Eugene Koonin, Ph.D.

NIH Distinguished 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. Yutin N, Makarova KS, Gussow AB, Krupovic M, Segall A, Edwards RA, Koonin EV. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol. 2018;3(1):38-46.
  3. Koonin EV, Makarova KS, Wolf YI, Krupovic M. Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire. Nat Rev Genet. 2020;21(2):119-131.
  4. Babajanyan SG, Wolf YI, Khachatryan A, Allahverdyan A, Lopez-Garcia P, Koonin EV. Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. Proc Natl Acad Sci U S A. 2023;120(14):e2301522120.
  5. Krupovic M, Dolja VV, Koonin EV. The virome of the last eukaryotic common ancestor and eukaryogenesis. Nat Microbiol. 2023;8(6):1008-1017.

Related Scientific Focus Areas

This page was last updated on Tuesday, August 8, 2023