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.
Novozhilov, A. S., and E. V. Koonin. (2009) Exceptional Error Minimization in Putative Primordial Genetic Codes. Biol Direct 4: 44.
Nunoura, T., Y. Takaki, J. Kakuta, S. Nishi, J. Sugahara, H. Kazama, G. J. Chee, M. Hattori, A. Kanai, H. Atomi, K. Takai, and H. Takami. (2010) Insights into the Evolution of Archaea and Eukaryotic Protein Modifier Systems Revealed by the Genome of a Novel Archaeal Group. Nucleic Acids Res Dec. 15 [Epub ahead of print].
O’Maille, P. E., A. Malone, N. Dellas, B. Andes Hess Jr., L. Smentek, I. Sheehan, B. T. Greenhagen, J. Chappell, G. Manning, and J. P. Noel. (2008) Quantitative Exploration of the Catalytic Landscape Separating Divergent Plant Sesquiterpene Synthases. Nat Chem Biol 4: 617–623.
O’Malley, M. A. (2009) What Did Darwin Say About Microbes, and How Did Microbiology Respond? Trends Microbiol 17: 341–347.
O’Malley, M. A., ed. (2010) Special Issue: The Tree of Life. Biology and Philosophy.
O’Malley, M. A., and Y. Boucher. (2005) Paradigm Change in Evolutionary Microbiology. Stud Hist Philos Biol Biomed Sci 36: 183–208.
Ochman, H. (2002) Distinguishing the Orfs from the Elfs: Short Bacterial Genes and the Annotation of Genomes. Trends Genet 18: 335–337.
Ohno, S. (1970). Evolution by Gene Duplication. New York: Springer-Verlag.
Ohta, T. (2002) Near-Neutrality in Evolution of Genes and Gene Regulation. Proc Natl Acad Sci USA 99: 16,134—16,137.
Omelchenko, M. V., M. Y. Galperin, Y. I. Wolf, and E. V. Koonin. (2010) Non-Homologous Isofunctional Enzymes: A Systematic Analysis of Alternative Solutions in Enzyme Evolution. Biol Direct 5: 31.
Omelchenko, M. V., Y. I. Wolf, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, M. J. Daly, E. V. Koonin, and K. S. Makarova. (2005) Comparative Genomics of Thermus Thermophilus and Deinococcus Radiodurans: Divergent Routes of Adaptation to Thermophily and Radiation Resistance. BMC Evol Biol 5: 57.
Oparin, A. I. (1924) The Origin of Life. Moscow: Moscow Worker. Oparin, A. I., and V. V. Fesenkov. (1956). Life in the Universe. Moscow: USSR Academy of Sciences Publisher.
Orgel, L. E. (1968) Evolution of the Genetic Apparatus. J Mol Biol 38: 381–393.
Orgel, L. E., and F. H. Crick. (1980) Selfish DNA: The Ultimate Parasite. Nature 284: 604–607.
Ostrowski, E. A., R. J. Woods, and R. E. Lenski. (2008) The Genetic Basis of Parallel and Divergent Phenotypic Responses in Evolving Populations of Escherichia Coli. Proc Biol Sci 275: 277–284.
Ouzounis, C. A., V. Kunin, N. Darzentas, and L. Goldovsky. (2006) A Minimal Estimate for the Gene Content of the Last Universal Common Ancestor — Exobiology from a Terrestrial Perspective. Res Microbiol 157: 57–68.
Pace, N. R. (1997) A Molecular View of Microbial Diversity and the Biosphere. Science 276: 734–740.
Pace, N. R. (2006) Time for a Change. Nature 441: 289.
Pace, N. R. (2009a) Mapping the Tree of Life: Progress and Prospects. Microbiol Mol Biol Rev 73: 565–576.
Pace, N. R. (2009b) Problems with «Procaryote». J Bacteriol 191: 2,008—2,010; discussion 2,011.
Pais, A. (1994) Niels Bohr’s Times: In Physics, Philosophy and Polity. Oxford: Oxford University Press.
Pal, C., B. Papp, and L. D. Hurst. (2001) Highly Expressed Genes in Yeast Evolve Slowly. Genetics 158: 927–931.
Pal, C., B. Papp, and M. J. Lercher. (2005) Adaptive Evolution of Bacterial Metabolic Networks by Horizontal Gene Transfer. Nat Genet 37: 1,372—1,375.
Pande, V. S., A. Grosberg, T. Tanaka, and D. S. Rokhsar. (1998) Pathways for Protein Folding: Is a New View Needed? Curr Opin Struct Biol 8: 68–79.
Patterson, D. J. (1999) The Diversity of Eukaryotes. Am Nat 154: S96—124.
Paul, J. H. (2008) Prophages in Marine Bacteria: Dangerous Molecular Time Bombs or the Key to Survival in the Seas? ISME J 2: 579–589.
Pennisi, E. (1999) Is It Time to Uproot the Tree of Life? Science 284: 1,305—1,307.
Pennisi, E. (2009) History of Science. The Case of the Midwife Toad: Fraud or Epigenetics? Science 325: 1,194—1,195.
Penny, D. (2005) An Interpretative Review of the Origin of Life Research. Biol Philos, in press.
Pereto, J., P. Lopez-Garcia, and D. Moreira. (2004) Ancestral Lipid Biosynthesis and Early Membrane Evolution. Trends Biochem Sci 29: 469–477.
Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch,