Robin Gutell

Email: robin.gutell@mail.utexas.edu

The remarkable advances in Nucleic Acid sequencing and Computer technology is transforming Biology to a new level of understanding. We are now attempting to understand many biological and biochemical processes, and complex structures from a molecular sequence and molecular evolution perspective, utilizing computational biology and bioinformatics. Within this new frontier the Gutell lab is primarily interested in RNA structure and the evolution of these RNAs.

Currently we are addressing the following topics:

  1. Structure Prediction with Comparative Methods: RNA secondary and tertiary structure prediction with comparative sequence analysis, with the computational tools the Gutell lab develops in #5.
  2. Principles of RNA Structure: Using the computational system in #5, determine relationships between RNA sequence and RNA higher order structure, including the identification and characterization of RNA structural motifs from an analysis of the data from #1 in parallel with the analysis of known high-resolution structures maintained in #5.
  3. RNA Folding: transforming a single RNA sequence into its biologically correct higher order structure based on the principles of RNA Structure determined in topic #2, and implemented in #5.
  4. Phylogenetic Analysis: Inferring phylogenetic and evolutionary relationships from RNA structures based on the information determined in #1 and 2, and implemented in #5.
  5. SQL-Server Databases: Develop computational tools for the analysis of multiple dimensions of data - RNA sequences, RNA structure-based alignments, secondary structure base pairing and loop information, RNA structural motifs, three-dimensional structure information for all sequences with a high-resolution crystal structure, and phyologenetic nodes for each sequence.

The lab seeks an interdisciplinary group of people, with interests in RNA structure, Molecular Biology, Molecular Evolution, Computer Science, and Applied Mathematics.

For more information, see the Gutell Lab’s Comparative RNA Web (CRW) Site at http://www.rna.ccbb.utexas.edu/

References:

Gutell R.R., Lee J.C., and Cannone J.J. (2002). The Accuracy of Ribosomal RNA Comparative Structure Models. Current Opinion in Structural Biology, 12:301-310.

Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Müller K.M., Pande N., Shang Z., Yu N., and Gutell R.R. (2002). The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and Other RNAs. BioMed Central Bioinformatics. 3:2.

Doshi K.J., Cannone J.J., Cobaugh C.W., and Gutell R.R. (2004). Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BioMed Central Bioinformatics, 5:105.

 

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