Last modified on 26 January 2016.
Overview:
Online appendices to published papers. Currently the Gutell Lab research focuses on six major categories: 1) RNA Structure, 2) Motifs, 3) Folding, 4) rRNA-based Phylogeny, 5) Lateral Gene Transfer, and 6) Computation and Software.
- 4A. Structure
- [2002] The Accuracy of Ribosomal RNA Comparative Structure Models (Current Opinion)
- [2002] Modeling a Minimal Ribosome Based on Comparative Sequence Analysis
- [2002] Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome
- [2003] The Exon Context and Distribution of Euascomycetes rRNA Spliceosomal Introns
- [2010] Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes
- [2012] A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions
- [2012] Structural Constraints Identified with Covariation Analysis in Ribosomal RNA
- [2012] The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum
- [PREP] Three-Dimensional Structure
- 4B. Motifs
- [2000] U-Turn Motif: Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis
- [2000] A Story: Unpaired Adenosines in Ribosomal RNAs
- [2001] AA.AG@Helix.Ends: A:A and A:G Base-pairs at the Ends of 16 S and 23 S rRNA Helices
- [2003] The Lonepair Triloop: A New Motif in RNA Structure
- [2004] Diversity of Basepair Conformations and Their Occurrence in rRNA Structure and RNA Structural Motifs
- [2006] The UAA/GAN Internal Loop Motif: A New RNA Structural Element That Forms a Cross-strand AAA Stack and Long-range Tertiary Interactions
- 4C. Folding
- [1995] Appendix to thermodynamic folding manuscript of 16S rRNAs
- [1996] Appendix to a large rRNA folding manuscript
- [2004] RNA Secondary Structure Prediction Metrics Website
- [2009] Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding
- [2010] Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures
- [2011] Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure
- 4D. Phylogenetic Analysis of Ribosomal RNA
- [2000] Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures
- [2001] Accelerated Evolution of Functional Plastid rRNA and Elongation Factor Genes Due to Reduced Protein Synthetic Load After the Loss of Photosynthesis in the Chlorophyte Alga Polytoma
- [2002] Reconstructing the Tree of Life with Ribosomal RNA Sequences and Structures: Integrating Phylogeny, Computational Methods, and a RNA Database
- [2003] ITS Secondary Structure Derived from Comparative Analysis: Implications for Sequence Alignment and Phylogeny of the Asteraceae
- [2006] The Evolution of Elongate Shape in Diatoms
- [2009] Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)
- [2009] The Limits of Nuclear-Encoded SSU rDNA for Resolving the Diatom Phylogeny
- [2010] Placement of Attine Ant-Associated Pseudonocardia in a Global Phylogeny (Pseudonocardiaceae, Actinomycetales): a Test of Two Symbiont-Association Models
- 4E. Lateral Gene Transfer: Group I Introns
- 4F. Computation and Software
- [2001] RNAMotif, an RNA Secondary Structure Definition and Search Algorithm
- [2007] CAT: the Comparative Analysis Toolkit
- [2011] RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure
- [2011] rCAD: A Novel Database Schema for the Comparative Analysis of RNA
- [2012] CRWAlign: An Accurate Scalable Template-based Alignment Algorithm
- [2013] Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems
- [2015] R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server
- [Links] Covariation Analysis
