Eugene V. Koonin

National Institutes of Health

Primary Section: 44, Microbial Biology
Secondary Section: 29, Biophysics and Computational Biology
Membership Type:
Member (elected 2016)


Eugene V. Koonin is the leader of the Evolutionary Genomics Group at the National Center for Biotechnology Information (NCBI) at the NIH. He is known primarily for his research on genome evolution, especially in microbes and viruses, host-parasite coevolution, and more specifically, functions and evolution of CRISPR-Cas systems. Koonin received his PhD in Molecular Biology in 1983 from the Department of Biology, Moscow State University. He was a research scientist at the Institute of Poliomyelitis of the Russian Academy of Sciences, and subsequently, a senior research scientist and laboratory chief at the Institute of Microbiology of the Russian Academy of Sciences. Koonin joined the NCBI in 1991 as a Visiting Scientist and became a Senior Investigator in 1996. He is the author of “The Logic of Chance: The nature and origin of biological evolution” (2011) and the founder and Editor-in-Chief of Biology Direct, an Open Access, open peer-review journal. Koonin is a Fellow of the American Academy of Arts and Sciences, American Academy of Microbiology, a member of the National Academy of Sciences of the USA, a Foreign Associate of the European Molecular Biology Organization, and Doctor Honoris Causa of Universite Aix-Marseille (France).

Research Interests

Eugene Koonin’s group is engaged in “post-genomic” computational biology research, i.e. utilization of genome sequences, expression, interaction and other data to advance our understanding of the evolution of life and functions of living cells. This research involves mathematical modeling of the evolution of genomes, pathways and networks; theory and practice of genome-wide phylogenetic analysis; construction of evolutionary scenarios for genomes and individual functional systems; evolutionary classification of proteins and RNA; identification of previously undetected protein domains and prediction of their functions. Koonin is particularly interested in evolution of viruses and virus-host coevolution including diversity and evolution of antivirus defense systems. This research involves extensive use of metagenomics sequences, in a focused effort to discover new defense systems and viruses. An important direction in the group is the characterization of novel variants of CRISPR-Cas systems, aiming at reconstruction of the evolution of adaptive immunity in prokaryotes as well as identification of potential new tools for genome engineering. Much of Koonin’s research involves direct collaboration with experimental laboratories on testing functional predictions made by computational approaches. Koonin and his colleagues also actively work on mathematical theory of genome evolution, host-parasite coevolution, and parasite-driven evolutionary transitions.

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