E V Koonin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. doi request reprint Diversity, classification and evolution of CRISPR-Cas systems
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA Electronic address
    Curr Opin Microbiol 37:67-78. 2017
  2. doi request reprint Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Life (Basel) 7:. 2017
  3. doi request reprint Evolutionary Genomics of Defense Systems in Archaea and Bacteria
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 email
    Annu Rev Microbiol 71:233-261. 2017
  4. doi request reprint Reconstruction of the evolution of microbial defense systems.
    Pere Puigb
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Evol Biol 17:94. 2017
  5. doi request reprint Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Curr Opin Virol 25:7-15. 2017
  6. doi request reprint Cellular origin of the viral capsid-like bacterial microcompartments
    Mart Krupovic
    Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
    Biol Direct 12:25. 2017
  7. doi request reprint The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis
    Sergei L Mekhedov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 12:13. 2017
  8. doi request reprint Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    Biol Direct 12:5. 2017
  9. pmc Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease
    Mart Krupovic
    Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, 75015, France
    Biol Direct 10:65. 2015
  10. pmc Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes
    Mart Krupovic
    Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, 75015, France
    Biol Direct 10:12. 2015

Collaborators

Detail Information

Publications310 found, 100 shown here

  1. doi request reprint Diversity, classification and evolution of CRISPR-Cas systems
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA Electronic address
    Curr Opin Microbiol 37:67-78. 2017
    ..Comparative analysis of the effector complexes indicates that Class 2 systems evolved from mobile genetic elements on multiple, independent occasions...
  2. doi request reprint Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Life (Basel) 7:. 2017
    ....
  3. doi request reprint Evolutionary Genomics of Defense Systems in Archaea and Bacteria
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 email
    Annu Rev Microbiol 71:233-261. 2017
    ....
  4. doi request reprint Reconstruction of the evolution of microbial defense systems.
    Pere Puigb
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Evol Biol 17:94. 2017
    ..Apart from the paucity and the low flux of defense genes in parasitic bacteria with deteriorating genomes, there is no clear connection between the evolutionary regime of defense systems and microbial life style...
  5. doi request reprint Polintons, virophages and transpovirons: a tangled web linking viruses, transposons and immunity
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Curr Opin Virol 25:7-15. 2017
    ..Taken together, these findings show that Polintons, PLV, virophages and transpovirons form a dynamic network of integrating mobile genetic elements that contribute to the cellular antivirus defense and host-virus coevolution...
  6. doi request reprint Cellular origin of the viral capsid-like bacterial microcompartments
    Mart Krupovic
    Department of Microbiology, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
    Biol Direct 12:25. 2017
    ..This finding is in line with the hypothesis that many major viral structural proteins have been recruited from cellular proteomes...
  7. doi request reprint The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis
    Sergei L Mekhedov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 12:13. 2017
    ..These findings suggest that SAMD9 is a hub of a novel, evolutionarily conserved defense network that remains to be characterized...
  8. doi request reprint Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    Biol Direct 12:5. 2017
    ..This article was reviewed by Mikhail Gelfand and Bojan Zagrovic...
  9. pmc Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease
    Mart Krupovic
    Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, 75015, France
    Biol Direct 10:65. 2015
    ..To our knowledge, this is the first described case of exaptation of an enzyme for a virus capsid protein function...
  10. pmc Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes
    Mart Krupovic
    Department of Microbiology, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, 75015, France
    Biol Direct 10:12. 2015
    ..The chimeric genomes of amalgaviruses are a testament to the effectively limitless gene exchange between viruses that shaped the evolution of the virosphere...
  11. pmc Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon
    Vladimir V Kapitonov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 10:20. 2015
    ....
  12. pmc A new family of hybrid virophages from an animal gut metagenome
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 10:19. 2015
    ..Virion proteins of mimiviruses were detected in the same metagenomes as the RVP suggesting that the virophages of the new family parasitize on giant viruses that infect protist inhabitants of the rumen...
