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.
Kurland, C. G. (2005) What Tangled Web: Barriers to Rampant Horizontal Gene Transfer. Bioessays 27: 741–747.
Kurland, C. G., B. Canback, and O. G. Berg. (2003) Horizontal Gene Transfer: A Critical View. Proc Natl Acad Sci USA 100: 9,658—9,662.
Kurland, C. G., L. J. Collins, and D. Penny. (2006) Genomics and the Irreducible Nature of Eukaryote Cells. Science 312: 1,011—1,014.
Lamarck, J.-B. (1809) Philosophie Zoologique, Ou Exposition Des Considerations Relatives А L’histoire Naturelle Des Animaux. Paris: Dentu.
Lambowitz, A. M., and S. Zimmerly. (2004) Mobile Group Ii Introns. Annu Rev Genet 38: 1—35.
Lane, C. E., and J. M. Archibald. (2008) The Eukaryotic Tree of Life: Endosymbiosis Takes Its Toll. Trends Ecol Evol 23: 268–275.
Lane, N., and W. Martin. (2010) The Energetics of Genome Complexity. Nature 467: 929–934.
Lang, A. S., and J. T. Beatty. (2007) Importance of Widespread Gene Transfer Agent Genes in Alpha-Proteobacteria. Trends Microbiol 15: 54–62.
Lang, B. F., M. W. Gray, and G. Burger. (1999) Mitochondrial Genome Evolution and the Origin of Eukaryotes. Annu Rev Genet 33: 351–397.
Lapierre, P., and J. P. Gogarten. (2009) Estimating the Size of the Bacterial Pan-Genome. Trends Genet 25: 107–110.
Lathe, W. C. III, B. Snel, and P. Bork. (2000) Gene Context Conservation of a Higher Order Than Operons. Trends Biochem Sci 25: 474–479.
Lawrence, J. (1999) Selfish Operons: The Evolutionary Impact of Gene Clustering in Prokaryotes and Eukaryotes. Curr Opin Genet Dev 9: 642–648.
Lawrence, J. G., R. W. Hendrix, and S. Casjens. (2001) Where Are the Pseudo-genes in Bacterial Genomes? Trends Microbiol 9: 535–540.
Le Hir, H., A. Nott, and M. J. Moore. (2003) How Introns Influence and Enhance Eukaryotic Gene Expression. Trends Biochem Sci 28: 215–220.
Leipe, D. D., L. Aravind, and E. V. Koonin. (1999) Did DNA Replication Evolve Twice Independently? Nucleic Acids Res 27: 3,389—3,401.
Leipe, D. D., E. V. Koonin, and L. Aravind. (2004) Stand, a Class of P-Loop NTPases Including Animal and Plant Regulators of Programmed Cell Death: Multiple, Complex Domain Architectures, Unusual Phyletic Pat terns, and Evolution by Horizontal Gene Transfer. J Mol Biol 343: 1—28.
Leipe, D. D., Y. I. Wolf, E. V. Koonin, and L. Aravind. (2002) Classification and Evolution of P-Loop GTPases and Related Atpases. J Mol Biol 317: 41–72.
Lenski, R. E., C. Ofria, R. T. Pennock, and C. Adami. (2003) The Evolutionary Origin of Complex Features. Nature 423: 139–144.
Lespinet, O., Y. I. Wolf, E. V. Koonin, and L. Aravind. (2002) The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes. Genome Res 12: 1,048—1,059.
Levy, S. F., and M. L. Siegal. (2008) Network Hubs Buffer Environmental Variation in Saccharomyces Cerevisiae. PLoS Biol 6: e264.
Li, W. H. (1997). Molecular Evolution. Sunderland, MA: Sinauer.
Lincoln, T. A., and G. F. Joyce. (2009) Self-Sustained Replication of an Rna Enzyme. Science 323: 1,229—1,232.
Lindberg, J., and J. Lundeberg. (2010) The Plasticity of the Mammalian Transcriptome. Genomics 95: 1–6.
Linde, A. D. (1986) Eternally Existing Self-Reproducing Chaotic Inflationary Universe. Phys Lett B 175: 395.
