	Robin Gutell Professor, Section of Integrative Biology see also: Institute for Cellular and Molecular Biology The Center for Computational Biology and Bioinformatics Comparative RNA Web (CRW) Site
Lab web page	Education \| Research Interests \| Instruction \| Grad Programs \| Publications
E-mail: robin.gutell@mail.utexas.edu Office: PAT 141MB, (512) 232-4814 Lab: (512) 232-4815 Fax: (512) 471-3878	Education B.A., Biology, University of California, San Diego, 1977, magna cum laude. Ph.D., Molecular Biology, University of California, Santa Cruz, 1984. postdoctoral fellow, University of Illinois, Urbana, 1985-1987. Research Interests The analysis of RNA sequences from an RNA structure and a molecular phylogenetic perspective can reveal the secondary and tertiary structure of RNA molecules, most notably for the 16S and 23S ribosomal RNAs, and phylogenetic relationships for organisms that span the entire tree of life. We utilize computational biology and bioinformatics to study: RNA secondary and tertiary structure prediction with comparative sequence analysis; RNA motifs: relationships between RNA sequences and their higher-order structures; RNA folding: transforming a single RNA sequence into its biologically correct higher-order structure; RNA structure-based phylogenetic analysis; and Comparative RNA Web site: RNA sequence/structure knowledge base. More information - see Dr. Gutell lab's Comparative RNA Web (CRW) Site. Instruction Spring and Fall 2009: Computational Biology lab: Analysis of Nucleic Acid and Protein Sequences. BIO 337J (for Undergraduate students); BIO 384 (for Graduate students) Spring 2010: Topics in RNA Folding/Structure Bio 384k.20 (Computational Biology) Associated Graduate Programs Cell and Molecular Biology bioinformatics & computational biology molecular genetics structural biology Biomedical Engineering Computational and Applied Mathematics Publications Below is a brief list of recent publications of Dr. Gutell. Visit the Gutell Lab Web Pages for a full interactive list of his publications. Click on article title for Medline abstract (where available). 109. Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009). The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology, 44(3):277-290. DOI 108. Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009). Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding. Journal of Molecular Biology, 391(4):769-783. PM 105. Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009). Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae). Zoologica Scripta, 38(1):43-62. PMC \| DOI 104. Smith T.F., Gutell R., Lee J., and Hartman H. (2008). The origin and evolution of the ribosome. Biology Direct, 3:16. 103. Chandramouli P., Topf M., Ménétret J.-F., Eswar N., Cannone J.J., Gutell R.R., Sali A., and Akey C.W. (2008). Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution. Structure, 16:535-548. 102. Wang S., Gutell R.R., and Miranker D.P. (2007). Biclustering as a Method for RNA Local Multiple Sequence Alignment. Bioinformatics, 23:3289-3296. 101. Lee C.-Y., Lee J.C., and Gutell R.R. (2007). Networks of interactions in the secondary and tertiary structure of ribosomal RNA. Physica A, 386:564-572. 100. Gillespie J.J., Johnston J.S., Cannone J.J., and Gutell R.R. (2006). Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta:Hymenoptera): structure, organization, and retrotransposable elements. Insect Molecular Biology, 15(5):657-686. PM \| PMC \| DOI 99. Weinstock et al. (81 authors), Gillespie J.J., Cannone J.J., Gutell R.R., et al. (100 authors) (2006). Insights into social insects from the genome of the honey bee Apis mellifera. Nature, 443:931-949. 98. Lee J.C., Gutell R.R., and Russell R. (2006). 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(5):978-988. PM \| DOI 97. Alverson A.J., Cannone J., Gutell R.R., and Theriot E.C. (2006). The Evolution of Elongate Shape in Diatoms. Journal of Phycology, 42:655-668. 93. Müller K.M., Ellenor D.W., Sherwood A.R., Sheath R.G., Cannone J.J., and Gutell R.R. (2005). Evidence for Lateral Transfer of an IE Intron Between Fungal and Red Algal Small Subunit rRNA Genes. Journal of Phycology, 41(2):380-390. DOI 92. Lee J.C. and Gutell R.R. (2004). Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs. Journal of Molecular Biology, 344(5):1225-1249. PM \| DOI 90. 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. PM \| PMC \| DOI 85. Lee J.C., Cannone J.J., and Gutell R.R. (2003). The Lonepair Triloop: A New Motif in RNA Structure. Journal of Molecular Biology, 325(1):65-83. PM \| DOI 81. 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(3):301-310. PM \| DOI 80. 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. PM \| PMC \| DOI Correction: BioMed Central Bioinformatics, 3:15. PMC \| DOI 76. Bhattacharya D., Cannone J.J., and Gutell R.R. (2001). Group I Intron Lateral Transfer Between Red and Brown Algae Ribosomal RNA. Current Genetics, 40(1):82-90. PM \| DOI 75. Elgavish T., Cannone J.J., Lee J.C., Harvey S.C., and Gutell R.R. (2001). 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(4):735-753. PM \| DOI 74. Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J. (2000). A Story: Unpaired Adenosine Bases in Ribosomal RNA. Journal of Molecular Biology, 304(3):335-354. PM \| DOI 71. Gutell R.R., Cannone J.J., Konings D., and Gautheret D. (2000). Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis. Journal of Molecular Biology, 300(4):791-803. PM \| DOI 34. Gutell R.R., Larsen N., and Woese C.R. (1994) Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective. Microbiological Reviews, 58(1):10-26. PM \| PMC 20. Woese C.R., Winker S. and Gutell R.R. (1990) Architecture of Ribosomal RNA: Constraints on the sequence of Tetra-loops. Proceedings of the National Academy of Sciences (USA), 87(21):8467-8471. PM \| PMC 18. Gutell, R.R. and C.R. Woese (1990) 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(2):663-667. PM \| PMC 16. Woese C.R. and Gutell R.R. (1989) Evidence for several higher order structural elements in ribosomal RNA. Proceedings of the National Academy of Sciences (USA), 86(9):3119-3122. PM \| PMC 14. Gutell R.R., Noller H.F., and Woese C.R. (1986). Higher order structure in ribosomal RNA. The EMBO Journal, 5(5):1111-1113. PM \| PMC 12. Gutell R.R., Weiser B., Woese C.R., and Noller H.F. (1985). Comparative anatomy of 16S-like ribosomal RNA. Progress in Nucleic Acid Research and Molecular Biology, 32:155-216. PM 5. Woese C.R., Gutell R., Gupta R., and Noller H.F. (1983). Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews, 47(4):621-669. PM \| PMC

