Searching journal content for articles similar to Wolf et al. 9 (8): 689.

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  1. LETTER: Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
    • Olga Zhaxybayeva,
    • J. Peter Gogarten,
    • Robert L. Charlebois,
    • W. Ford Doolittle,
    • and R. Thane Papke
    Genome Res. September 2006 16: 1099-1108; Published in Advance August 9, 2006, doi:10.1101/gr.5322306
    ...genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available s. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial s reveal...
  2. ARTICLE: Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context
    • Yuri I. Wolf,
    • Igor B. Rogozin,
    • Alexey S. Kondrashov,
    • and Eugene V. Koonin
    Genome Res. March 1, 2001 11: 356-372; Published in Advance February 8, 2001, doi:10.1101/gr.161901
    ...conservation shows a much lower variance than the cooccurrence of genomes in COGs, which indicates that intragenome homogenization via recombination occurs in evolution much faster than intergenome homogenization via horizontal gene transfer and lineage-specific gene loss. The potential of using template...
  3. LETTER: Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels
    • Jimmy Lin and
    • Mark Gerstein
    Genome Res. June 1, 2000 10: 808-818; doi:10.1101/gr.10.6.808
    ...– 164 . ↵ Hennig W. ( 1965 ) Phylogenetic systematics. Ann. Rev. Entomol. 10 : 97 – 116 . ↵ Hilario E. , Gogarten J.P. ( 1993 ) Horizontal transfer of ATPase genes—the tree of life becomes a net of life. Biosystems 31 : 111 – 119 . ↵ Himmelreich R. , Hilbert H. , Plagens H. , Pirkl E. , Li B...
  4. ARTICLE: Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
    • Minglei Wang,
    • Liudmila S. Yafremava,
    • Derek Caetano-Anollés,
    • Jay E. Mittenthal,
    • and Gustavo Caetano-Anollés
    Genome Res. November 2007 17: 1572-1585; Published in Advance October 1, 2007, doi:10.1101/gr.6454307
    ...or cellular features that have been analyzed. The canonical view, stemming mostly from ribosomal RNA (rRNA), elongation factors, and other molecules of the “informational” class, suggests that the ancestor was simple and prokaryotic-like ( Woese et al. 1990 ; Woese 1998 ) and that horizontal gene transfer...
  5. LETTER: Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System
    • L. Aravind and
    • Eugene V. Koonin
    Genome Res. August 1, 2000 10: 1172-1184; doi:10.1101/gr.10.8.1172
    ....I. , Aravind L. , Grishin N.V. , Koonin E.V. ( 1999 ) Evolution of aminoacyl-tRNA synthetases—analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9 : 689 – 710 . ↵ Wootton J.C. , Federhen S. ( 1996 ) Analysis...
  6. ARTICLE: An Evolutionarily Structured Universe of Protein Architecture
    • Gustavo Caetano-Anollés and
    • Derek Caetano-Anollés
    Genome Res. July 2003 13: 1563-1571; doi:10.1101/gr.1161903
    ....F. 1999 . Phylogenetic classification and the universal tree. Science 284 : 2124 -2128. ↵ Doolittle, W.F. 2000 . The nature of the universal ancestor and the evolution of the proteome. Curr. Opin. Struct. Biol. 10 : 355 -358. ↵ Eisen, J.A. 2000 . Horizontal gene transfer among microbial s: New insights...
  7. LETTER: The Genetic Core of the Universal Ancestor
    • J. Kirk Harris,
    • Scott T. Kelley,
    • George B. Spiegelman,
    • and Norman R. Pace
    Genome Res. March 1, 2003 13: 407-412; Published in Advance February 12, 2003, doi:10.1101/gr.652803
    ..., and identifies them as potentially fruitful targets for further experimentation. The universal COGs that are not three-domain primarily contain genes that encode proteins that are not integrated into specific large macromolecular complexes, for instance, the aminoacyl tRNA synthetases (14 of 28 COGs, reviewed...
  8. LETTER: Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast
    • Fiona S.L. Brinkman,
    • Jeffrey L. Blanchard,
    • Artem Cherkasov,
    • Yossef Av-Gay,
    • Robert C. Brunham,
    • Rachel C. Fernandez,
    • B. Brett Finlay,
    • Sarah P. Otto,
    • B.F. Francis Ouellette,
    • Patrick J. Keeling,
    • Ann M. Rose,
    • Robert E.W. Hancock,
    • and Steven J.M. Jones
    Genome Res. August 1, 2002 12: 1159-1167; Published in Advance July 19, 2002, doi:10.1101/gr.341802
    ...—Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9 : 689 – 710 . ↵ Wolf Y.I. , Aravind L. , Koonin E.V. ( 1999b ) Rickettsiae and Chlamydiae: Evidence of horizontal gene transfer and gene exchange. Trends Genet. 15 : 173 – 175...
  9. ARTICLE: Biosynthesis of Isoprenoids via Mevalonate in Archaea: The Lost Pathway
    • Arian Smit and
    • Arcady Mushegian
    Genome Res. October 1, 2000 10: 1468-1484; doi:10.1101/gr.145600
    ..., sequences of mevalonate pathway genes from these bacteria are deep branches on the phylogenetic trees (Fig. 3 and data not shown), and they do not cluster with the orthologs from animal s, which would seem an obvious source of horizontally transferred genes. This tree topology could, in principle...
  10. LETTER: From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins
    • Nick V. Grishin,
    • Yuri I. Wolf,
    • and Eugene V. Koonin
    Genome Res. July 1, 2000 10: 991-1000; doi:10.1101/gr.10.7.991
    ...) Evolution of aminoacyl-tRNA synthetases — Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9 : 689 – 710 . ↵ Wootton J.C. ( 1994 ) Non-globular domains in protein sequences: Automated segmentation using complexity...
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