Евгений Кунин - Логика случая. О природе и происхождении биологической эволюции

Makarova, K. S., L. Aravind, Y. I. Wolf, R. L. Tatusov, K. W. Minton, E. V. Koonin, and M. J. Daly. (2001a) Genome of the Extremely Radiation-Resistant Bacterium Deinococcus Radiodurans Viewed from the Perspective of Comparative Genomics. Microbiol Mol Biol Rev 65: 44–79.

Makarova, K. S., N. V. Grishin, S. A. Shabalina, Y. I. Wolf, and E. V. Koonin. (2006) A Putative RNA-Interference-Based Immune System in Prokaryotes: Computational Analysis of the Predicted Enzymatic Machinery, Functional Analogies with Eukaryotic Rnai, and Hypothetical Mechanisms of Action. Biol Direct 1: 7.

Makarova, K. S., M. V. Omelchenko, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, A. Lapidus, A. Copeland, E. Kim, M. Land, K. Mavrommatis, S. Pitluck, P. M. Richardson, C. Detter, T. Brettin, E. Saunders, B. Lai, B. Ravel, K. M. Kemner, Y. I. Wolf, A. Sorokin, A. V. Gerasimova, M. S. Gelfand, J. K. Fredrickson, E. V. Koonin, and M. J. Daly. (2007a) Deinococcus Geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks. PLoS ONE 2: e955.

Makarova, K. S., V. A. Ponomarev, and E. V. Koonin. (2001b) Two C or Not Two C: Recurrent Disruption of Zn-Ribbons, Gene Duplication, Lineage-Specific Gene Loss, and Horizontal Gene Transfer in Evolution of Bacterial Ribosomal Proteins. Genome Biol 2: RESEARCH 0033.

Makarova, K. S., A. V. Sorokin, P. S. Novichkov, Y. I. Wolf, and E. V. Koonin. (2007b) Clusters of Orthologous Genes for 41 Archaeal Genomes and Implications for Evolutionary Genomics of Archaea. Biol Direct 2: 33.

Makarova, K. S., Y. I. Wolf, and E. V. Koonin. (2003) Potential Genomic Determinants of Hyperthermophily. Trends Genet 19: 172–176.

Makarova, K. S., Y. I. Wolf, and E. V. Koonin. (2009a) Comprehensive Comparative-Genomic Analysis of Type 2 Toxin-Antitoxin Systems and Related Mobile Stress Response Systems in Prokaryotes. Biol Direct 4: 19.

Makarova, K. S., Y. I. Wolf, S. L. Mekhedov, B. G. Mirkin, and E. V. Koonin. (2005) Ancestral Paralogs and Pseudoparalogs and Their Role in the Emergence of the Eukaryotic Cell. Nucleic Acids Res 33: 4,626—4,638.

Makarova, K. S., Y. I. Wolf, J. van der Oost, and E. V. Koonin. (2009b) Prokaryotic Homologs of Argonaute Proteins Are Predicted to Function As Key Components of a Novel System of Defense Against Mobile Genetic Elements. Biol Direct 4: 29.

Makarova, K. S., N. Yutin, S. D. Bell, and E. V. Koonin. (2010) Evolution of Diverse Cell Division and Vesicle Formation Systems in Archaea. Nat Rev Microbiol 8: 731–741.

Mans, B. J., V. Anantharaman, L. Aravind, and E. V. Koonin. (2004) Comparative Genomics, Evolution, and Origins of the Nuclear Envelope and Nuclear Pore Complex. Cell Cycle 3: 1,612—1,637.

Mansy, S. S., J. P. Schrum, M. Krishnamurthy, S. Tobe, D. A. Treco, and J. W. Szostak. (2008) Template-Directed Synthesis of a Genetic Polymer in a Model Protocell. Nature 454: 122–125.

Margulis, L. (2009) Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis. Methods Mol Biol 532: 181–191.

Margulis, L., M. Chapman, R. Guerrero, and J. Hall. (2006) The Last Eukaryotic Common Ancestor (LECA): Acquisition of Cytoskeletal Motility from Aerotolerant Spirochetes in the Proterozoic Eon. Proc Natl Acad Sci USA 103: 13,080—13,085.

Margulis, L., and D. Sagan. (2003). Acquiring Genomes: The Theory of the Origin of Species. New York: Basic Books.

Marinsek, N., E. R. Barry, K. S. Makarova, I. Dionne, E. V. Koonin, and S. D. Bell. (2006) GINS, a Central Nexus in the Archaeal DNA Replication Fork. EMBO Rep 7: 539–545.

Marraffini, L. A., and E. J. Sontheimer. (2008) CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA. Science 322: 1,843—1,845.

Martin, W. (1999) Mosaic Bacterial Chromosomes: A Challenge En Route to a Tree of Genomes. Bioessays 21: 99—104.