  13. pmc Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae
    Isabelle Pagnier
    URMITE, CNRS UMR IRD 6236, Faculte de Medecine, Universite de la Mediterranee, 27 Bd Jean Moulin, 13385, Marseille Cedex 5, France
    Biol Direct 10:13. 2015
    ....
  14. pmc Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation
    Fyodor A Kondrashov
    Section on Ecology, Behavior and Evolution, Division of Biological Sciences, University of California at San Diego, 2218 Muir Biology Building, La Jolla, CA 92093, USA
    Biol Direct 1:31. 2006
    ..In order to clarify the status of the MS and ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic study...
  15. pmc Mathematical modeling of tumor therapy with oncolytic viruses: regimes with complete tumor elimination within the framework of deterministic models
    Artem S Novozhilov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:6. 2006
    ..The interaction between an oncolytic virus and tumor cells is amenable to mathematical modeling using adaptations of techniques employed previously for modeling other types of virus-cell interaction...
  16. pmc On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:14. 2007
    ....
  17. pmc Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 1:34. 2006
    ....
  18. pmc Mutational hotspots in the TP53 gene and, possibly, other tumor suppressors evolve by positive selection
    Galina V Glazko
    Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
    Biol Direct 1:4. 2006
    ..The origin of hotspots is of major importance because it has been suggested that mutable contexts could be used to infer mechanisms of mutagenesis contributing to tumorigenesis...
  19. pmc Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics
    Georgy P Karev
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:30. 2006
    ..There is no unifying theoretical framework in mathematical modeling of carcinogenesis that would account for parametric heterogeneity...
  20. pmc MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes
    Sivakumar Kannan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Evol Biol 14:237. 2014
    ..Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire...
  21. pmc Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems
    Jaime Iranzo
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Evol Biol 15:43. 2015
    ..Coevolution of these different but interacting defense strategies yields complex evolutionary regimes...
  22. pmc Patterns of intron gain and conservation in eukaryotic genes
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Evol Biol 7:192. 2007
    ..To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions...
  23. pmc A novel group of diverse Polinton-like viruses discovered by metagenome analysis
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Biol 13:95. 2015
    ..Here we report the metagenomic discovery of a distinct group of diverse viruses that are distantly related to the eukaryotic virus-like transposons of the Polinton superfamily...
  24. pmc Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection
    Nobuto Takeuchi
    Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
    BMC Biol 13:20. 2015
    ..These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena...
  25. doi request reprint Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.
    Pere Puigb
    BMC Biol 12:66. 2014
    ....
  26. pmc A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea
    David M Kristensen
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 16:380. 2015
    ....
  27. pmc Disentangling the effects of selection and loss bias on gene dynamics
    Jaime Iranzo
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
    Proc Natl Acad Sci U S A 114:E5616-E5624. 2017
    ..The horizontal gene transfer to loss ratio, but not duplication to loss ratio, correlates with genome size, potentially explaining increased abundance of neutral and costly elements in larger genomes...
  28. pmc Multiple origins of viral capsid proteins from cellular ancestors.
    Mart Krupovic
    Proc Natl Acad Sci U S A 114:E2401-E2410. 2017
    ....
  29. pmc Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Stud Hist Philos Biol Biomed Sci 59:125-34. 2016
    ....
  30. pmc The meaning of biological information
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Philos Trans A Math Phys Eng Sci 374:. 2016
    ..Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology. ..
  31. pmc Viruses and mobile elements as drivers of evolutionary transitions
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Philos Trans R Soc Lond B Biol Sci 371:. 2016
    ..This article is part of the themed issue 'The major synthetic evolutionary transitions'. ..
  32. pmc Splendor and misery of adaptation, or the importance of neutral null for understanding evolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    BMC Biol 14:114. 2016
    ..To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none...
  33. pmc Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD, 20894, USA
    Biol Direct 11:9. 2016
    ..These findings emphasize the continuity between random and directed mutations and the critical importance of evolved mechanisms that govern the mutational process...
