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

Seshasayee, A. S., G. M. Fraser, and N. M. Luscombe. (2010) Comparative Genomics of Cyclic-Di-Gmp Signalling in Bacteria: Post-Translational Regulation and Catalytic Activity. Nucleic Acids Res 38: 5,970—5,981.

Shabalina, S. A., and E. V. Koonin. (2008) Origins and Evolution of Eukaryotic RNA Interference. Trends Ecol Evol 23: 578–587.

Shiflett, A. M., and P. J. Johnson. (2010) Mitochondrion-Related Organelles in Eukaryotic Protists. Annu Rev Microbiol 64: 409–429.

Shnol, S. E. (2001) Heroes, Villains, Conformists of Russian Science. Moscow: Kron-Press.

Sicheritz-Ponten, T., and S. G. Andersson. (2001) A Phylogenomic Approach to Microbial Evolution. Nucleic Acids Res 29: 545–552.

Simpson, G. G. (1983) Tempo and Mode in Evolution. New York: Columbia University Press.

Smith, M. W., D. F. Feng, and R. F. Doolittle. (1992) Evolution by Acquisition: The Case for Horizontal Gene Transfers. Trends Biochem Sci 17: 489–493.

Smolin, L. (1999) The Life of the Cosmos. Oxford: Oxford University Press.

Sniegowski, P. D., P. J. Gerrish, and R. E. Lenski. (1997) Evolution of High Mutation Rates in Experimental Populations of E. coli. Nature 387: 703–705.

Snel, B., P. Bork, and M. A. Huynen. (2002) Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content. Genome Res 12: 17–25.

Soyfer, V. N. (1994) Lysenko and the Tragedy of Soviet Science. New Brunswick, NJ: Rutgers University Press.

Soyfer, V. N. (2001) The Consequences of Political Dictatorship for Russian Science. Nat Rev Genet 2: 723–729.

Spiegelman, S. (1971) An Approach to the Experimental Analysis of Precellular Evolution. Q Rev Biophys 4: 213–253.

Srivastava, M., E. Begovic, J. Chapman, N. H. Putnam, U. Hellsten, T. Kawashima, A. Kuo, T. Mitros, A. Salamov, M. L. Carpenter, A. Y. Signorovitch, M. A. Moreno, K. Kamm, J. Grimwood, J. Schmutz, H. Shapiro, I. V. Grigoriev, L. W. Buss, B. Schierwater, S. L. Dellaporta, and D. S. Rokhsar. (2008) The Trichoplax Genome and the Nature of Placozoans. Nature 454: 955–960.

Srivastava, M., O. Simakov, J. Chapman, B. Fahey, M. E. Gauthier, T. Mitros, G. S. Richards, C. Conaco, M. Dacre, U. Hellsten, C. Larroux, N. H. Putnam, M. Stanke, M. Adamska, A. Darling, S. M. Degnan, T. H. Oakley, D. C. Plachetzki, Y. Zhai, M. Adamski, A. Calcino, S. F. Cummins, D. M. Goodstein, C. Harris, D. J. Jackson, S. P. Leys, S. Shu, B. J. Woodcroft, M. Vervoort, K. S. Kosik, G. Manning, B. M. Degnan, and D. S. Rokhsar. (2010) The Amphimedon Queenslandica Genome and the Evolution of Animal Complexity. Nature 466: 720–726.

Stalder, L., and O. Muhlemann. (2008) The Meaning of Nonsense. Trends Cell Biol 18: 315–321.

Stanier, R. Y., and C. B. Van Niel. (1962) The Concept of a Bacterium. Arch Mikrobiol 42: 17–35.

Stechmann, A., and T. Cavalier-Smith. (2003) The Root of the Eukaryote Tree Pinpointed. Curr Biol 13: R665—666.

Stern, A., L. Keren, O. Wurtzel, G. Amitai, and R. Sorek. (2010) Self-Targeting by CRISPR: Gene Regulation or Autoimmunity? Trends Genet 26: 335–340.

Stoltzfus, A. (1999) On the Possibility of Constructive Neutral Evolution. J Mol Evol 49: 169–181.

Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory, and M. V. Olson. (2000) Complete Genome Sequence of Pseudomonas Aeruginosa Pao1, an Opportunistic Pathogen. Nature 406: 959–964.

Sullivan, M. B., D. Lindell, J. A. Lee, L. R. Thompson, J. P. Bielawski, and S. W. Chisholm. (2006) Prevalence and Evolution of Core Photosystem II Genes in Marine Cyanobacterial Viruses and Their Hosts. PLoS Biol 4: e234.