Martin, W., J. Baross, D. Kelley, and M. J. Russell. (2008) Hydrothermal Vents and the Origin of Life. Nat Rev Microbiol 6: 805–814.

Martin, W., and E. V. Koonin. (2006a) Introns and the Origin of Nucleus-Cytosol Compartmentalization. Nature 440: 41–45.

Martin, W., and E. V. Koonin. (2006b) A Positive Definition of Prokaryotes. Nature 442: 868.

Martin, W., and K. V. Kowallik. (1999) Annotated English Translation of Mereschkowsky’s 1905 Paper «über Natur Und Ursprung Der Chromatophoren Im Pflanzenreiche». Eur J Phycol 34: 287–296.

Martin, W., and M. Muller. (1998) The Hydrogen Hypothesis for the First Eukaryote. Nature 392: 37–41.

Martin, W., and M. J. Russell. (2003) On the Origins of Cells: A Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautotrophic Prokaryotes, and from Prokaryotes to Nucleated Cells. Philos Trans R Soc Lond B Biol Sci 358: 59–83; discussion 83–55.

Martin, W., and M. J. Russell. (2007) On the Origin of Biochemistry at an Alkaline Hydrothermal Vent. Philos Trans R Soc Lond B Biol Sci 362: 1,887—1,925.

Martinez, J. L. (2008) Antibiotics and Antibiotic Resistance Genes in Natural Environments. Science 321: 365–367.

Masel, J., and A. Bergman. (2003) The Evolution of the Evolvability Properties of the Yeast Prion [Psi+]. Evolution 57: 1,498—1,512.

Masel, J., and M. L. Siegal. (2009) Robustness: Mechanisms and Consequences. Trends Genet 25: 395–403.

Masel, J., and M. V. Trotter. (2010) Robustness and Evolvability. Trends Genet 26: 406–414.

Maslov, S., S. Krishna, T. Y. Pang, and K. Sneppen. (2009) Toolbox Model of Evolution of Prokaryotic Metabolic Networks and Their Regulation. Proc Natl Acad Sci USA 106: 9,743—9,748.

Mayr, E. (1963). Animal Species and Evolution. Cambridge: Harvard University Press.

McCarthy, B. J., and J. J. Holland. (1965) Denatured DNA as a Direct Template for in Vitro Protein Synthesis. Proc Natl Acad Sci USA 54: 880–886.

McClain, W. H., L. B. Lai, and V. Gopalan. (2010) Trials, Travails, and Triumphs: An Account of RNA Catalysis in RNase P. J Mol Biol 397: 627–646.

McClintock, B. (1984) The Significance of Responses of the Genome to Challenge. Science 226: 792–801.

McCutcheon, J. P., B. R. McDonald, and N. A. Moran. (2009) Convergent Evolution of Metabolic Roles in Bacterial Co-Symbionts of Insects. Proc Natl Acad Sci USA 106: 15,394—15,399.

McDaniel, L. D., E. Young, J. Delaney, F. Ruhnau, K. B. Ritchie, and J. H. Paul. (2010) High Frequency of Horizontal Gene Transfer in the Oceans. Science 330: 50.

McDonald, J. H., and M. Kreitman. (1991) Adaptive Protein Evolution at the Adh Locus in Drosophila. Nature 351: 652–654.

McGeoch, A. T., and S. D. Bell. (2008) Extra-Chromosomal Elements and the Evolution of Cellular DNA Replication Machineries. Nat Rev Mol Cell Biol 9: 569–574.

Medvedev, Z. A. (1969) The Rise and Fall of T. D. Lysenko. New York: Columbia University Press.

Mendell, J. E., K. D. Clements, J. H. Choat, and E. R. Angert. (2008) Extreme Polyploidy in a Large Bacterium. Proc Natl Acad Sci USA 105: 6,730—6,734.

Mendes Soares, L. M., and J. Valcarcel. (2006) The Expanding Transcriptome: The Genome as the «Book of Sand». Embo J 25: 923–931.

Merkl, R. (2006) A Comparative Categorization of Protein Function Encoded in Bacterial or Archeal Genomic Islands. J Mol Evol 62: 1—14.

Mielke, R. E., M. J. Russell, P. R. Wilson, S. E. McGlynn, M. Coleman, R. Kidd, and I. Kanik. (2010) Design, Fabrication, and Test of a Hydrothermal Reactor for Origin-of-Life Experiments. Astrobiology 10: 799–810.

Mills, D. R., F. R. Kramer, and S. Spiegelman. (1973) Complete Nucleotide Sequence of a Replicating RNA Molecule. Science 180: 916–927.

Mira, A., A. B. Martin-Cuadrado, G. D’Auria, and F. Rodriguez-Valera. (2010) The Bacterial Pan-Genome: A New Paradigm in Microbiology. Int Microbiol 13: 45–57.

