E V Koonin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Virology: Gulliver among the Lilliputians
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Curr Biol 15:R167-9. 2005
  2. doi request reprint 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
  3. doi request reprint 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. doi request reprint 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

Collaborators

Detail Information

Publications234 found, 100 shown here

  1. ncbi request reprint Virology: Gulliver among the Lilliputians
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Curr Biol 15:R167-9. 2005
    ..2 Mb genome of the mimivirus is predicted to contain 1262 genes and is much bigger than the genomes of many parasitic bacteria...
  2. doi request reprint 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
    ..This article was reviewed by Patrick Forterre and Lakshminarayan Iyer. For the full reviews, see the Reviewers' reports section. ..
  3. doi request reprint 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. ..
  4. 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. ..
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. doi request reprint 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
    ....
  11. 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
    ....
  12. 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...
  13. 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
    ....
  14. 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...
  15. 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...
  16. 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
    ....
  17. 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...
  18. 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
    ....
  19. 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
    ....
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. pmc Archaeal origin of tubulin
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 7:10. 2012
    ..These findings expand the emerging picture of the origin of key components of eukaryotic functional systems from ancestral forms that are scattered among the extant archaea...
  25. pmc Nature and intensity of selection pressure on CRISPR-associated genes
    Nobuto Takeuchi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    J Bacteriol 194:1216-25. 2012
    ..However, we failed to detect evidence of strong positive selection in any of the cas genes...
  26. pmc Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virol J 6:223. 2009
    ....
  27. pmc Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biol 8:59. 2009
    ..However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'...
  28. pmc Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
    Jimmy H Saw
    Department of Microbiology, University of Hawai i, 2538 The Mall, Honolulu, HI 96822, USA
    Genome Biol 9:R161. 2008
    ..The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life...
  29. pmc A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans
    Mircea Podar
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Genome Biol 9:R158. 2008
    ..Little is known about the mechanisms that enable this relationship...
  30. pmc Evolution of gene fusions: horizontal transfer versus independent events
    Itai Yanai
    Bioinformatics Graduate Program and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Genome Biol 3:research0024. 2002
    ..Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution...
  31. pmc How stands the Tree of Life a century and a half after The Origin?
    Maureen A O'Malley
    Department of Philosophy, Quadrangle A14, University of Sydney, NSW 2006, Australia
    Biol Direct 6:32. 2011
    ..The original TOL hypothesis has failed but a new "statistical TOL hypothesis" is promising. The TOL heuristic usefully organizes data without positing fundamental evolutionary truth...
  32. pmc Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Biol Direct 6:38. 2011
    ..Comparative analysis of the Cas protein sequences and structures led to the classification of the CRISPR-Cas systems into three Types (I, II and III)...
  33. pmc A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
    Diana Chernikova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 6:26. 2011
    ..Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya...
  34. pmc The prokaryotic V4R domain is the likely ancestor of a key component of the eukaryotic vesicle transport system
    Mircea Podar
    Biosciences Division and the Bioenergy Science Center, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
    Biol Direct 3:2. 2008
    ..This suggests, for the first time, a prokaryotic origin for one of the key eukaryotic trafficking proteins...
  35. pmc A highly conserved family of inactivated archaeal B family DNA polymerases
    Igor B Rogozin
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD, 20894, USA
    Biol Direct 3:32. 2008
    ..The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication...
  36. pmc Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:51. 2009
    ..However, the details of the evolution of these genes that bear on the complexity of the putative ancestral NCLDV and on the evolutionary relationships between viruses and their hosts are not well understood...
  37. pmc Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 4:19. 2009
    ....
  38. pmc U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
    Malay Kumar Basu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Biol Direct 3:19. 2008
    ....
  39. pmc The origins of phagocytosis and eukaryogenesis
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:9. 2009
    ....
  40. pmc Exceptional error minimization in putative primordial genetic codes
    Artem S Novozhilov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:44. 2009
    ....
  41. pmc Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia
    Shaobin Hou
    Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall 319, Honolulu, Hawaii, 96822, USA
    Biol Direct 3:26. 2008
    ..Similar organisms were independently isolated from geothermal systems in Italy and Russia...
  42. pmc Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health Bethesda, Maryland 20894, USA
    Biol Direct 5:33. 2010
    ....
  43. pmc Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:33. 2007
    ..One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes...
  44. pmc Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements
    Kira S Makarova
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 4:29. 2009
    ..Many prokaryotes also encode homologs of Argonaute-PIWI proteins but their functions remain unknown...
  45. pmc Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
    Maxim Y Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:40. 2008
    ....
  46. pmc Accumulation of GC donor splice signals in mammals
    Alexander Churbanov
    Loyola University Medical Center, 2160 S First Ave, Maywood, IL, 60153, USA
    Biol Direct 3:30. 2008
    ..Thus, there was substantive accumulation of GC donor splice sites during the evolution of mammals. Accumulation of GC sites might have been driven by selection for alternative splicing...
  47. pmc Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 3:7. 2008
    ..However, a non-negligible level of homoplasy was detected...
  48. pmc Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Biol Direct 5:31. 2010
    ..In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins...
