Overview

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.

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9780323998864

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Igor Mokrousov, 53 years old, PhD, DSc, is the Head of Laboratory of Molecular Epidemiology and Evolutionary Genetics at St. Petersburg Pasteur Institute, Russia. His research interests include study of evolution, phylogenomics, and molecular epidemiology of tuberculosis; phylogeography of Mycobacterium tuberculosis and co-evolution with humans; molecular mechanisms and genotypic detection of drug resistance. His current projects focus on the application of next-generation sequencing for genome-wide analysis to understand the pathogenetic characteristics and evolutionary trajectory of various M. tuberculosis lineages and emerging clones. Dr Mokrousov made a recognized contribution to the study of human-M. tuberculosis coevolution and put forward a hypothesis that evolutionary histories of H. sapiens and human pathogens are comirrored and coshaped. He proposed a new simple measure of genetic distance between geographic populations within a microbial species based on the observed difference in the frequencies of its genotypes. 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.

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