Koonin's principal research goals include the comparative analysis of sequenced genomes and automatic methods for genome-scale annotation of gene functions. His research also investigates the application of comparative genomics for phylogenetic analysis, reconstruction of ancestral life forms and building large-scale evolutionary scenarios, as well as mathematical modeling of genome evolution. Koonin's research also investigates computational study of the major transitions in the evolution of life (such as the origin of eukaryotes), the evolution of eukaryotic signaling and developmental pathways from the comparative-genomic perspective.
The rapidly growing genomic and metagenomic sequence database provide researchers with a rapidly expanding and diversifying resource for discovery of novel genetic elements. Unlike the more traditional databases of complete genomes, this new resource is not restricted by the ability of microbes to grow in culture and therefore represents unbiased sampling of biological diversity. We developed computational pipelines for identification of novel mobile elements as well as cellular defence systems in genomic and metagenomics systems. Application of these approaches resulted in the discovery of several families of new viruses and transposable elements as well as new types of CRISPR-Cas adaptive immunity systems. Comparative analysis of the discovered novel defence systems prompted the scenario of independent evolution of different types of CRISPR-Cas systems from distinct mobile elements. Experimental validation of the predictions produced by our searches led to the identification of novel mechanisms of CRISPR-mediated defence that could be exploited in new tools for genome engineering.