  34. pmc The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    J Mol Evol 80:244-50. 2015
    ....
  35. pmc Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Philos Trans R Soc Lond B Biol Sci 370:20140333. 2015
    ....
  36. pmc Why the Central Dogma: on the nature of the great biological exclusion principle
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Instittues of Health, Bethesda, MD, 20894, USA
    Biol Direct 10:52. 2015
    ....
  37. pmc Archaeal ancestors of eukaryotes: not so elusive any more
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    BMC Biol 13:84. 2015
    ..The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis. ..
  38. doi request reprint Origins and evolution of viruses of eukaryotes: The ultimate modularity
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Virology 479:2-25. 2015
    ..Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes. ..
  39. pmc Virus world as an evolutionary network of viruses and capsidless selfish elements
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    Microbiol Mol Biol Rev 78:278-303. 2014
    ..Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host...
  40. pmc Chordopoxvirus protein F12 implicated in enveloped virion morphogenesis is an inactivated DNA polymerase
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 9:22. 2014
    ..Thus, F12 appears to present a rare example of a drastic, exaptive functional change in virus evolution...
  41. pmc Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 11:20-7. 2015
    ..Such analyses are expected to yield disagreements with the predictions of the current, oversimplified models and to trigger a new round of theoretical developments. ..
  42. pmc Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    Extremophiles 18:877-93. 2014
    ....
  43. pmc Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses
    Mart Krupovic
    Department of Microbiology, Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris 75015, France
    Biol Direct 9:6. 2014
    ..We propose the name 'Polintoviruses' to denote these putative viruses that could have played a central role in the evolution of several groups of DNA viruses of eukaryotes...
  44. pmc Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity
    Mart Krupovic
    Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Docteur Roux, 75015 Paris, France
    BMC Biol 12:36. 2014
    ..With the growth in the number and diversity of sequenced genomes, previously unnoticed mobile elements continue to be discovered...
  45. pmc Impairment of translation in neurons as a putative causative factor for autism
    Eugenia Poliakov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 9:16. 2014
    ....
  46. pmc Calorie restriction à Lamarck
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Cell 158:237-8. 2014
    ..Combined with recent findings in prokaryotes, these results suggest that Lamarckian-type inheritance of acquired traits is a major evolutionary phenomenon...
  47. pmc Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis
    Faina S Berezovskaya
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 9:13. 2014
    ..Mathematical modeling and initial experimental studies of CRISPR-carrying microbes and viruses reveal complex coevolutionary dynamics...
  48. doi request reprint The origins of cellular life
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, MD, 20894, USA
    Antonie Van Leeuwenhoek 106:27-41. 2014
    ....
  49. pmc Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
    Nucleic Acids Res 42:7132-44. 2014
    ..The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns. ..
  50. pmc Relative contributions of intrinsic structural-functional constraints and translation rate to the evolution of protein-coding genes
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
    Genome Biol Evol 2:190-9. 2010
    ..Together the intrinsic constraints and translation rate account for approximately 50% of the variance of the ERs. The contribution of constraints is estimated to be 3- to 5-fold greater than the contribution of translation rate...
  51. pmc Quoderat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences
    L M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 2:RESEARCH0051. 2001
    ..Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction seems to be supported by experiment...
  52. pmc Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:4626-38. 2005
    ..The results of this study demonstrate a major increase in the level of gene paralogy as a hallmark of the early evolution of eukaryotes...
  53. pmc Conservation versus parallel gains in intron evolution
    Alexander V Sverdlov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:1741-8. 2005
    ..Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation...
  54. pmc Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes
    Alexander Churbanov
    Department of Computer Science, College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA
    Nucleic Acids Res 33:5512-20. 2005
    ....
  55. doi request reprint A community experiment with fully open and published peer review.
    Eugene V Koonin
    Biol Direct 1:1. 2006
  56. pmc The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:22. 2006
    ..Beyond the formal dilemma, the more substantial side of this debate has to do with possible roles of introns in the evolution of eukaryotes...
