Eugene Koonin, Ph.D.

Senior Investigator

Evolutionary Genomics Research Group


Building 38A, Room 5N503
8600 Rockville Pike
Bethesda, MD 20894


Research Topics

The major research directions in Dr. Koonin's group include:
Evolutionary systems biology: emergence and evolution of genomic and organizational complexity in biological systems; comparative analysis of sequenced genomes and automatic methods for genome-scale annotation of gene functions; application of comparative genomics for phylogenetic analysis, reconstruction of ancestral life forms and building large-scale evolutionary scenarios; mathematical modeling of genome evolution; comparative-genomic study of the major transitions in the evolution of life, such as the origin of eukaryotes; origin of cells and viruses; evolution of eukaryotic signaling and developmental pathways from the comparative-genomic perspective; testing fundamental predictions of evolutionary theory, in particular, the relationship between neutral evolution and various modes of selection, using genome-wide sequence comparison; developing a general theory of evolution using principles and models of statistical physics.

Dr. Koonin's group performs research in many areas of evolutionary genomics. The overall gist of Dr. Koonin's research is to take advantages of the advances of comparative genomics and systems biology to address fundamental problems in evolutionary biology.


Dr. Koonin graduated from Moscow State University, Moscow, Russia and received his Ph.D. in Molecular Biology from the same University in 1983. He has been working in the fields of Computational Biology and Evolutionary Genomics since 1984. Dr. Koonin moved to the US in 1991, first, as a Visiting Scientist, and then, since 1996, as a Senior Investigator at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD. Dr. Koonin's group performs research in many areas of evolutionary genomics.

Selected Publications

  1. Krupovic M, Koonin EV. Multiple origins of viral capsid proteins from cellular ancestors. Proc Natl Acad Sci U S A. 2017;114(12):E2401-E2410.

  2. Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciordia S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol. 2017;2:17081.

  3. Koonin EV, Krupovic M. Evolution of adaptive immunity from transposable elements combined with innate immune systems. Nat Rev Genet. 2015;16(3):184-92.

  4. Krupovic M, Koonin EV. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol. 2015;13(2):105-15.

  5. Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV. Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol. 2017;15(3):169-182.

This page was last updated on September 6th, 2018