Koonin, E. V., A. E. Gorbalenya, and K. M. Chumakov. (1989) Tentative Identification of RNA-Dependent RNA Polymerases of dsRNA Viruses and Their Relationship to Positive Strand RNA Viral Polymerases. FEBS Lett 252: 42–46.

Koonin, E. V., and K. S. Makarova. (2009) CRISPR-Cas: An Adaptive Immunity System in Prokaryotes. F1000 Biol Rep 1: 95.

Koonin, E. V., K. S. Makarova, and L. Aravind. (2001a) Horizontal Gene Transfer in Prokaryotes: Quantification and Classification. Annu Rev Microbiol 55: 709–742.

Koonin, E. V., and W. Martin. (2005) On the Origin of Genomes and Cells within Inorganic Compartments. Trends Genet 21: 647–654.

Koonin, E. V., and A. R. Mushegian. (1996) Complete Genome Sequences of Cellular Life Forms: Glimpses of Theoretical Evolutionary Genomics. Curr Opin Genet Dev 6: 757–762.

Koonin, E. V., A. R. Mushegian, and K. E. Rudd. (1996) Sequencing and Analysis of Bacterial Genomes. Curr Biol 6: 404–416.

Koonin, E. V., and A. S. Novozhilov. (2009) Origin and Evolution of the Genetic Code: The Universal Enigma. IUBMB Life 61: 99—111.

Koonin, E. V., T. G. Senkevich, and V. V. Dolja. (2006) The Ancient Virus World and Evolution of Cells. Biol Direct 1: 29.

Koonin, E. V., and Y. I. Wolf. (2006) Evolutionary Systems Biology: Links Between Gene Evolution and Function. Curr Opin Biotechnol 17: 481–487.

Koonin, E. V., and Y. I. Wolf. (2008a). Evolutionary Systems Biology. Evolutionary Genomics and Proteomics. Ed. by M. Pagel and A. Pomiankowski. Sunder-land, MA: Sinauer Associates, Inc.: 11–25.

Koonin, E. V., and Y. I. Wolf. (2008b) Genomics of Bacteria and Archaea: The Emerging Dynamic View of the Prokaryotic World. Nucleic Acids Res 36: 6,688—6,719.

Koonin, E. V., and Y. I. Wolf. (2009a) The Fundamental Units, Processes and Patterns of Evolution, and the Tree of Life Conundrum. Biol Direct 4: 33.

Koonin, E. V., and Y. I. Wolf. (2009b) Is Evolution Darwinian or/and Lamarckian? Biol Direct 4: 42.

Koonin, E. V., and Y. I. Wolf. (2010a) The Common Ancestry of Life. Biol Direct 5: 64.

Koonin, E. V., and Y. I. Wolf. (2010b) Constraints and Plasticity in Genome and Molecular-Phenome Evolution. Nat Rev Genet 11: 487–498.

Koonin, E. V., Y. I. Wolf, and L. Aravind. (2000b) Protein Fold Recognition Using Sequence Profiles and Its Application in Structural Genomics. Adv Protein Chem 54: 245–275.

Koonin, E. V., Y. I. Wolf, and L. Aravind. (2001b) Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach. Genome Res 11: 240–252.

Koonin, E. V., Y. I. Wolf, and G. P. Karev. (2002) The Structure of the Protein Universe and Genome Evolution. Nature 420: 218–223.

Koonin, E. V., Y. I. Wolf, K. Nagasaki, and V. V. Dolja. (2008) The Big Bang of Picorna-Like Virus Evolution Antedates the Radiation of Eukaryotic Supergroups. Nat Rev Microbiol 6: 925–939.

Koonin, E. V., and N. Yutin. (2010) Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses. Intervirology 53: 284–292.

Kristensen, D. M., A. R. Mushegian, V. V. Dolja, and E. V. Koonin. (2010) New Dimensions of the Virus World Discovered Through Metagenomics. Trends Microbiol 18: 11–19.

Krylov, D. M., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. (2003) Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution. Genome Res 13: 2,229—2,235.