Searching journal content for articles similar to Wolf et al. 9 (1): 17.

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  1. 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
    ...Whole-genome Trees Based on the Occurrence of Folds and Orthologs: Implications for Comparing Genomes on Different Levels Jimmy Lin 1 and Mark Gerstein 1 , 2 1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA...
  2. 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
    ...in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold...
  3. 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
    ..., Illinois 61801, USA Abstract Protein structural diversity encompasses a finite set of architectural designs. Embedded in these topologies are evolutionary histories that we here uncover using cladistic principles and measurements of protein-fold usage and sharing. The reconstructed phylogenies...
  4. LETTER: Evolution of protein domain promiscuity in eukaryotes
    • Malay Kumar Basu,
    • Liran Carmel,
    • Igor B. Rogozin,
    • and Eugene V. Koonin
    Genome Res. March 2008 18: 449-461; Published in Advance January 29, 2008, doi:10.1101/gr.6943508
    ...structural folds ( Doolittle 1995 ; Vogel et al. 2004 ; Orengo and Thornton 2005 ; Fong et al. 2007 ; Han et al. 2007 ). Some of these domain combinations are stable during evolution whereas others are more labile. Accordingly, domains differ in their tendency to appear in variable multidomain contexts...
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  5. RESOURCE: Links from Genome Proteins to Known 3-D Structures
    • Yanli Wang,
    • Stephen Bryant,
    • Roman Tatusov,
    • and Tatiana Tatusova
    Genome Res. October 1, 2000 10: 1643-1647; doi:10.1101/gr.143200
    ...names and protein names, and one may search for a protein of interest using the find feature of a WWW browser. One may also select a region from the physical map of the , or use the listing of BLAST sequence neighbors grouped by taxonomic superkingdom. These routes also lead to a listing of any...
  6. LETTER: Prokaryotic phylogenies inferred from protein structural domains
    • Eric J. Deeds,
    • Hooman Hennessey,
    • and Eugene I. Shakhnovich
    Genome Res. March 2005 15: 393-402; doi:10.1101/gr.3033805
    .... The structural domains used in this work also have advantages when compared with structural information that has been used to infer phylogenies in previous studies ( Wolf et al. 1999 ; Lin and Gerstein 2000 ). These studies were based on the “fold” level of structural classification, which correspond to clusters...
  7. 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
    .... The known PMK enzymes encoded by metazoan s are unrelated to the galactokinase family, and their evolutionary origin was unclear. We found that metazoan PMK are distantly related to nucleoside monophosphate kinases found in all superkingdoms of life and in viruses. The database searches revealed moderate...
  8. Methods: Visualizing Sequence Similarity of Protein Families
    • Vamsi Veeramachaneni and
    • Wojciech Makałowski
    Genome Res. June 2004 14: 1160-1169; Published in Advance May 12, 2004, doi:10.1101/gr.2079204
  9. ARTICLE: Structural Characterization of the Human Proteome
    • Arne Müller,
    • Robert M. MacCallum,
    • and Michael J.E. Sternberg
    Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
    ...structural and functional features are common and which confer species specificity. In this paper, we present an integrated analysis of the proteomes of human and 13 other species considering the folds of globular domains, the presence of transmembrane proteins, and the extent to which the proteomes can...
  10. RESEARCH: Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell
    • Kira S. Makarova,
    • L. Aravind,
    • Michael Y. Galperin,
    • Nick V. Grishin,
    • Roman L. Tatusov,
    • Yuri I. Wolf,
    • and Eugene V. Koonin
    Genome Res. July 1, 1999 9: 608-628; doi:10.1101/gr.9.7.608
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