Eugene V. Koonin
National Institutes of Health
GeneComparative genomicsGenomePeptide sequenceGenome evolutionGenomicsPhylogenetic treeConserved sequenceSequence alignmentGeneticsArchaeaDNABiochemistryRNAComputational biologyEvolutionary biologyBiologyPhylogeneticsHorizontal gene transferCRISPR
1,079Publications
218H-index
152kCitations
Publications 1031
Newest
#1Sofiya Garushyants (NIH: National Institutes of Health)
#2Igor B. RogozinH-Index: 71
Last. Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
view all 0 authors...
The appearance of multiple new SARS-CoV-2 variants during the winter of 2020-2021 is a matter of grave concern. Some of these new variants, such as B.1.351 and B.1.1.17, manifest higher infectivity and virulence than the earlier SARS-CoV-2 variants, with potential dramatic effects on the course of the COVID-19 pandemic. So far, analysis of new SARS-CoV-2 variants focused primarily on point nucleotide substitutions and short deletions that are readily identifiable by comparison to consensus genom...
Source
#1Sean Benler (NIH: National Institutes of Health)H-Index: 3
#2Guilhem Faure (Broad Institute)H-Index: 18
Last. Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
view all 0 authors...
Transposition is a major mechanism of horizontal gene mobility in prokaryotes. However, exploration of the genes mobilized by transposons (cargo) is hampered by the difficulty in delineating integrated transposons from their surrounding genetic context. Here, we present a computational approach that allowed us to identify the boundaries of 6,549 Tn7-like transposons at base pair resolution. We found that 96% of these transposons carry at least one cargo gene. Delineation of distinct communities ...
Source
#1Tao Wen (SUTD: Singapore University of Technology and Design)H-Index: 10
#2Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
Last. Kang Hao Cheong (SUTD: Singapore University of Technology and Design)H-Index: 17
view all 0 authors...
BACKGROUND Dormancy is widespread in nature, but while it can be an effective adaptive strategy in fluctuating environments, the dormant forms are costly due to the inability to breed and the relatively high energy consumption. We explore mathematical models of predator-prey systems, in order to assess whether dormancy can be an effective adaptive strategy to outcompete perennially active (PA) prey, even when both forms of the dormitive prey (active and dormant) are individually disadvantaged. R...
Source
#1Michael SegelH-Index: 1
Last. Feng ZhangH-Index: 155
view all 0 authors...
Eukaryotic genomes contain domesticated genes from integrating viruses and mobile genetic elements. Among these are homologs of the capsid protein (known as Gag) of long terminal repeat (LTR) retrotransposons and retroviruses. We identified several mammalian Gag homologs that form virus-like particles and one LTR retrotransposon homolog, PEG10, that preferentially binds and facilitates vesicular secretion of its own messenger RNA (mRNA). We showed that the mRNA cargo of PEG10 can be reprogrammed...
Source
#1Kira S. Makarova (NIH: National Institutes of Health)H-Index: 100
#2Yuri I. Wolf (NIH: National Institutes of Health)H-Index: 107
Last. Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
view all 0 authors...
Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig doma...
Source
#1Matthew A. Nethery (NCSU: North Carolina State University)H-Index: 4
#2Michael Korvink (NIH: National Institutes of Health)
Last. Rodolphe Barrangou (NCSU: North Carolina State University)H-Index: 68
view all 0 authors...
Detection and classification of CRISPR-Cas systems in metagenomic data have become increasingly prevalent in recent years due to their potential for diverse applications in genome editing. Traditio...
Source
#1Sean Benler (NIH: National Institutes of Health)H-Index: 3
Metagenomics and metatranscriptomics have become the principal approaches for discovery of novel bacteriophages and preliminary characterization of their ecology and biology. Metagenomic sequencing dramatically expanded the known diversity of tailed and non-tailed phages with double-stranded DNA genomes and those with single-stranded DNA genomes, whereas metatranscriptomics led to the discovery of thousands of new single-stranded RNA phages. Apart from expanding phage diversity, metagenomics stu...
Source
#1Sofia Medvedeva (Pasteur Institute)H-Index: 8
#2Jiarui Sun (UQ: University of Queensland)H-Index: 1
Last. Mart Krupovic (Pasteur Institute)H-Index: 59
view all 7 authors...
Asgardarchaeota encode many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level...
Source
#1Eugene V. Koonin (NIH: National Institutes of Health)H-Index: 218
#2Mart KrupovicH-Index: 59
Last. Vadim I. Agol (RAS: Russian Academy of Sciences)H-Index: 60
view all 3 authors...
Fifty years ago, David Baltimore published a brief conceptual paper delineating the classification of viruses by the routes of genome expression. The six "Baltimore classes" of viruses, with a subsequently added 7th class, became the conceptual framework for the development of virology during the next five decades. During this time, it became clear that the Baltimore classes, with relatively minor additions, indeed cover the diversity of virus genome expression schemes that also define the repli...
Source
#2Natalya Yutin (NIH: National Institutes of Health)H-Index: 37
Last. Bernard MossH-Index: 171
view all 5 authors...
The survival of viruses depends on their ability to resist host defenses and, of all animal virus families, the poxviruses have the most antidefense genes. Orthopoxviruses (ORPV), a genus within the subfamily Chordopoxvirinae, infect diverse mammals and include one of the most devastating human pathogens, the now eradicated smallpox virus. ORPV encode ∼200 genes, of which roughly half are directly involved in virus genome replication and expression as well as virion morphogenesis. The remaining ...
Source