Robin Gutell

Professor, Section of Integrative Biology
see also:
Institute for Cellular and Molecular Biology
The Center for Computational Biology and Bioinformatics
Comparative RNA Web (CRW) Site

Lab web page

Education | Research Interests | Instruction | Grad Programs | Publications

E-mail:
robin.gutell@mail.utexas.edu
Office:
PAT 141MB,
(512) 232-4814
Lab:
(512) 232-4815
Fax:
(512) 471-3878

Education

B.A., Biology, University of California, San Diego, 1977, magna cum laude.
Ph.D., Molecular Biology, University of California, Santa Cruz, 1984.
postdoctoral fellow, University of Illinois, Urbana, 1985-1987.

Research Interests

The analysis of RNA sequences from an RNA structure and a molecular phylogenetic perspective can reveal the secondary and tertiary structure of RNA molecules, most notably for the 16S and 23S ribosomal RNAs, and phylogenetic relationships for organisms that span the entire tree of life. We utilize computational biology and bioinformatics to study:

RNA secondary and tertiary structure prediction with comparative sequence analysis;
RNA motifs: relationships between RNA sequences and their higher-order structures;
RNA folding: transforming a single RNA sequence into its biologically correct higher-order structure;
RNA structure-based phylogenetic analysis; and
Comparative RNA Web site: RNA sequence/structure knowledge base.

More information - see Dr. Gutell lab's Comparative RNA Web (CRW) Site.

Instruction

Spring and Fall 2009:

Computational Biology lab: Analysis of Nucleic Acid and Protein Sequences.
BIO 337J (for Undergraduate students); BIO 384 (for Graduate students)

Spring 2010:

Topics in RNA Folding/Structure
Bio 384k.20 (Computational Biology)

Associated Graduate Programs

Publications

Below is a brief list of recent publications of Dr. Gutell. Visit the Gutell Lab Web Pages for a full interactive list of his publications. Click on article title for Medline abstract (where available).

109. Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009).
The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.
European Journal of Phycology, 44(3):277-290.
DOI
108. Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009).
Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.
Journal of Molecular Biology, 391(4):769-783.
PM
105. Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009).
Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).
Zoologica Scripta, 38(1):43-62.
PMC | DOI
104. Smith T.F., Gutell R., Lee J., and Hartman H. (2008). The origin and evolution of the ribosome. Biology Direct, 3:16.
103. Chandramouli P., Topf M., Ménétret J.-F., Eswar N., Cannone J.J., Gutell R.R., Sali A., and Akey C.W. (2008). Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution. Structure, 16:535-548.
102. Wang S., Gutell R.R., and Miranker D.P. (2007). Biclustering as a Method for RNA Local Multiple Sequence Alignment. Bioinformatics, 23:3289-3296.
101. Lee C.-Y., Lee J.C., and Gutell R.R. (2007). Networks of interactions in the secondary and tertiary structure of ribosomal RNA. Physica A, 386:564-572.
100. Gillespie J.J., Johnston J.S., Cannone J.J., and Gutell R.R. (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta:Hymenoptera): structure, organization, and retrotransposable elements.
Insect Molecular Biology, 15(5):657-686.
PM | PMC | DOI
99. Weinstock et al. (81 authors), Gillespie J.J., Cannone J.J., Gutell R.R., et al. (100 authors) (2006). Insights into social insects from the genome of the honey bee Apis mellifera. Nature, 443:931-949.
98. Lee J.C., Gutell R.R., and Russell R. (2006).
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(5):978-988.
PM | DOI
97. Alverson A.J., Cannone J., Gutell R.R., and Theriot E.C. (2006). The Evolution of Elongate Shape in Diatoms. Journal of Phycology, 42:655-668.
93. Müller K.M., Ellenor D.W., Sherwood A.R., Sheath R.G., Cannone J.J., and Gutell R.R. (2005).
Evidence for Lateral Transfer of an IE Intron Between Fungal and Red Algal Small Subunit rRNA Genes.
Journal of Phycology, 41(2):380-390.
DOI
92. Lee J.C. and Gutell R.R. (2004).
Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs.
Journal of Molecular Biology, 344(5):1225-1249.
PM | DOI
90. 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.
PM | PMC | DOI
85. Lee J.C., Cannone J.J., and Gutell R.R. (2003).
The Lonepair Triloop: A New Motif in RNA Structure.
Journal of Molecular Biology, 325(1):65-83.
PM | DOI
81. 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(3):301-310.
PM | DOI
80. 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.
PM | PMC | DOI
Correction: BioMed Central Bioinformatics, 3:15. PMC | DOI
76. Bhattacharya D., Cannone J.J., and Gutell R.R. (2001).
Group I Intron Lateral Transfer Between Red and Brown Algae Ribosomal RNA.
Current Genetics, 40(1):82-90.
PM | DOI
75. Elgavish T., Cannone J.J., Lee J.C., Harvey S.C., and Gutell R.R. (2001).
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(4):735-753.
PM | DOI
74. Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J. (2000).
A Story: Unpaired Adenosine Bases in Ribosomal RNA.
Journal of Molecular Biology, 304(3):335-354.
PM | DOI
71. Gutell R.R., Cannone J.J., Konings D., and Gautheret D. (2000).
Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis.
Journal of Molecular Biology, 300(4):791-803.
PM | DOI
34. Gutell R.R., Larsen N., and Woese C.R. (1994)
Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective.
Microbiological Reviews, 58(1):10-26.
PM | PMC
20. Woese C.R., Winker S. and Gutell R.R. (1990)
Architecture of Ribosomal RNA: Constraints on the sequence of Tetra-loops.
Proceedings of the National Academy of Sciences (USA), 87(21):8467-8471.
PM | PMC
18. Gutell, R.R. and C.R. Woese (1990)
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(2):663-667.
PM | PMC
16. Woese C.R. and Gutell R.R. (1989)
Evidence for several higher order structural elements in ribosomal RNA.
Proceedings of the National Academy of Sciences (USA), 86(9):3119-3122.
PM | PMC
14. Gutell R.R., Noller H.F., and Woese C.R. (1986).
Higher order structure in ribosomal RNA.
The EMBO Journal, 5(5):1111-1113.
PM | PMC
12. Gutell R.R., Weiser B., Woese C.R., and Noller H.F. (1985).
Comparative anatomy of 16S-like ribosomal RNA.
Progress in Nucleic Acid Research and Molecular Biology, 32:155-216.
PM
5. Woese C.R., Gutell R., Gupta R., and Noller H.F. (1983).
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids.
Microbiological Reviews, 47(4):621-669.
PM | PMC