  57. pmc The ancient Virus World and evolution of cells
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, USA
    Biol Direct 1:29. 2006
    ....
  58. pmc Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:39. 2006
    ..This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology...
  59. pmc The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:15. 2007
    ..This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception...
  60. pmc Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda
    Genome Biol Evol 2009:99-113. 2009
    ....
  61. doi request reprint CRISPR-Cas: an adaptive immunity system in prokaryotes.
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    F1000 Biol Rep 1:95. 2009
    ..The CRISPR-Cas system is a case of apparent Lamarckian inheritance...
  62. pmc The tree and net components of prokaryote evolution
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 2:745-56. 2010
    ..Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT...
  63. doi request reprint Archaeal ubiquitin-like proteins: functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
    Archaea 2010:. 2010
    ....
  64. pmc Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes
    Philippe Colson
    Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Centre National de la Recherche Scientifique UMR IRD 6236, Faculte de Medecine, Universite de la Mediterranee, Marseille, France
    Genome Biol Evol 3:737-42. 2011
    ..Detailed analysis of the protein sequences of the two Mimiviruses led to a substantial amendment of the functional annotation of the viral genomes...
  65. pmc Divergence and convergence in enzyme evolution
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Biol Chem 287:21-8. 2012
    ....
  66. pmc Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
    David Managadze
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 3:1390-404. 2011
    ....
  67. pmc Predictability of evolutionary trajectories in fitness landscapes
    Alexander E Lobkovsky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Comput Biol 7:e1002302. 2011
    ..We suggest that smoothness and the substantial deficit of peaks in the fitness landscapes of protein evolution are fundamental consequences of the physics of protein folding...
  68. pmc A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland
    Genome Biol Evol 4:1286-94. 2012
    ..We conclude that, at least in prokaryotes, genes for which independent evidence of orthology is available typically form BBH and, conversely, BBH can serve as a strong indication of gene orthology...
  69. pmc Universal pacemaker of genome evolution
    Sagi Snir
    Department of Evolutionary and Environmental Biology and the Institute of Evolution, University of Haifa Mount Carmel, Haifa, Israel
    PLoS Comput Biol 8:e1002785. 2012
    ..Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life...
  70. pmc Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage
    Niyaz Yoosuf
    Aix Marseille University, URMITE, Faculte de Medecine et de Pharmacie, Marseille, France
    Genome Biol Evol 4:1324-30. 2012
    ..Comparative genome analysis of the three lineages of the Mimiviridae revealed significant mobility of Group I self-splicing introns, with the highest intron content observed in the moumouvirus genome...
  71. pmc Replaying the tape of life: quantification of the predictability of evolution
    Alexander E Lobkovsky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
    Front Genet 3:246. 2012
    ....
  72. pmc Gene frequency distributions reject a neutral model of genome evolution
    Alexander E Lobkovsky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 5:233-42. 2013
    ..These findings indicate that, unlike some other universal distributions of genomic variables, for example, the distribution of paralogous gene family membership, the gene frequency distribution is substantially affected by selection...
  73. pmc The vast, conserved mammalian lincRNome
    David Managadze
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 9:e1002917. 2013
    ..The orthologous mammalian lincRNAs can be predicted to perform equivalent functions; accordingly, it appears likely that thousands of evolutionarily conserved functional roles of lincRNAs remain to be characterized...
  74. pmc Comparative genomics of defense systems in archaea and bacteria
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 41:4360-77. 2013
    ....
  75. doi request reprint Biology Direct: celebrating 7 years of open, published peer review.
    Eugene V Koonin
    Biol Direct 8:11. 2013
  76. pmc Stability along with extreme variability in core genome evolution
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 5:1393-402. 2013
    ..Because of this high variance, the gene-specific rate is a poor predictor of the conservation rank for any gene in any particular lineage. ..
