Comparative RNA Web Site and Project The Gutell Lab

Recent CRW Site Publications
(Complete List »)

2017: (Pub #133) RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Research, 45(D1):D128-D134. [ PM | PMC | DOI ]

2015: (Pub #132) R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server. Nucleic Acids Research, 43(W1):W15-W23. [ PM | PMC | DOI ]

2015: (Pub #131) rRNA -- the evolution of that magic molecule. RNA, 21:627-629. [ PM | PMC | DOI ]

2015: (Pub #130) RNAcentral: an international database of ncRNA sequences. Nucleic Acids Research, 43(D1):D123-D129. [ PM | PMC | DOI ]

2014: (Pub #129) Multiple entries in: Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey.

2014: (Pub #128) Ten Lessons with Carl Woese about RNA and Comparative Analysis. RNA Biology, 11(3):254-272. [ PM | pmc | DOI ]

2014: (Pub #127) Introduction to Special Carl Woese Issue in RNA Biology. RNA Biology, 11(3):170-171. [ PM | PMC | DOI ]

2014: (Pub #126) Helix Capping in RNA Structure. PLOS One, 9(4):e93664. [ PM | PMC | DOI ]

2013: (Pub #125) Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems. BMC Systems Biology, 7(S4):S13. [ PM | PMC | DOI ]

2013: (Pub #124) You tell Carl that some of my best friends are Eukaryotes: Carl R. Woese (1928-2012). RNA 19(4):vii-xi. [ pm | pmc | doi ]

2013: (Pub #123) Specificity between Lactobacilli and Hymenoptera Hosts is the Exception Rather than the Rule. Applied and Environmental Microbiology, 79:1803-1812. [ PM | pmc | DOI ]

2013: (Pub #122) Comparative Analysis of the Higher-Order Structure of RNA. In: Biophysics of RNA Folding ("Biophysics for the Life Sciences" Series). pp. 11-22. Springer, New York, NY. [ pm | pmc | DOI ]

2012: (Pub #121) An Accurate Scalable Template-based Alignment Algorithm. Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. pp. 237-243. [ PM | PMC | DOI ]

2012: (Pub #120) The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum. PLoS One, 7(6):e38320. [ PM | PMC | DOI ]

2012: (Pub #119) Structural Constraints Identified with Covariation Analysis in Ribosomal RNA. PLos One, 7(6):e39383. [ PM | PMC | DOI ]

2012: (Pub #118) A Comparison of the Crystal Structures of the Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions. PLos One, 7(5):e38203. [ PM | PMC | DOI ]

2011: (Pub #117) rCAD: A Novel Database Schema for the Comparative Analysis of RNA. 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22. [ PM | PMC | DOI ]

2011: (Pub #116) R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm. 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), pp. 618-622. [ PM | PMC | DOI ]

2011: (Pub #115) RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure. 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), pp. 613-617. [ PM | PMC | DOI ]

2011: (Pub #114) Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure. Journal of Molecular Biology, 413(2):473-483. [ PM | PMC | DOI ]

2011: (Pub #113) Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA. PLoS ONE, 6(4):e18768. [ PM | PMC | DOI ]

2010: (Pub #112) Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures. The Journal of Physical Chemistry B, 114(42):13497-13506. [ PM | pmc | DOI ]

2010: (Pub #111) Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes. BMC Genomics, 11(1):485. [ PM | PMC | DOI ]

2010: (Pub #110) Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212. [ PM | PMC | DOI ]

Recent CRW Site Updates
(More Updates »)

2014-present: Ongoing collaboration with the Leontis-Zirbel group at BGSU.

• R3D-2-MSA Server (website at BGSU, database at UT-Austin)
• 2015-02-01: Poster at Gordon Research Conference (Converging Disciplines for the Advancement of Inter-RNA Interactions; website).
• 2015-05-09: R3D-2-MSA manuscript (Nucleic Acids Research, 43(W1):W15-W23.
• 2015-05-26: Poster at the RNA Society Meeting (Madison 2015; website).
• 2016-01-25: Added manuscript appendix (Pub #132)

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2016-06-06: Began officially hosting the RNA Mutation Database, authored by Kathy Triman.

2016-01-26: Added appendices for RNAMotif, an RNA Secondary Structure Definition and Search Algorithm, CAT: the Comparative Analysis Toolkit, and Covariation Analysis.

2014-09-10: RNAcentral press release (2015-01-20: See also (Pub #130)).

2013-07-08: Added 1E. Modeling the Comparative Structure of Ribosomal RNAs in the 1980s.

2013-03-07: Added manuscript appendix for Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems (Pub #125).

2012-08-27: Added multiple manuscript appendices: 1) Correlation of Structure Statistics (Pub #108); 2) Coarse-Grained Model (Pub #112); 3) RNA2DMap: Visual Exploration of RNA Structure (Pub #115); 4) rCAD: The RNA Comparative Analysis Database (Pub #117); 5) CRWAlign: Template-based Alignment Algorithm (Pub #121).

2012-08-07: Released the CRWAlign: RNA Multiple Sequence Alignment feature.

2012 May: Added three manuscript appendices: 1) Plasmodium Mitochondrion (Pub #120); 2) Hypervariable SSU rRNA (Pub #118); 3) Structural Constraint Identification (Pub #119).

2011-11-23: The CRW Site runs on a new web server (more powerful and larger disk capacity).

2011-10-11: Added Pre-Primary Alignments for 16S rRNA to the Sequence Alignment Retrieval page.

2011-10-03: Added the Three-Dimensional Structure presentation (under development). Includes the following pages: 1) Identification of Basepairs and Conformations; 2) Motif: Adenosine Platform; 3) Motif: A-minor; 4) Motif: C Loop; 5) Motif: E Loop; 6) Motif: E-like Loop; 7) Motif: E and E-like Loop; 8) Motif: GAAA Receptor; 9) Motif: H-turn; 10) Motif: K-turn; 11) Motif: Lonepair Triloop; 12) Motif: Tandem G:A Internal Loop; 13) Motif: Tetraloop; 14) Motif: U-turn; 15) Motif: UAA/GAN, UNA/GAN, GA/GAA.

2011-09-02: (Pub #114) Added the Appendix to new Statistical Potentials presentation.

2011-09-01: Additions to Structural Statstics: new statistic (Hairpin Comparative/Potential Ratio) and statistics for eight additional RNAs.

2011-08-29: Added the RNA Families section (under development).

2011-08-08: Added RNA2DMap Examples.