Yuri Wolf

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
  2. pmc Genome reduction as the dominant mode of evolution
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MA, USA
    Bioessays 35:829-37. 2013
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

Detail Information

Publications81

  1. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
    ..These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies...
  2. pmc Genome reduction as the dominant mode of evolution
    Yuri I Wolf
    National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MA, USA
    Bioessays 35:829-37. 2013
    ..Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification...
  3. 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...
  4. 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...
  5. 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...
  6. 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
    ....
  7. 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'...
  8. 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...
  9. 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)...
  10. 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
    ....
  11. 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
    ....
  12. 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
    ....
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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
    ....
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. 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...
  28. pmc Long-term trends in evolution of indels in protein sequences
    Yuri Wolf
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 7:19. 2007
    ..We studied relatively early evolutionary events and focused on protein domains which are conserved among various taxonomy groups...
  29. pmc Genome trees constructed using five different approaches suggest new major bacterial clades
    Y I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Evol Biol 1:8. 2001
    ..Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes...
  30. ncbi request reprint Coping with the quantitative genomics 'elephant': the correlation between the gene dispensability and evolution rate
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 22:354-7. 2006
    ..These studies highlight the need for truly multidimensional approaches to the issues of quantitative genomics...
  31. pmc Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    Dmitri M Krylov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 13:2229-35. 2003
    ..Thus, propensity of a gene to be lost during evolution seems to be a direct reflection of its biological importance...
  32. pmc The role of lineage-specific gene family expansion in the evolution of eukaryotes
    Olivier Lespinet
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 12:1048-59. 2002
    ..LSEs seem to be one of the principal means of adaptation and one of the most important sources of organizational and regulatory diversity in crown-group eukaryotes...
  33. pmc Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 14:29-36. 2004
    ..All of these approaches supported the coelomate clade and showed concordance between evolution of protein sequences and higher-level evolutionary events, such as domain fusion or gene loss...
  34. 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...
  35. ncbi request reprint A universal trend of amino acid gain and loss in protein evolution
    I King Jordan
    National Center for Biotechnology Information, NIH, Bethesda, Maryland 20894, USA
    Nature 433:633-8. 2005
    ..Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day...
  36. pmc The deep archaeal roots of eukaryotes
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:1619-30. 2008
    ..Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer...
  37. pmc Connected gene neighborhoods in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:2212-23. 2002
    ..Gene neighborhoods appear to evolve via complex rearrangement, with different combinations of genes from a neighborhood fixed in different lineages...
  38. 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...
  39. ncbi request reprint Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?
    Georgy P Karev
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 19:1889-900. 2003
    ....
  40. pmc Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes
    Pavel S Novichkov
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Bacteriol 191:65-73. 2009
    ....
  41. ncbi request reprint Genome trees and the tree of life
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:472-9. 2002
    ..However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution...
  42. pmc The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 106:7273-80. 2009
    ..Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation...
  43. pmc Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Res 12:962-8. 2002
    ..In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales...
  44. pmc Congruent evolution of different classes of non-coding DNA in prokaryotic genomes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:4264-71. 2002
    ..In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non-coding regions...
  45. ncbi request reprint Classification and evolution of P-loop GTPases and related ATPases
    Detlef D Leipe
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 317:41-72. 2002
    ..In addition to the classification of previously known families of GTPases and related ATPases, we introduce several previously undetected families and describe new functional predictions...
  46. pmc Unifying measures of gene function and evolution
    Yuri I Wolf
    National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine Bethesda, MD 20894, USA
    Proc Biol Sci 273:1507-15. 2006
    ....
  47. pmc Evolutionarily conserved genes preferentially accumulate introns
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 17:1045-50. 2007
    ..This apparent functional importance of introns is likely to be due, at least in part, to their multiple effects on gene expression...
  48. ncbi request reprint Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Mol Biol Evol 24:1080-90. 2007
    ..It is expected that RGC_CAM and other RGC-based methods will be crucial for these future, definitive phylogenetic studies...
  49. ncbi request reprint Purifying and directional selection in overlapping prokaryotic genes
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 18:228-32. 2002
    ..This could be a general evolutionary mode for genes emerging from noncoding sequences, in which the protein sequence has not been subject to selection...
  50. pmc Evolutionary plasticity of protein families: coupling between sequence and structure variation
    Anna R Panchenko
    Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Proteins 61:535-44. 2005
    ..Similar sequence-structure analysis performed for protein loop regions shows that evolutionary plasticity of loop regions is greater than for the protein core...
  51. pmc Selection in the evolution of gene duplications
    Fyodor A Kondrashov
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:RESEARCH0008. 2002
    ....
  52. 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
    ....
