Koonin, E. V. (2007a) The Biological Big Bang Model for the Major Transitions in Evolution. Biol Direct 2: 21.

Koonin, E. V. (2007b) The Cosmological Model of Eternal Inflation and the Transition from Chance to Biological Evolution in the History of Life. Biol Direct 2: 15.

Koonin, E. V. (2007c) An RNA-Making Reactor for the Origin of Life. Proc Natl Acad Sci USA 104: 9,105—9,106.

Koonin, E. V. (2009a) Evolution of Genome Architecture. Int J Biochem Cell Biol 41: 298–306.

Koonin, E. V. (2009b) Intron-Dominated Genomes of Early Ancestors of Eukaryotes. J Hered 100: 618–623.

Koonin, E. V. (2009c) On the Origin of Cells and Viruses: Primordial Virus World Scenario. Ann N Y Acad Sci 1,178: 47–64.

Koonin, E. V. (2010a) The Origin and Early Evolution of Eukaryotes in the Light of Phylogenomics. Genome Biol 11: 209.

Koonin, E. V. (2010b) Preview. The Incredible Expanding Ancestor of Eukaryotes. Cell 140: 606–608.

Koonin, E. V. (2010c) Taming of the Shrewd: Novel Eukaryotic Genes from RNA Viruses. BMC Biol 8: 2.

Koonin, E. V. (2010d) The Two Empires and the Three Domains of Life in the Postgenomic Age. Nature Education 3: 27.

Koonin, E. V., and L. Aravind. (2002) Origin and Evolution of Eukaryotic Apoptosis: The Bacterial Connection. Cell Death Differ 9: 394–404.

Koonin, E. V., L. Aravind, and A. S. Kondrashov. (2000a) The Impact of Comparative Genomics on Our Understanding of Evolution. Cell 101: 573–576.

Koonin, E. V., and V. V. Dolja. (1993) Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences. Crit Rev Biochem Mol Biol 28: 375–430.

Koonin, E. V., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, D. M. Krylov, K. S. Makarova, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, I. B. Rogozin, S. Smirnov, A. V. Sorokin, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. (2004) A Comprehensive Evolutionary Classification of Proteins Encoded in Complete Eukaryotic Genomes. Genome Biol 5: R7.

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.

Kuhn, T. S. (1962) The Structure of Scientific Revolutions. Chicago: University of Chicago Press.

Kun, A., M. Santos, and E. Szathmary. (2005) Real Ribozymes Suggest a Relaxed Error Threshold. Nat Genet 37: 1,008—1,011.

Kunin, V., L. Goldovsky, N. Darzentas, and C. A. Ouzounis. (2005) The Net of Life: Reconstructing the Microbial Phylogenetic Network. Genome Res 15: 954–959.

Kunin, V., and C. A. Ouzounis. (2003) The Balance of Driving Forces During Genome Evolution in Prokaryotes. Genome Res 13: 1,589—1,594.