  49. pmc Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors
    Tahir H Tahirov
    Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198 7696, USA
    Biol Direct 4:11. 2009
    ..However, the details of the evolutionary relationships between DNA polymerases of archaea and eukaryotes remain unresolved...
  50. pmc Evolutionary primacy of sodium bioenergetics
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Biol Direct 3:13. 2008
    ..The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments...
  51. pmc Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape
    Artem S Novozhilov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 2:24. 2007
    ..However, it remains unclear how much evolution the standard code underwent, what is the level of optimization, and what is the likely starting point...
  52. pmc Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea
    Fabian Blombach
    Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    Biol Direct 4:39. 2009
    ..These findings suggest that functional separation of RNA polymerases for protein-coding genes and non-coding RNAs might predate the origin of the Eukaryotes...
  53. pmc Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein
    C Leong Ng
    York Structural Biology Laboratory, Chemistry Department, University of York, York, YO10 5YW, UK
    BMC Struct Biol 9:32. 2009
    ..Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown...
  54. pmc Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Struct Biol 3:1. 2003
    ..No evolutionary relationship between RDRP and other polymerases has been reported so far, hence the origin of this eukaryote-specific polymerase remains a mystery...
  55. pmc Evolution of alternative and constitutive regions of mammalian 5'UTRs
    Alissa M Resch
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    BMC Genomics 10:162. 2009
    ..By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized...
  56. pmc Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    Colin N Dewey
    National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Genomics 7:311. 2006
    ..We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons...
  57. pmc The relationship of protein conservation and sequence length
    David J Lipman
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 2:20. 2002
    ..However, additional evolutionary forces that affect the length of a protein may be revealed by studying the length distributions of proteins evolving under weaker functional constraints...
  58. pmc Duplicated genes evolve slower than singletons despite the initial rate increase
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 4:22. 2004
    ..It has been shown that, shortly after the duplication, genes seem to experience a considerable relaxation of purifying selection...
  59. pmc No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 3:1. 2003
    ..However, the extent to which the number of protein-protein interactions influences evolutionary rates remains unclear. Here, we address this question at several different levels of evolutionary relatedness...
  60. pmc 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
    Boris G Mirkin
    School of Information Systems and Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK
    BMC Evol Biol 3:2. 2003
    ..This complicates the notion of a species tree, which needs to be re-interpreted as a prevailing evolutionary trend, rather than the full depiction of evolution, and makes reconstruction of ancestral genomes a non-trivial task...
  61. pmc Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance
    Marina V Omelchenko
    Department of Pathology, F E Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814 4799, USA
    BMC Evol Biol 5:57. 2005
    ..radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria...
  62. pmc Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models
    Georgy P Karev
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 4:32. 2004
    ..Evolution of ensembles of gene families can be described with Birth, Death, and Innovation Models (BDIMs). Analysis of the properties of different versions of BDIMs has the potential of revealing important features of genome evolution...
  63. pmc Birth and death of protein domains: a simple model of evolution explains power law behavior
    Georgy P Karev
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 2:18. 2002
    ..Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution...
  64. pmc Global similarity and local divergence in human and mouse gene co-expression networks
    Panayiotis Tsaparas
    Basic Research Unit, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
    BMC Evol Biol 6:70. 2006
    ..Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species...
  65. pmc Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis
    Vladimir N Babenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
    BMC Cancer 6:36. 2006
    ..This conclusion is supported by accumulating experimental evidence of evolution of new functions of p53 in tumors. These findings prompted a genome-wide analysis of possible positive selection during tumor evolution...
  66. pmc The COG database: an updated version includes eukaryotes
    Roman L Tatusov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Bioinformatics 4:41. 2003
    ..Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies...
  67. pmc Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
    Marina V Omelchenko
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R55. 2003
    ....
  68. ncbi request reprint Beyond complete genomes: from sequence to structure and function
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Curr Opin Struct Biol 8:355-63. 1998
    ..Taken together, sequence and structure comparisons provide a powerful methodology that can successfully complement traditional experimental approaches...
  69. ncbi request reprint Horizontal gene transfer: the path to maturity
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Microbiol 50:725-7. 2003
  70. pmc Comparative genomics of Archaea: how much have we learned in six years, and what's next?
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:115. 2003
    ..The majority of archaeal genes have not been experimentally characterized, but novel functional pathways have been predicted...
  71. ncbi request reprint Genomics: re-evaluation of translation machinery evolution
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Curr Biol 8:R266-9. 1998
    ....
  72. ncbi request reprint p53 gain-of-function: tumor biology and bioinformatics come together
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 4:686-8. 2005
    ..The latter observation suggests an unexpected level of complexity of p53 evolution in tumors, with distinct novel function gained in different tumors...
  73. pmc Getting positive about selection
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:331. 2003
    ..A report on the 68th Symposium on Quantitative Biology, The Genome of Homo Sapiens', Cold Spring Harbor, USA, 28 May-2 June 2003...
  74. pmc Darwinian evolution in the light of genomics
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Nucleic Acids Res 37:1011-34. 2009
    ..Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future...
  75. ncbi request reprint How many genes can make a cell: the minimal-gene-set concept
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Annu Rev Genomics Hum Genet 1:99-116. 2000
    ....
