Area of research
Molecular Biology · Ecology
Research interest
Dr. Eugene Koonin is a Senior Investigator at the National Center for Biotechnology Information of the National Library of Medicine. Over the course of his career, Koonin has contributed to nearly every area of evolutionary genomics. He developed the concept of Clusters of Orthologous Genes (COGs) that is central to functional and evolutionary analysis of genomes. With his colleagues, he conducted extensive comparative work on nearly every feature of cell biology, thereby elucidating the likely features of key members of the tree of life, including LECA (Last Eukaryotic Common Ancestor). For example, he thoroughly characterized the evolutionary dynamics of introns in eukaryotes, showing that LECA must have been intron-rich, leading to a novel hypothesis on the origin of the nucleus as defense against intron invasion. Using comparative genomic methods, he also predicted the existence and mechanism of action of a system of adaptive immunity in Archaea and Bacteria (known as CRISPR). With colleagues, Koonin also demonstrated the universal shape of the distribution of evolutionary rates of orthologous genes among diverse genomes, showing that this pattern can be explained by fundamental principles of protein folding. The hallmark of his genomic work is a thorough understanding of the cell biological context in which evolution occurs. His research continues to focus on developing our understanding the evolution of life, employing existing and new methods of computational biology to further scientific knowledge. Koonin is the author of the books The Logic of Chance: The Nature and Origin of Biological Evolution and Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. His scientific publications appear in BMC Biology, Cell, Nature, and Science.
Dominant contribution of Asgard archaea to eukaryogenesis
Diverse bacterial pattern recognition receptors sense the core phage proteome
The paradox of immune systems conservation between prokaryotes and eukaryotes
Structural visualization of the molecular evolution of CRISPR–Cas9
Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea
Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis
Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism
Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily
Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily
The heterogeneous selection landscape of genome evolution in prokaryotes
A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination
A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination
Organization and evolution of the virosphere and the replicator space
An updated evolutionary classification of CRISPR–Cas systems including rare variants
An updated evolutionary classification of CRISPR–Cas systems including rare variants
TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses
TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses
Reprogrammable RNA-targeting CRISPR systems evolved from RNA toxin-antitoxins
The hidden bacterial microproteome
Jumbo phage killer immune system targets early infection of nucleus-forming phages
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025
Naturally ornate RNA-only complexes revealed by cryo-EM
Translon: a single term for translated regions
Activation of bacterial programmed cell death by phage inhibitors of host immunity
Naturally ornate RNA-only complexes revealed by cryo-EM
The protein structurome of Orthornavirae and its dark matter
In silico evolution of globular protein folds from random sequences
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal DNA Viruses and Retroviruses Subcommittee, 2025
Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems
Translon: a single term for translated regions