Foundations, Methods, and Pathogen Analysis

1st Edition - October 1, 2023

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  • Editors: Igor Mokrousov, Egor Shitikov
  • Paperback ISBN: 9780323998864

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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 on methods offering 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. Part 3 offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Shigella, Vibrio cholera, and Mycobacterium tuberculosis, among others.

Key Features

  • 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 analysis medically significant microorganisms
  • Considers examples of phylogenomic analysis across a range of medically significant pathogens
  • Includes chapter contributions from leading international experts


Researchers in Genomics, Genetics, Pathology, Epidemiology, Developmental Biology, Evolutionary Biology, Microbiology, and Immunology, Students and clinicians

Table of Contents

    1. Genome-based taxonomy of viruses
    2. Genome-based taxonomy of Bacteria
    3. Pangenome
    4. Horizontal Gene Transfer and the History of Life
    5. Genomic insight into deciphering bacterial outbreaks
    6. Evolution of bacterial resistance
    7. Evolution of bacterial virulence
    8. Ancient DNA and contribution to dating the emergence and evolutionary reconstruction in bacterial pathogens

    9. Bayesian Evaluation of Temporal Signal
    10. Phylogenomic networks and new insight into evolutionary reconstruction
    11. Maximum Likelihood Tree Building Methods

    12. Yersinia pestis
    13. Salmonella
    14. Shigella   
    15. Corynebacterium diphtheria
    16. Phylogenomics of Mycobacterium tuberculosis Beijing genotype
    17. Mycobacterium kansasii
    18. Leptospira
    19. Measles virus
    20. Dengue and Zika viruses
    21. Human immunodeficiency virus
    22. SARS-CoV-2
    23. Respiratory RSV viruses
    24. Flaviviruses (beyond Zika and Dengue)
    25. Norovirus

Product details

  • No. of pages: 520
  • Language: English
  • Copyright: © Academic Press 2023
  • Published: October 1, 2023
  • Imprint: Academic Press
  • Paperback ISBN: 9780323998864

About the Editors

Igor Mokrousov

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.

Affiliations and Expertise

Head of the Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, Russia

Egor Shitikov

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.

Affiliations and Expertise

Head of the Laboratory of Molecular Genetics of Microorganisms, Federal Research and Clinical Center of Physical-Chemical Medicine, Russia

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