  76. ncbi request reprint A non-adaptationist perspective on evolution of genomic complexity or the continued dethroning of man
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bldg 38A, Bethesda, Maryland 20894, USA
    Cell Cycle 3:280-5. 2004
    ..I further consider the far-reaching biological and philosophical implications of this theory...
  77. pmc Towards a postmodern synthesis of evolutionary biology
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Cell Cycle 8:799-800. 2009
    ..This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas...
  78. pmc The wonder world of microbial viruses
    Eugene V Koonin
    National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health, Building 38A, Room 5N503, 8600 Rockville Pike, Bethesda, MA 20894, USA
    Expert Rev Anti Infect Ther 8:1097-9. 2010
    ..Viruses, in particular viruses that infect prokaryotes and unicellular eukaryotes, are emerging as the most abundant class of biological entities on earth and a major evolutionary and geochemical force...
  79. pmc Two domains of superfamily I helicases may exist as separate proteins
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland 20894, USA
    Protein Sci 5:178-80. 1996
    ..It is speculated that PhoH and YjhR have evolved from helicases through deletion of the portions of the helicase genes coding for the C- and N-terminal domain, respectively...
  80. pmc Intron-dominated genomes of early ancestors of eukaryotes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Hered 100:618-23. 2009
    ..An organism with such an unusual genome architecture could survive only under conditions of a severe population bottleneck...
  81. pmc The phylogenetic forest and the quest for the elusive tree of life
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Cold Spring Harb Symp Quant Biol 74:205-13. 2009
    ..The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process...
  82. ncbi request reprint Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Curr Opin Genet Dev 6:757-62. 1996
    ..A comparison of the protein sequences encoded in these genes with those of the proteins encoded in the complete yeast genome suggests that the last common ancestor of all extant life might have had an RNA genome...
  83. ncbi request reprint Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Microbiol 25:619-37. 1997
    ..It is likely that the evolution of archaea included at least one major merger between ancestral cells from the bacterial lineage and the lineage leading to the eukaryotic nucleocytoplasm...
  84. ncbi request reprint Comparative genomics, minimal gene-sets and the last universal common ancestor
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, NIH Building 38A, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 1:127-36. 2003
    ..The present estimate suggests a simple last universal common ancestor with only 500-600 genes...
  85. ncbi request reprint Prokaryotic genomes: the emerging paradigm of genome-based microbiology
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland 20894, USA
    Curr Opin Genet Dev 7:757-63. 1997
    ....
  86. pmc The fundamental units, processes and patterns of evolution, and the tree of life conundrum
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:33. 2009
    ..The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject...
  87. pmc A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 5:R7. 2004
    ....
  88. pmc The Origin at 150: is a new evolutionary synthesis in sight?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Trends Genet 25:473-5. 2009
    ..The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution...
  89. ncbi request reprint Paralogs and mutational robustness linked through transcriptional reprogramming
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
    Bioessays 27:865-8. 2005
    ....
  90. ncbi request reprint On the origin of genomes and cells within inorganic compartments
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 21:647-54. 2005
    ....
  91. pmc Origin and evolution of the genetic code: the universal enigma
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    IUBMB Life 61:99-111. 2009
    ..A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system...
  92. pmc Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Nucleic Acids Res 36:6688-719. 2008
    ....
  93. pmc The common ancestry of life
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 5:64. 2010
    ....
  94. ncbi request reprint Horizontal gene transfer in prokaryotes: quantification and classification
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Annu Rev Microbiol 55:709-42. 2001
    ....
  95. pmc New variants of known folds: do they bring new biology?
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1226-9. 2010
    ..These structures do not supplant direct biochemical experiments, but are indispensable for the complete characterization of proteins...
  96. ncbi request reprint Origin and evolution of eukaryotic apoptosis: the bacterial connection
    E V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Cell Death Differ 9:394-404. 2002
    ....
  97. pmc The origin and early evolution of eukaryotes in the light of phylogenomics
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 11:209. 2010
    ..Phylogenomics of eukaryote supergroups suggest a highly complex last common ancestor of eukaryotes and a key role of mitochondrial endosymbiosis in the origin of eukaryotes...
  98. pmc 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
    K S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 2:RESEARCH 0033. 2001
    ..Here we analyze all such cases and attempt to reconstruct the evolutionary history of these ribosomal proteins...
  99. pmc Constraints and plasticity in genome and molecular-phenome evolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Rev Genet 11:487-98. 2010
    ..Taken together, these findings are starting to reveal complex networks of evolutionary processes that must be integrated to attain a new synthesis of evolutionary biology...
  100. pmc Is evolution Darwinian or/and Lamarckian?
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Biol Direct 4:42. 2009
    ..In contrast, Darwin assigned a greater importance to random, undirected change that provided material for natural selection...
  101. ncbi request reprint Evolutionary systems biology: links between gene evolution and function
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Opin Biotechnol 17:481-7. 2006
    ..These developments show that, although the methodological basis of evolutionary systems biology is not yet fully solidified, this area of research is already starting to yield fundamental biological insights...