Mira, A., H. Ochman, and N. A. Moran. (2001) Deletional Bias and the Evolution of Bacterial Genomes. Trends Genet 17: 589–596.

Mirkin, B. G., T. I. Fenner, M. Y. Galperin, and E. V. Koonin. (2003) Algorithms for Computing Parsimonious Evolutionary Scenarios for Genome Evolution, the Last Universal Common Ancestor, and Dominance of Horizontal Gene Transfer in the Evolution of Prokaryotes. BMC Evol Biol 3: 2.

Mojica, F. J., C. Diez-Villasenor, J. Garcia-Martinez, and E. Soria. (2005) Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements. J Mol Evol 60: 174–182.

Molina, N., and E. van Nimwegen. (2009) Scaling Laws in Functional Genome Content Across Prokaryotic Clades and Lifestyles. Trends Genet 25: 243–247.

Monier, A., J. M. Claverie, and H. Ogata. (2008) Taxonomic Distribution of Large DNA Viruses in the Sea. Genome Biol 9: R106.

Monod, J. (1972). Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology. New York: Vintage.

Moreira, D., and P. Lopez-Garcia. (2009) Ten Reasons to Exclude Viruses from the Tree of Life. Nat Rev Microbiol 7: 306–311.

Mulkidjanian, A. Y. (2009) On the Origin of Life in the Zinc World: 1. Photosynthesizing, Porous Edifices Built of Hydrothermally Precipitated Zinc Sulfide as Cradles of Life on Earth. Biol Direct 4: 26.

Mulkidjanian, A. Y., M. Y. Galperin, K. S. Makarova, Y. I. Wolf, and E. V. Koonin. (2008) Evolutionary Primacy of Sodium Bioenergetics. Biol Direct 3: 13.

Mulkidjanian, A. Y., E. V. Koonin, K. S. Makarova, S. L. Mekhedov, A. Sorokin, Y. I. Wolf, A. Dufresne, F. Partensky, H. Burd, D. Kaznadzey, R. Haselkorn, and M. Y. Galperin. (2006) The Cyanobacterial Genome Core and the Origin of Photosynthesis. Proc Natl Acad Sci USA 103: 13,126—13,131.

Mulkidjanian, A. Y., K. S. Makarova, M. Y. Galperin, and E. V. Koonin. (2007) Inventing the Dynamo Machine: The Evolution of the F-Type and V-Type Atpases. Nat Rev Microbiol 5: 892–899.

Müller, F., T. Brissac, N. Le Bris, H. Felbeck, and O. Gros. (2010) First Description of Giant Archaea (Thaumarchaeota) Associated with Putative Bacterial Ectosymbionts in a Sulfidic Marine Habitat. Env Microbiol 12: 2,371—2,383.

Müller, H. J. (1964) The Relation of Recombination to Mutational Advance. Mutat Res 106: 2–9.

Mushegian, A. R., and E. V. Koonin. (1996a) Gene Order Is Not Conserved in Bacterial Evolution. Trends Genet 12: 289–290.

Mushegian, A. R., and E. V. Koonin. (1996b) A Minimal Gene Set for Cellular Life Derived by Comparison of Complete Bacterial Genomes. Proc Natl Acad Sci USA 93: 10,268—10,273.

Nelson, K. E., R. A. Clayton, S. R. Gill, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, W. C. Nelson, K. A. Ketchum, L. McDonald, T. R. Utterback, J. A. Malek, K. D. Linher, M. M. Garrett, A. M. Stewart, M. D. Cotton, M. S. Pratt, C. A. Phillips, D. Richardson, J. Heidelberg, G. G. Sutton, R. D. Fleischmann, J. A. Eisen, O. White, S. L. Salzberg, H. O. Smith, J. C. Venter, and C. M. Fraser. (1999) Evidence for Lateral Gene Transfer Between Archaea and Bacteria from Genome Sequence of Thermotoga Maritima. Nature 399: 323–329.

Netzer, N., J. M. Goodenbour, A. David, K. A. Dittmar, R. B. Jones, J. R. Schneider, D. Boone, E. M. Eves, M. R. Rosner, J. S. Gibbs, A. Embry, B. Dolan, S. Das, H. D. Hickman, P. Berglund, J. R. Bennink, J. W. Yewdell, and T. Pan. (2009) Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity. Nature 462: 522–526.

Neupert, W., and J. M. Herrmann. (2007) Translocation of Proteins into Mitochondria. Annu Rev Biochem 76: 723–749.

Novichkov, P. S., M. V. Omelchenko, M. S. Gelfand, A. A. Mironov, Y. I. Wolf, and E. V. Koonin. (2004) Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution. J Bacteriol, in press.

Novichkov, P. S., Y. I. Wolf, I. Dubchak, and E. V. Koonin. (2009) Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes. J Bacteriol 191: 65–73.