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# Reference Reference Links
39. The RNAcentral Consortium (2017).
RNAcentral: a comprehensive database of non-coding RNA sequences.
Nucleic Acids Research, 45(D1):D128-D134.
PM | PMC | DOI ]
38. Cannone J.J., Sweeney B.A., Petrov A.I., Gutell R.R., Zirbel C.L., and Leontis N.B. (2015).
R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server.
Nucleic Acids Research, 43(W1):W15-W23.
PM | PMC | DOI ]
37. Cannone J.J. and Gutell R.R. (2014).
Multiple entries in: Concise Encyclopaedia of Bioinformatics and Computational Biology, 2nd Edition, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey.
[ pm | pmc | doi ]
ALT )
36. Shang L., Gardner D.P., Xu W., Cannone J.J., Miranker D.P., Ozer S., and Gutell R.R. (2013).
Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems.
BMC Systems Biology, 7(S4):S13.
[ pm | pmc | DOI ]
35. McFrederick Q.S., Cannone J.J., Gutell R.R., Kellner K., Plowes R.M., and Mueller U.G. (2013).
Specificity between Lactobacilli and Hymenopteran Hosts is the Exception Rather than the Rule.
Applied and Environmental Microbiology, 79:1803-1812.
PM | PMC | DOI ]
34. Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
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. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
PM | PMC | DOI ]
33. Feagin J.E., Harrell M.I., Lee J.C., Coe K.J., Sands B.H., Cannone J.J., Tami G., Schnare M.N., and Gutell R.R. (2012).
The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum.
PLoS One, 7(6):e38320.
PM | PMC | DOI ]
32. Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617.
PM | PMC | DOI ]
31. Milbury C.A., Lee J.C., Cannone J.J., Gaffney P.M., and Gutell R.R. (2010).
Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes.
BMC Genomics, 11(1):485.
PM | PMC | DOI ]
30. 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.
PM | PMC | DOI ]
29. 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.
[ pm | PMC | DOI ]
28. 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(4):535-548.
PM | PMC | DOI ]
27. 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 ]
26. 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 honeybee Apis mellifera.
Nature, 443(7114):931-949.
PM | PMC | DOI ]
Corrigenda: Nature, 444(7118):512. [ pm | pmc | DOI ]
25. Alverson A.J., Cannone J.J., Gutell R.R., and Theriot E.C. (2006).
The Evolution of Elongate Shape in Diatoms.
Journal of Phycology, 42(3):655-668.
[ pm | pmc | DOI ]
24. Qiu Y.-L., Dombrovska O., Lee J., Li L., Whitlock B.A., Bernasconi-Quadroni F., Rest J.S., Davis C.C., Borsch T., Hilu K.W., Renner S.S., Soltis D.E., Soltis P.S., Zanis M.J., Cannone J.J., Gutell R.R., Powell M., Savolainen V., Chatrou L.W., and Chase M.W. (2005).
Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes.
International Journal of Plant Sciences, 166(5):815-842.
[ pm | pmc | DOI ]
23. 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.
[ pm | pmc | DOI ]
22. Müller K.M., Cannone J.J., and Sheath R.G. (2005).
A molecular phylogenetic analysis of the Bangiales (Rhodophyta) and description of a new genus and species, Pseadobangia [sic] kaycoleia.
Phycologia, 44(2):146-155.
[ pm | pmc | DOI ]
21. Gillespie J., Cannone J., Gutell R., and Cognato A. (2004).
A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae).
Insect Molecular Biology, 13(5):495-518.
PM | pmc | DOI ]
20. 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 ]
19. Cannone J.J. and Gutell R.R. (2004).
Multiple entries in: Dictionary of Bioinformatics and Computational Biology, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey.
 
18. Hewitt E.A., Müller K.M., Cannone J., Hogan D.J., Gutell R., and Prescott D.M. (2003).
Phylogenetic Relationships Among 28 Spirotrichous Ciliates Defined by rDNA.
Molecular Phylogenetics and Evolution, 29(2):258-267.
PM | pmc | DOI ]
17. Goertzen L.R., Cannone J.J., Gutell R.R., and Jansen R.K. (2003).
ITS Secondary Structure Derived from Comparative Analysis: Implications for Sequence Alignment and Phylogeny of the Asteraceae.
Molecular Phylogenetics and Evolution, 29(2):216-234.
PM | pmc | DOI ]
16. Bhattacharya D, Simon D., Huang J., Cannone J.J., and Gutell R.R. (2003).
The Exon Context and Distribution of Euascomycetes rRNA Spliceosomal Introns.
BioMed Central Evolutionary Biology, 3:7.
PM | PMC | DOI ]
15. 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 | pmc | DOI ]
14. Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R., and Woodson S.A. (2002).
Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome.
Journal of Molecular Biology, 323(1):35-52.
PM | pmc | DOI ]
13. Mears J.A., Cannone J.J., Stagg S.M., Gutell R.R., Agrawal R.K., and Harvey S.C. (2002).
Modeling a Minimal Ribosome Based on Comparative Sequence Analysis.
Journal of Molecular Biology, 321(2):215-234.
PM | pmc | DOI ]
12. 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 | pmc | DOI ]
11. 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. [ pm | PMC | DOI ]
10. Cannone J.J., Barnes C.L., Achari A., and Kundrot C.E. (2001).
Crystallization of bFGF-DNA aptamer complexes using a Sparse Matrix designed for protein-nucleic acid complexes.
Journal of Crystal Growth, 232(1-4):409-417.
[ pm | pmc | DOI ]
9. Vernon D., Gutell R.R., Cannone J.J., Rumpf R.W., and Birky C.W. Jr. (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.
Molecular Biology and Evolution, 18(9):1810-1822.
PM | pmc | doi ]
8. Müller K.M., Cannone J.J., Gutell R.R., and Sheath R.G. (2001).
A structural and phylogenetic analysis of the Group IC1 introns in the order Bangiales (Rhodophyta).
Molecular Biology and Evolution, 18(9):1654-1667.
PM | pmc | doi ]
7. 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 | pmc | DOI ]
6. 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 | pmc | DOI ]
5. 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 | pmc | DOI ]
4. Mavridou A., Cannone J., and Typas M.A. (2000).
Identification of Group-I Introns at Three Different Positions within the 28S rDNA Gene of the Entomopathogenic Fungus Metarhizium anisopliae var. anisopliae.
Fungal Genetics and Biology, 31(2):79-90.
PM | pmc | DOI ]
3. Ragan M.A., MacCallum G.S., Murphy C.A., Cannone J.J., Gutell R.R., and McGladdery S.E. (2000).
Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota.
Diseases of Aquatic Organisms, 42(3):185-190.
PM | pmc | DOI ]
2. 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 | pmc | DOI ]
1. Rand T.G., White K., Cannone J.J., Gutell R.R., Murphy C.A., and Ragan M.A. (2000).
Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea from the Nova Scotia shelf.
Diseases of Aquatic Organisms, 41(1):31-36.
PM | pmc | DOI ]

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