Browsing Biomolecular Engineering Research Center Papers by Title

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Browsing Biomolecular Engineering Research Center Papers by Title

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  • Favaretto, Paola; Bhutkar, Arjun; Smith, Temple F. (Oxford University Press, 2005-09-09)
    Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study reports a computational ...
  • Hartman, Hyman; Smith, Temple F (BioMed Central, 2010-5-20)
    BACKGROUND. This paper is an attempt to trace the evolution of the ribosome through the evolution of the universal P-loop GTPases that are involved with the ribosome in translation and with the attachment of the ribosome ...
  • Bhutkar, Arjun; Gelbart, William M; Smith, Temple F (BioMed Central, 2007-11-8)
    A simple, fast, and biologically inspired computational approach for inferring genome-scale rearrangement phylogeny and ancestral gene order has been developed. This has been applied to eight Drosophila genomes. Existing ...
  • Smith, Temple F; Lee, Jung C; Gutell, Robin R; Hartman, Hyman (BioMed Central, 2008-4-22)
    BACKGROUND. The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the ...
  • Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor (Public Library of Science, 2008-10-10)
    Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic ...
  • Plasterer, Thomas N; Smith, Temple F; Mohr, Scott C (BioMed Central, 2001-06-01)
    BACKGROUND. We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein ...
  • Blanco, Enrique; Messeguer, Xavier; Smith, Temple F; Guigó, Roderic (Public Library of Science, 2006-5-26)
    We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed ...

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