  77. pmc Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea
    Wenqi Ran
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    MBio 5:e00956-14. 2014
    ..This work establishes the coupling between selection at the level of protein sequence and at the level of codon choice optimization as a distinct aspect of genome evolution...
  78. pmc Pandoraviruses are highly derived phycodnaviruses
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 8:25. 2013
    ..We conclude that, despite their many unusual characteristics, Pandoraviruses are highly derived phycodnaviruses. These findings imply that giant viruses have independently evolved from smaller NCLDV on at least two occasions...
  79. pmc A virocentric perspective on the evolution of life
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Electronic address
    Curr Opin Virol 3:546-57. 2013
    ..Together with the fundamental inevitability of the emergence of genomic parasites in any evolving replicator system, these multiple lines of evidence reveal the central role of viruses in the entire evolution of life. ..
  80. pmc CRISPR-Cas: evolution of an RNA-based adaptive immunity system in prokaryotes
    Eugene V Koonin
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD, USA
    RNA Biol 10:679-86. 2013
    ..Such coupling could manifest in the persistence state being induced and potentially providing conditions for more effective action of the immune system or in cell death being triggered when immunity fails. ..
  81. pmc Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
    Biol Direct 8:9. 2013
    ..A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes...
  82. pmc Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:46. 2012
    ..Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea...
  83. pmc 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
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 1:7. 2006
    ..However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis...
  84. pmc Parabolic replicator dynamics and the principle of minimum Tsallis information gain
    Georgy P Karev
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 8:19. 2013
    ..We sought to identify a more general form of the MaxEnt principle that would be applicable to parabolic growth...
  85. pmc Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes
    Alexander E Lobkovsky
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 9:1627-31. 2013
    ....
  86. pmc Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies
    Natalya Yutin
    National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virol J 10:158. 2013
    ....
  87. pmc Evolution of microbes and viruses: a paradigm shift in evolutionary biology?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
    Front Cell Infect Microbiol 2:119. 2012
    ....
  88. pmc Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virol J 10:106. 2013
    ..In the light of these findings, a reassessment of the relationships between the mimiviruses and other NCLDV and reconstruction of the evolution of giant virus genomes emerge as interesting and timely goals...
  89. pmc Elaborate security TRAINing to fight against expression of genomic junk
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Cell Cycle 12:553-4. 2013
    ....
  90. doi request reprint Evolution of cell division: from shear mechanics to complex molecular machineries
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Cell 152:942-4. 2013
    ..Mercier et al. (2013) show that this "mechanical" division can be activated by increased lipid synthesis. Conceivably, the first cells divided via this route...
  91. doi request reprint Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes
    Eugene V Koonin
    National Center for Biotechnology Information NLM NIH, Bethesda, MD, USA
    Wiley Interdiscip Rev RNA 4:93-105. 2013
    ..Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins...
  92. pmc Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
    Biol Direct 7:40. 2012
    ....
  93. pmc Proteorhodopsin genes in giant viruses
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:34. 2012
    ..We hypothesize that viral rhodopsins modulate light-dependent signaling, in particular phototaxis, in infected protists...
  94. pmc Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virol J 9:161. 2012
    ....
  95. pmc Origin and evolution of spliceosomal introns
    Igor B Rogozin
    National Center for Biotechnology Information NLM NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA
    Biol Direct 7:11. 2012
    ....
  96. pmc Does the central dogma still stand?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 7:27. 2012
    ..This direction of the information flow is likely to be one of the important routes of environment-genome interaction and could substantially contribute to the evolution of complex adaptive traits...
  97. pmc A half-century after the molecular clock: new dimensions of molecular evolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
    EMBO Rep 13:664-6. 2012
    ..The meeting focused on phenomena that are not part of the traditional narrative of molecular evolution and which might signal a paradigm shift in the field...
  98. pmc Expanding networks of RNA virus evolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Biol 10:54. 2012
    ..Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver...
  99. pmc The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 7:7. 2012
    ..Here we present the results of in-depth phylogenomic analysis of RecJ homologs in archaea...