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Robin Gutell

Gutell, Robin
Professor in Integrative Biology

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Main Office: PAT 141MB Phone: (512) 232-4814

Alternate Office: PAT 141 Phone: (512) 232-4815

Mailing Address:
The University of Texas at Austin
Integrative Biology, 1 University Station - C0930
PAT 141, 2401 Speedway
Austin,TX 78712

Research Lab Members:
  • Cannone, Jamie
  • Gardner, David
  • Jiang, Yanan
  • Jung, Hee Young
  • Lee, Jung Chull
  • Shang, Lei

    • Research Summary:

    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 my lab is primarily interested in RNA structure and the evolution of these RNAs.

    Currently we are addressing the following topics -

    (1) STRUCTURE PREDICTION: RNA secondary and tertiary structure prediction with comparative sequence analysis.
    (2) PRINCIPLES OF RNA STRUCTURE: Relationships between RNA sequence and RNA higher order structure.
    (3) RNA FOLDING: transforming a single RNA sequence into its biologically correct higher order structure.
    (4) PHYLOGENETIC ANALYSIS: Inferring phylogenetic and evolutionary relationships from RNA structures.
    (5) DEVELOPMENT OF COMPUTATIONAL METHODS: rCAD - RNA Comparative Analysis Database - SQL-Server, template-based alignment methods, covariation analysis, visualization methods
    (6) Comparative RNA Web (CRW) Site: RNA sequence/structure knowledgebase.

