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.
