Dr. Koonin and his research group employ existing and new methods of computational biology to perform research in three main areas:
i) Empirical comparative and evolutionary genomics - comparison of prokaryotic and eukaryotic genomes with the aim of predicting gene functions, constructing evolutionary scenarios for particular gene families and functional categories, and deciphering general evolutionary trends. One of the products of this research direction is the database of Clusters of Orthologous Groups of proteins (COGs).
ii) Exploitation of genome comparisons, particularly those between relatively close genomes, for addressing fundamental issues of evolutionary biology such as the nature of adaptation and selection in different categories of genes.
iii) Classification and evolutionary analysis of protein domains and domain architectures. An important dimension in this type of research is the discovery of "new" domains that are shared by many diverse proteins but have not been defined previously.
iv) Construction of a general physical theory of evolution.
Dr. Koonin is the author of “Sequence - Evolution – Function Computational Approaches in Comparative Genomics” (2003, with Michael Galperin) and “The Logic of Chance: The nature and origin of biological evolution” (2011). He is the founder and Editor-in-Chief (with Laura Landweber and David Lipman) of Biology Direct, an Open Access journal that also employs open peer-review. Dr. Koonin was elected Member of the American Academy of Microbiology, Fellow of the American College of Medical Informatics, Fellow of the American Academy of Arts and Sciences, Foreign Associate of the European Molecular Biology Organization, and Doctor Honoris Causa of Universite Aix-Marseille (France).