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


    Publications:
    2012 Feagin J.E., Harrell M.I., Lee J.C., Coe K.J., Sands B., Cannone J.J., Tami G., Schnare M.N., and Gutell R.R., The Fragmented Mitochondrial rRNAs of Plasmodium falciparum, PLoS ONE 7: e38320 view
    2012 Shang L., Xu W., Ozer S., and Gutell R.R., Structural Constraints identified with Covariation Analysis in 16S ribosomal RNA, PLoS ONE 7: e39383 view
    2012 Lee J.C. and Gutell R.R. , A Comparison of the Crystal Structures of Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions, PLoS ONE 7: e38203 view
    2011 Ozer S., Doshi K.J., Xu W., and Gutell R.R., rCAD: A Novel Database Schema for the Comparative Analysis of RNA, 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011 15-22 view
    2011 Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R., RNA2DMap: A Visual Exploration Tool of the Information in RNA’s Higher-Order Structure., 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011) November 12-15, 2011 in Atlanta, Georgia 613-617 view
    2011 Gardner D.P., Ren P., Ozer S., and Gutell R.R., Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure. , Journal of Molecular Biology 413: 473-483 view
    2011 Muralidhara C., Gross A.M., Gutell R.R., and Alter O., Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA. , PLoS ONE 6: e18768 view
    2010 Xia Z., Gardner D.P., Gutell R.R., and Ren P., Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures, The Journal of Physical Chemistry B, 114: 13497-13506 view
    2010 Milbury C.A., Lee J.C., Cannone J.J., Gaffney P.M., and Gutell R.R., Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes, BMC Genomics 11: 485 view
    2009 Xu W., Ozer S., Gutell R.R., Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA, 21st International Conference on Scientific and Statistical Database Management. conference/book: 200-216 view
    2007 Lee C.-Y., Lee J.C., and Gutell R.R. , Networks of interactions in the secondary and tertiary structure of ribosomal RNA., Physica A 386: 564-572 view
    2006 Lee J.C., Gutell R.R., and Russell R., The UAA/GAN Internal Loop Motif: A New RNA Structural Element That Forms a Cross-strand AAA stack and Long-range Tertiary Interactions., Journal of Molecular Biology 360: 978-988 view
    2005 M�ller K.M., Ellenor D.W., Sherwood A.R., Sheath R.G., Cannone J.J., and Gutell R.R., Evidence for Lateral Transfer of an IE Intron Between Fungal and Red Algal Small Subunit rRNA Genes, Journal of Phycology 41: 380-390 view
    2004 Lee J.C. and Gutell R.R., Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs, Journal of Molecular Biology 344: 1225-1249 view
    2004 Doshi K.J., Cannone J.J., Cobaugh C.W., and Gutell R.R., Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction, BioMed Central Bioinformatics 5: 105 view
    2003 Lee J.C., Cannone J.J., and Gutell R.R., The Lonepair Triloop: A New Motif in RNA Structure, Journal of Molecular Biology 325: 65-83 view
    2002 Gutell R.R., Lee J.C., and Cannone J.J., The Accuracy of Ribosomal RNA Comparative Structure Models, Current Opinion in Structural Biology 12: 301-310 view
    2002 Cannone J.J, Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., M�ller K.M., Pande N.,Shang Z., Yu N., and Gutell R.R. , 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 (and 15) view
    2001 Elgavish T., Cannone J.J., Lee J.C., Harvey S.C., and Gutell R.R., AA.AG@Helix.Ends: A:A and A:G Base-pairs at the Ends of 16 S and 23 S rRNA Helices., Journal of Molecular Biology 310: 735-753 view
    2000 Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J., A Story: Unpaired Adenosine Bases in Ribosomal RNA. , Journal of Molecular Biology, 304: 335-354 view
    2000 Gutell R.R., Cannone J.J., Konings D., and Gautheret D., Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis. , Journal of Molecular Biology 300: 791-803 view
    1997 Gautheret D. and Gutell R.R, Inferring the Conformation of RNA Base Pairs and Triples from Patterns of Sequence Variation, Nucleic Acids Research 25: 1559-1564 view
    1996 Fields D.S. and Gutell R.R., An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method, Folding and Design 1: 419-430 view
    1996 Schnare M.N., Damberger S.H., Gray M.W., and Gutell R.R. , Comprehensive Comparison of Structural Characteristics in Eukaryotic Cytoplasmic Large Subunit (23S-like) Ribosomal RNA, Journal of Molecular Biology 256: 701-719 view
    1995 Gautheret D., Konings D., and Gutell R.R., G.U Base pairing Motifs in Ribosomal RNAs, RNA 1: 807-814 view
    1995 Ragan M.A. and Gutell R.R., Are red algae plants? , Botanical Journal of the Linnean Society 118: 81-105 view
    1995 Konings D.A.M. and Gutell R.R., A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs, RNA 1: 559-574 view
    1995 Gautheret D., Damberger S.H., and Gutell R.R., Identification of Base Triples in RNA Using Comparative Sequence Analysis, ournal of Molecular Biology 248: 27-43 view
    1994 Gautheret D., Konings D., and Gutell R.R., A Major Family of Motifs Involving G-A Mismatches in Ribosomal RNA, Journal of Molecular Biology 242: 1-8 view
    1994 Trust T.J., Logan S.M., Gustafson C., Romaniuk P.J., Kim N.W., Chan V.L., Ragan M.A., Guerry P., and Gutell R.R., Phylogenetic and molecular characterization of a 23S ribosomal RNA gene positions the Genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp. , Journal of Bacteriology 176: 4597-4609 view
    1994 Gutell R.R., Larsen N., and Woese C.R., Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective, Microbiological Reviews 58: 10-26 view
    1992 Gutell R.R., Power A., Hertz G., Putz E., and Stormo G., Identifying Constraints on the Higher-Order Structure of RNA: Continued Development and Application of Comparative Sequence Analysis Methods. , Nucleic Acids Research, 20: 5785-5795 view
    1990 Woese C.R., Winker S. and Gutell R.R., Architecture of Ribosomal RNA: Constraints on the sequence of Tetra-loops, Proceedings of the National Academy of Sciences (USA) 87: 8467-8471 view
    1990 Gutell, R.R. and C.R. Woese, Higher order structural elements in ribosomal RNAs: Pseudo-knots and the use of non-canonical pairs, Proceedings of the National Academy of Sciences (USA) 87: 663-667 view
    1989 Woese C.R. and Gutell R.R., Evidence for several higher order structural elements in ribosomal RNA., Proceedings of the National Academy of Sciences (USA) 86: 3119-3122 view
    1986 Gutell R.R., Noller H.F., and Woese C.R., Higher order structure in ribosomal RNA, The EMBO Journal 5: 1111-1113 view
    1985 Gutell R.R., Weiser B., Woese C.R., and Noller H.F. , Comparative anatomy of 16S-like ribosomal RNA., Progress in Nucleic Acid Research and Molecular Biology 32: 155-216 view