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

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, and F. R. Blattner. (2001) Genome Sequence of Enterohaemorrhagic Escherichia Coli O157:H7. Nature 409: 529–533.

Pisani, D., J. A. Cotton, and J. O. McInerney. (2007) Supertrees Disentangle the Chimerical Origin of Eukaryotic Genomes. Mol Biol Evol 24: 1,752—1,760.

Poole, A. M. (2009) Horizontal Gene Transfer and the Earliest Stages of the Evolution of Life. Res Microbiol 160: 473–480.

Poole, A. M., D. C. Jeffares, and D. Penny. (1998) The Path from the Rna World. J Mol Evol 46: 1—17.

Poole, A. M., and D. Penny. (2007) Evaluating Hypotheses for the Origin of Eukaryotes. Bioessays 29: 74–84.

Popper, K. R. (1982) Unended Quest: An Intellectual Autobiography. London: Open Court Publishing Company.

Prangishvili, D., P. Forterre, and R. A. Garrett. (2006a) Viruses of the Archaea: A Unifying View. Nat Rev Microbiol 4: 837–848.

Prangishvili, D., R. A. Garrett, and E. V. Koonin. (2006b) Evolutionary Genomics of Archaeal Viruses: Unique Viral Genomes in the Third Domain of Life. Virus Res 117: 52–67.

Price, M.N., P. S. Dehal, and A. P. Arkin. (2010) FastTree 2 — approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.

Prusiner, S. B. (1998) Prions. Proc Natl Acad Sci USA 95: 13,363—13,383.

Puigbo, P., Y. I. Wolf, and E. V. Koonin. (2009) Search for a «Tree of Life» in the Thicket of the Phylogenetic Forest. J Biol 8: 59.

Puigbo, P., Y. I. Wolf, and E. V. Koonin. (2010) The Tree and Net Components of Prokaryote Evolution. Genome Biol Evol 2: 745–756.