E V Koonin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint 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
  2. ncbi request reprint 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
  3. ncbi request reprint 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
  4. 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
  5. ncbi 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications265 found, 100 shown here

  1. ncbi request reprint 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
    ....
  2. ncbi request reprint 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. ..
  3. ncbi request reprint 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...
  4. 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. ..
  5. ncbi 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
    ....
  6. 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...
  7. 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...
  8. 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...
  9. 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
    ....
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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...
  14. 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
    ....
  15. 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
    ....
  16. 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...
  17. 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...
  18. 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
    ....
  19. 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...
  20. 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...
  21. 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
    ....
  22. 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. ..
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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. ..
  28. 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. ..
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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
    ....
  34. 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
    ....
  35. 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
    ....
  36. 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...
  37. 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
    ....
  38. 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...
  39. 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...
  40. 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
    ....
  41. 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...
  42. 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
    ....
  43. 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
    ....
  44. 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...
  45. 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...
  46. 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...
  47. 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...
  48. 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...
  49. 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...
  50. 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
    ....
  51. 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'...
  52. 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...
  53. 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...
  54. 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...
  55. 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...
  56. 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)...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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
    ....
  62. 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
    ....
  63. 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
    ....
  64. 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
    ....
  65. 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...
  66. 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
    ....
  67. 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...
  68. 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...
  69. 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...
  70. 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...
  71. 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
    ....
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. 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...
  78. 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...
  79. 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...
  80. 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...
  81. 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...
  82. 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...
  83. 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...
  84. 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...
  85. 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...
  86. 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...
  87. 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...
  88. 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...
  89. 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...
  90. 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...
  91. 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...
  92. 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
    ....