Ruben E Valas

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc History of biological metal utilization inferred through phylogenomic analysis of protein structures
    Christopher L Dupont
    Microbial and Environmental Genomics Group, J Craig Venter Institute, La Jolla, CA 92121, USA
    Proc Natl Acad Sci U S A 107:10567-72. 2010
  2. pmc Rethinking proteasome evolution: two novel bacterial proteasomes
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, La Jolla, CA 92093, USA
    J Mol Evol 66:494-504. 2008
  3. pmc Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life
    Ruben E Valas
    Bioinformatics Program, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 4:30. 2009
  4. pmc Save the tree of life or get lost in the woods
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 5:44. 2010
  5. pmc The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 6:16. 2011
  6. pmc Nothing about protein structure classification makes sense except in the light of evolution
    Ruben E Valas
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 0743, USA
    Curr Opin Struct Biol 19:329-34. 2009
  7. pmc Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
    Talina Konotchick
    J Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
    New Phytol 198:398-407. 2013

Collaborators

Detail Information

Publications7

  1. pmc History of biological metal utilization inferred through phylogenomic analysis of protein structures
    Christopher L Dupont
    Microbial and Environmental Genomics Group, J Craig Venter Institute, La Jolla, CA 92121, USA
    Proc Natl Acad Sci U S A 107:10567-72. 2010
    ..The results presented here provide an evolutionary timeline based on genomic characteristics, and key hypotheses can be tested by alternative geochemical methods...
  2. pmc Rethinking proteasome evolution: two novel bacterial proteasomes
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, La Jolla, CA 92093, USA
    J Mol Evol 66:494-504. 2008
    ..We have found different combinations of Anbu, BPH, and HslV within these bacterial genomes, which raises questions about specialized protein degradation systems...
  3. pmc Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life
    Ruben E Valas
    Bioinformatics Program, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 4:30. 2009
    ..However the two most comprehensive attempts at this strategy, performed by Cavalier-Smith and Lake et al., have excluded each other's rootings...
  4. pmc Save the tree of life or get lost in the woods
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 5:44. 2010
    ..We argue that trees may still be a useful representation for evolutionary histories in light of new data...
  5. pmc The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon
    Ruben E Valas
    Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Biol Direct 6:16. 2011
    ..The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed...
  6. pmc Nothing about protein structure classification makes sense except in the light of evolution
    Ruben E Valas
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 0743, USA
    Curr Opin Struct Biol 19:329-34. 2009
    ..The desired classification scheme is then one in which a fold is merely semantics and structure can be classified as either ancestral or derived...
  7. pmc Transcriptomic analysis of metabolic function in the giant kelp, Macrocystis pyrifera, across depth and season
    Talina Konotchick
    J Craig Venter Institute, 10355 Science Center Drive, San Diego, CA, USA
    New Phytol 198:398-407. 2013
    ..g. nitrite reductase) were upregulated at depth compared with the surface, supporting a conceptual biological model of depth-dependent physiology...