Susskind, L. (2003) The Anthropic Landscape of String Theory. arXiv: hep-th/0302219.

Susskind, L. (2006a) The Cosmic Landscape. String Theory and the Illusion of Intelligent Design. New York-Boston: Little, Brown and Company.

Susskind, L. (2006b) The Cosmic Landscape: String Theory and the Illusion of Intelligent Design. San Francisco: Back Bay Books.

Suttle, C. A. (2005) Viruses in the Sea. Nature 437: 356–361.

Suttle, C. A. (2007) Marine Viruses – Major Players in the Global Ecosystem. Nat Rev Microbiol 5: 801–812.

Sydow, J. F., and P. Cramer. (2009) RNA Polymerase Fidelity and Transcriptional Proofreading. Curr Opin Struct Biol 19: 732–739.

Syvanen, M. (1994) Horizontal Gene Transfer: Evidence and Possible Consequences. Annu Rev Genet 28: 237–261.

Szathmary, E. (1993) Coding Coenzyme Handles: A Hypothesis for the Origin of the Genetic Code. Proc Natl Acad Sci USA 90: 9,916—9,920.

Szathmary, E. (1999) The Origin of the Genetic Code: Amino Acids as Cofactors in an RNA World. Trends Genet 15: 223–229.

Szathmary, E. (2000) The Evolution of Replicators. Philos Trans R Soc Lond B Biol Sci 355: 1,669—1,676.

Szathmary, E., and L. Demeter. (1987) Group Selection of Early Replicators and the Origin of Life. J Theor Biol 128: 463–486.

Szathmary, E., and J. Maynard Smith. (1997) From Replicators to Reproducers: The First Major Transitions Leading to Life. J Theor Biol 187: 555–571.

Takeuchi, N., and P. Hogeweg. (2008) Evolution of Complexity in RNA-Like Replicator Systems. Biol Direct 3: 11.

Takeuchi, N., P. Hogeweg, and E. V. Koonin. (2011) On the Origin of DNA Genomes: Evolution of the Division of Labor Between Template and Catalyst in Model Replicator Systems. PLoS Comput Biol, in press.

Tatusov, R. L., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, B. Kiryutin, E. V. Koonin, D. M. Krylov, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, S. Smirnov, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. (2003) The Cog Database: An Updated Version Includes Eukaryotes. BMC Bioinformatics 4: 41.

Tatusov, R. L., E. V. Koonin, and D. J. Lipman. (1997) A Genomic Perspective on Protein Families. Science 278: 631–637.

Tejero, H., A. Marin, and F. Montero. (2011) The Relationship Between Error Catastrophe, Survival of the Flattest, and Natural Selection. BMC Evol Biol 11: 2.

Theobald, D. L. (2010) A Formal Test of the Theory of Universal Common Ancestry. Nature 465: 219–222.

Toor, N., K. S. Keating, S. D. Taylor, and A. M. Pyle. (2008) Crystal Structure of a Self-Spliced Group Ii Intron. Science 320: 77–82.

Treangen, T. J., and E. P. Rocha. (2011) Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes. PLoS Genet 7: e1001284.

Trifonov, E. N. (2004) The Triplet Code from First Principles. J Biomol Struct Dyn 22: 1—11.

Trifonov, E. N., I. Gabdank, D. Barash, and Y. Sobolevsky. (2006) Primordia Vita. Deconvolution from Modern Sequences. Orig Life Evol Biosph 36: 559–565.

Tuite, M. F., and T. R. Serio. (2010) The Prion Hypothesis: From Biological Anomaly to Basic Regulatory Mechanism. Nat Rev Mol Cell Biol 11: 823–833.

Turk, R. M., N. V. Chumachenko, and M. Yarus. (2010) Multiple Translational Products from a Five-Nucleotide Ribozyme. Proc Natl Acad Sci USA 107: 4,585—4,589.

Tyedmers, J., M. L. Madariaga, and S. Lindquist. (2008) Prion Switching in Response to Environmental Stress. PLoS Biol 6: e294.

Ulrich, L. E., E. V. Koonin, and I. B. Zhulin. (2005) One-Component Systems Dominate Signal Transduction in Prokaryotes. Trends Microbiol 13: 52–56.

Vabulas, R. M., S. Raychaudhuri, M. Hayer-Hartl, and F. U. Hartl. (2010) Protein Folding in the Cytoplasm and the Heat Shock Response. Cold Spring Harb Perspect Biol 2: a004390.