  53. 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
    ....
  54. 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...
  55. ncbi request reprint Conservation and coevolution in the scale-free human gene coexpression network
    I King Jordan
    National Center for Biotechnology Information, National Institutes of Health Bethesda, Maryland, USA
    Mol Biol Evol 21:2058-70. 2004
    ....
  56. ncbi request reprint Computational approaches for the analysis of gene neighbourhoods in prokaryotic genomes
    Igor B Rogozin
    NCBI NLM NIH, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA
    Brief Bioinform 5:131-49. 2004
    ..In this review, we discuss various computational approaches for identification of conserved gene strings and construction of local alignments of gene orders in prokaryotic genomes...
  57. 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
    ....
  58. ncbi request reprint The structure of the protein universe and genome evolution
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nature 420:218-23. 2002
    ..These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle...
  59. 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...
  60. pmc Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 2:e955. 2007
    ....
  61. pmc Universal distribution of protein evolution rates as a consequence of protein folding physics
    Alexander E Lobkovsky
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Proc Natl Acad Sci U S A 107:2983-8. 2010
    ..The results suggest that the universal distribution of the evolutionary rates of protein-coding genes is a direct consequence of the basic physics of protein folding...
  62. pmc A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 541:357-71. 2009
    ..Since the method works with intron presence-absence maps, it is expected to be instrumental for the analysis of the evolution of other binary characters as well...
  63. ncbi request reprint Potential genomic determinants of hyperthermophily
    Kira S Makarova
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Trends Genet 19:172-6. 2003
    ....
  64. doi request reprint The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups
    Eugene V Koonin
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
    Nat Rev Microbiol 6:925-39. 2008
    ..The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages...
  65. ncbi request reprint Microevolutionary genomics of bacteria
    I King Jordan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Theor Popul Biol 61:435-47. 2002
    ..This suggests the possibility that nonessential genes are responsible for driving the evolutionary diversification between strains...
  66. pmc Three distinct modes of intron dynamics in the evolution of eukaryotes
    Liran Carmel
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Genome Res 17:1034-44. 2007
    ..Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features...
  67. ncbi request reprint Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
    Igor B Rogozin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Curr Biol 13:1512-7. 2003
    ..In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent...
  68. ncbi request reprint Scale-free networks in biology: new insights into the fundamentals of evolution?
    Yuri I Wolf
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioessays 24:105-9. 2002
    ....
  69. ncbi request reprint Duplicated gelsolin family genes in zebrafish: a novel scinderin-like gene (scinla) encodes the major corneal crystallin
    Sujuan Jia
    Laboratory of Molecular and Development Biology, National Eye Institute, National Institutes of Health, 7 Memorial Dr, Bldg 7, Rm 100, Bethesda, MD 20892, USA
    FASEB J 21:3318-28. 2007
    ..Our data suggest that scinla and scinlb are diverged paralogs of the vertebrate scinderin gene and show that scinla encodes the zebrafish corneal crystallin previously called C/L-gelsolin...
  70. pmc Genome-wide molecular clock and horizontal gene transfer in bacterial evolution
    Pavel S Novichkov
    Department of Bioengineering and Bioinformatics, Moscow State University, Russia
    J Bacteriol 186:6575-85. 2004
    ..The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale...
  71. pmc The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
    Alexei I Slesarev
    Fidelity Systems, Gaithersburg, MD 20879, USA
    Proc Natl Acad Sci U S A 99:4644-9. 2002
    ..Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism...
  72. pmc Genome sequence of the deep-sea gamma-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
    Shaobin Hou
    Department of Microbiology, University of Hawaii, Snyder Hall 111, 2538 The Mall, Honolulu, HI 96822, USA
    Proc Natl Acad Sci U S A 101:18036-41. 2004
    ..In summary, the I. loihiensis genome reveals an integrated mechanism of metabolic adaptation to the constantly changing deep-sea hydrothermal ecosystem...
  73. pmc The cyanobacterial genome core and the origin of photosynthesis
    Armen Y Mulkidjanian
    School of Physics, University of Osnabruck, D 49069 Osnabruck, Germany
    Proc Natl Acad Sci U S A 103:13126-31. 2006
    ..From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer...
  74. 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...
  75. ncbi request reprint Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family
    Ekaterina Kuznetsova
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    J Biol Chem 281:36149-61. 2006
    ..Many of the secondary activities of HADs might have no immediate physiological function but could comprise a reservoir for evolution of novel phosphatases...
  76. pmc Role of hypermutability in the evolution of the genus Oenococcus
    Angela M Marcobal
    Department of Viticulture and Enology, University of California, One Shields Ave, Davis, CA 95616, USA
    J Bacteriol 190:564-70. 2008
    ..The hypermutable status of the genus Oenococcus explains the observed high level of allelic polymorphism among known O. oeni isolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments...
  77. pmc Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome
    Alexis Dufresne
    Station Biologique, Unité Mixte de Recherche 7127, Centre National de la Recherche Scientifique et Université Paris 6, BP74, 29682 Roscoff Cedex, France
    Proc Natl Acad Sci U S A 100:10020-5. 2003
    ..Because of its remarkable compactness, the genome of P. marinus SS120 might approximate the minimal gene complement of a photosynthetic organism...
  78. pmc Global analysis of posttranslational protein arginylation
    Catherine C L Wong
    The Scripps Research Institute, LaJolla, California, United States of America
    PLoS Biol 5:e258. 2007
    ..The results of our study suggest that protein arginylation is a general mechanism for regulation of protein structure and function and outline the potential role of protein arginylation in cell metabolism and embryonic development...
  79. ncbi request reprint Analysis of rare amino acid replacements supports the Coelomata clade
    Igor B Rogozin
    Mol Biol Evol 24:2594-7. 2007
    ..Direct estimation of the level of homoplasy, combined with taxon sampling with different sets of outgroup species, reinforces the support for Coelomata, whereas the effect of reversals is shown to be relatively minor...