Lindell, D., J. D. Jaffe, Z. I. Johnson, G. M. Church, and S. W. Chisholm. (2005) Photosynthesis Genes in Marine Viruses Yield Proteins During Host Infection. Nature 438: 86–89.
Ling, J., H. Roy, and M. Ibba. (2007) Mechanism of Trna-Dependent Editing in Translational Quality Control. Proc Natl Acad Sci USA 104: 72–77.
Ling, J., and D. Soll. (2010) Severe Oxidative Stress Induces Protein Mistranslation Through Impairment of an Aminoacyl-Trna Synthetase Editing Site. Proc Natl Acad Sci USA 107: 4,028—4,033.
Liu, Y., J. Zhou, M. V. Omelchenko, A. S. Beliaev, A. Venkateswaran, J. Stair, L. Wu, D. K. Thompson, D. Xu, I. B. Rogozin, E. K. Gaidamakova, M. Zhai, K. S. Makarova, E. V. Koonin, and M. J. Daly. (2003) Transcriptome Dynamics of Deinococcus Radiodurans Recovering from Ionizing Radiation. Proc Natl Acad Sci USA 100: 4,191—4,196.
Livio, M., and M. J. Rees. (2005) Cosmology. Anthropic Reasoning. Science 309: 1,022—1,023.
Lobkovsky, A. E., Y. I. Wolf, and E. V. Koonin. (2010) Universal Distribution of Protein Evolution Rates As a Consequence of Protein Folding Physics. Proc Natl Acad Sci USA 107: 2,983—2,988.
Loewe, L. (2009) A framework for evolutionary systems biology. BMC Syst Biol 3: 27.
Lopez-Garcia, P., and D. Moreira. (2006) Selective Forces for the Origin of the Eukaryotic Nucleus. Bioessays 28: 525–533.
Lozada-Chavez, I., S. C. Janga, and J. Collado-Vides. (2006) Bacterial Regulatory Networks Are Extremely Flexible in Evolution. Nucleic Acids Res 34: 3,434—3,445.
Luria, S. E., and J. Darnell. (1967). General Virology. New York: John Wiley.
Luscombe, N. M., J. Qian, Z. Zhang, T. Johnson, and M. Gerstein. (2002) The Dominance of the Population by a Selected Few: Power-Law Behaviour Applies to a Wide Variety of Genomic Properties. Genome Biol 3: RESEARCH0040.
Lynch, M. (2006) The Origins of Eukaryotic Gene Structure. Mol Biol Evol 23: 450–468.
Lynch, M. (2007a) The Evolution of Genetic Networks by Non-Adaptive Processes. Nat Rev Genet 8: 803–813.
Lynch, M. (2007b) The Frailty of Adaptive Hypotheses for the Origins of Organismal Complexity. Proc Natl Acad Sci USA 104 Suppl 1: 8,597—8,604.
Lynch, M. (2007c) The Origins of Genome Archiecture. Sunderland, MA: Sinauer Associates.
Lynch, M. (2010) Evolution of the Mutation Rate. Trends Genet 26: 345–352.
Lynch, M., R. Burger, D. Butcher, and W. Gabriel. (1993) The Mutational Meltdown in Asexual Populations. J Hered 84: 339–344.
Lynch, M., and J. S. Conery. (2000) The Evolutionary Fate and Consequences of Duplicate Genes. Science 290: 1,151—1,155.
Lynch, M., and J. S. Conery. (2003) The Origins of Genome Complexity. Science 302: 1,401—1,404.
Lynch, M., and V. Katju. (2004) The Altered Evolutionary Trajectories of Gene Duplicates. Trends Genet 20: 544–549.
Lyotard, J. F. (1979) La Condition Postmoderne: Rapport Sur Le Savoir. Paris: Minuit.
Makarova, K. S., L. Aravind, N. V. Grishin, I. B. Rogozin, and E. V. Koonin. (2002) A DNA Repair System Specific for Thermophilic Archaea and Bacteria Predicted by Genomic Context Analysis. Nucleic Acids Res 30: 482–496.