Van den Born, E., M. V. Omelchenko, A. Bekkelund, V. Leihne, E. V. Koonin, V. V. Dolja, and P. O. Falnes. (2008) Viral Alkb Proteins Repair RNA Damage by Oxidative Demethylation. Nucleic Acids Res 36: 5,451—5,461.

Van der Giezen, M. (2009) Hydrogenosomes and Mitosomes: Conservation and Evolution of Functions. J Eukaryot Microbiol 56: 221–231.

Van der Oost, J., M. M. Jore, E. R. Westra, M. Lundgren, and S. J. Brouns. (2009) CRISPR-Based Adaptive and Heritable Immunity in Prokaryotes. Trends Biochem Sci 34: 401–407.

Van Etten, J. L., L. C. Lane, and D. D. Dunigan. (2010) DNA Viruses: The Really Big Ones (Giruses). Annu Rev Microbiol 64: 83–99.

Van Melderen, L. (2010) Toxin – Antitoxin Systems: Why So Many, What For? Curr Opin Microbiol 13: 781–785.

Van Melderen, L., and M. Saavedra De Bast. (2009) Bacterial Toxin – Antitoxin Systems: More Than Selfish Entities? PLoS Genet 5: e1000437.

Van Niel, C. B. (1955) Natural Selection in the Microbial World. J Gen Microbiol 13: 201–217.

Van Nimwegen, E. (2003) Scaling Laws in the Functional Content of Genomes. Trends Genet 19: 479–484.

Van Valen, L. (1973) A New Evolutionary Law. Evol. Tehory 1: 1—30.

Vargas, A. O. (2009) Did Paul Kammerer Discover Epigenetic Inheritance? A Modern Look at the Controversial Midwife Toad Experiments. J Exp Zool B Mol Dev Evol 312: 667–678.

Venn, J. (1866) The Logic of Chance: An Essay on the Foundations and Province of the Theory of Probability, with Especial Reference to its Application to Moral and Socila Science. London and Cambridge: MacMillan and Co.

Venters, B. J., and B. F. Pugh. (2009) How Eukaryotic Genes Are Transcribed. Crit Rev Biochem Mol Biol 44: 117–141.

Veretnik, S., C. Wills, P. Youkharibache, R. E. Valas, and P. E. Bourne. (2009) Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome. PLoS Comput Biol 5: e1000315.

Vetsigian, K., C. Woese, and N. Goldenfeld. (2006) Collective Evolution and the Genetic Code. Proc Natl Acad Sci USA 103: 10,696—10,701.

Vilenkin, A. (1983) The Birth of Inflationary Universes. Phys. Rev. D 27: 2,848.

Vilenkin, A. (2007) Many Worlds in One: The Search for Other Universes. Boston: Hill and Wang.

Vogel, G. (1997) Prusiner Recognized for Once-Heretical Prion Theory. Science 278: 214.

Vogel, G., and E. Pennisi. (2009) Physiology Nobel. U.S. Researchers Recognized for Work on Telomeres. Science 326: 212–213.

Volker, C., and A. N. Lupas. (2002) Molecular Evolution of Proteasomes. Curr Top Microbiol Immunol 268: 1—22.

Von Dohlen, C. D., S. Kohler, S. T. Alsop, and W. R. McManus. (2001) Mealybug Beta-Proteobacterial Endosymbionts Contain Gamma-Proteobacterial Symbionts. Nature 412: 433–436.

Von Neumann, J. (1966) Theory of Self-Reproducing Automata. Urbana, IL: University of Illinois Press.

Wachtershauser, G. (1997) The Origin of Life and Its Methodological Challenge. J Theor Biol 187: 483–494.

Waddington, C. H., and E. Robertson. (1966) Selection for Developmental Canalisation. Genet Res 7: 303–312.

Wagner, A. (2008a) Neutralism and Selectionism: A Network-Based Reconciliation. Nat Rev Genet 9: 965–974.

Wagner, A. (2008b) Robustness and Evolvability: A Paradox Resolved. Proc Biol Sci 275: 91—100.

Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. (1982) Distantly Related Sequences in the Alpha – and Beta-Subunits of Atp Synthase, Myosin, Kinases, and Other Atp-Requiring Enzymes and a Common Nucleotide Binding Fold. Embo J 1: 945–951.

Wang, E. T., R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. F. Kingsmore, G. P. Schroth, and C. B. Burge. (2008) Alternative Isoform Regulation in Human Tissue Transcriptomes. Nature 456: 470–476.

Wang, X., Y. Kim, Q. Ma, S. H. Hong, K. Pokusaeva, J. M. Sturino, and T. K. Wood. (2010) Cryptic Prophages Help Bacteria Cope with Adverse Environments. Nat Commun 1: 147.