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Showing 1–8 of 8 results
Advanced filters: Author: Sergey A. Shmakov Clear advanced filters

  • Sergey A. Shmakov et al. investigate the origin of the CRISPR spacers. They examine the distribution of partial matches between the spacers, viral genomes, and the host genomes and report that most of the spacers originate from host specific viromes. They demonstrate that most of the viruses are unknown although are likely related to known viruses.

    • Sergey A. Shmakov
    • Yuri I. Wolf
    • Eugene V. Koonin
    ResearchOpen Access
    Communications Biology
    Volume: 3, P: 1-9

  • CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude.

    • Ayal B. Gussow
    • Allyson E. Park
    • Eugene V. Koonin
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-12

  • This computational protocol functionally links bacterial or archaeal genes within a dataset, enabling reliable functional predictions to be extracted for uncharacterized genes. As one example, the authors describe the ‘CRISPRicity’ metric to link genes to CRISPR–Cas systems.

    • Sergey A. Shmakov
    • Guilhem Faure
    • Eugene V. Koonin
    Protocols
    Nature Protocols
    Volume: 14, P: 3013-3031

  • Class 2 CRISPR–Cas systems are characterized by effector modules that consist of a single multidomain protein. In this Analysis, using a computational pipeline, the authors discover three novel families of class 2 effectors that correspond to three new CRISPR–Cas subtypes and present a comprehensive census of class 2 systems that are encoded in complete and draft bacterial and archaeal genomes.

    • Sergey Shmakov
    • Aaron Smargon
    • Eugene V. Koonin
    Research
    Nature Reviews Microbiology
    Volume: 15, P: 169-182

  • CRISPR–Cas systems in bacteria and archaea have multifaceted evolutionary relationships with mobile genetic elements (MGEs), including viruses, plasmids and transposons. CRISPR–Cas systems or their components have also been recruited by MGEs on many independent occasions. In this Analysis article, Koonin and colleagues investigate and substantially expand the range of CRISPR–Cas components carried by MGEs.

    • Guilhem Faure
    • Sergey A. Shmakov
    • Eugene V. Koonin
    Research
    Nature Reviews Microbiology
    Volume: 17, P: 513-525

  • The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. In this Review, Koonin and colleagues provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on major developments, and outline a complete scenario for the origins and evolution of CRISPR–Cas systems.

    • Kira S. Makarova
    • Yuri I. Wolf
    • Eugene V. Koonin
    Reviews
    Nature Reviews Microbiology
    Volume: 18, P: 67-83