordonnateurs : Mokrousov Igor, Shitikov Egor
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 analysis of viruses and bacteria, deciphering bacterial outbreaks, and evolution of drug resistance and virulence, with a second section on methods offering instruction in tools for SNP calling and dealing with big datasets, use of Bayesian approach in molecular epidemiology, bacterial evolution modeling and evolutionary reconstruction in the presence of mosaic sequences. Part 3 offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Mycobacterium tuberculosis, HIV-1, measles virus as well as ancient pathogens research.
PART I. GENERAL TOPICS AND FOUNDATIONS 1. Phylogenomic analysis and the origin and early evolution of viruses 2. 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 sequences 9. Tools for SNP calling and the way to deal with big datasets PART III. PHYLOGENOMICS OF SPECIFIC PATHOGENS 10. Phylogenomics of Yersinia pestis 11. Salmonella Phylogenomics 12. The phylogenomics of Shigella spp. 13. Phylogenomic diversity within Corynebacterium diphtheriae, a re-emerging threat to global public health 14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis 15. Mycobacterium kansasii 16. Taxonomy and phylogenomics of Leptospira 17. Phylogenomics and evolution of Measles virus 18. Phylogenomics of HIV-1 19. Respiratory syncytial virus 20. Phylogenomics of Flaviviruses 21. How clonal is Staphylococcus aureus? 22. Genomic research of ancient pathogens in Central Asia 23. Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution (PCE) model 24. Phylogenomics of Mycobacterium leprae
Egor Shitikov, PhD, is the Head of Laboratory of Molecular Genetics of Microorganisms at Federal Research and Clinical Center of Physical-Chemical Medicine, Russia. His research interests are closely related to the systematic analysis of Mycobacterium tuberculosis: phylogenetic relationship of various strains, their definition and classification; the search for new drug-resistance determinants, virulence factors, and pathogenicity; development of rapid screening systems for certain pathogen groups; experiments on model organisms. The current topic focuses on the deep machine learning methods in Mycobacterium tuberculosis genomics for the building of an open platform for the analysis of the pathogen’s evolutionary signatures.
- 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
Date de parution : 05-2024
Ouvrage de 520 p.
19x23.3 cm
