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# Reference Reference Links
127. Cannone J.J. and Gutell R.R. (2013).
Multiple entries in: Concise Encyclopaedia of Bioinformatics and Computational Biology, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey. (In press.)
 
126. Lee J.C. and Gutell R.R. (2014).
Helix Capping in RNA Structure.
PLOS One, 9(4):e93664.
PM | PMC | DOI ]
125. 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 ]
124. Gutell R.R. (2013).
You tell Carl that some of my best friends are Eukaryotes: Carl R. Woese (1928-2012).
RNA, 19(4):vii-xi.
 
123. 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 ]
122. Gutell R.R. (2013).
Comparative Analysis of the Higher-Order Structure of RNA.
in: Biophysics of RNA Folding. Volume editor: Rick Russell. Series title: Biophysics for the Life Sciences. Series editors: Norma Allewell, Ivan Rayment, Bertrand Garcia-Moreno, Jonathan Dinman, and Michael McCarthy. pp. 11-22. Publisher: Springer, New York, NY.
[ pm | pmc | DOI ]
121. 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 ]
120. 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 ]
119. Shang L., Xu W., Ozer S., and Gutell R.R. (2012).
Structural Constraints Identified with Covariation Analysis in Ribosomal RNA.
PLoS ONE, 7(6):e39383.
PM | PMC | DOI ]
118. Lee J.C. and Gutell R.R. (2012).
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 ]
117. Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
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 ]
116. Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D. (2011).
R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.
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. 618-622.
[ pm | pmc | DOI ]
115. 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 ]
114. Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
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 ]
113. Muralidhara C., Gross A.M., Gutell R.R., and Alter O. (2011).
Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA.
PLoS ONE, 6(4):e18768.
PM | PMC | DOI ]
112. Xia Z., Gardner D.P., Gutell R.R., and Ren P. (2010).
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures.
The Journal of Physical Chemistry B, 114(42):13497-13506.
PM | PMC | DOI ]
111. 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 ]
110. Mueller U.G., Ishak H., Lee J.C., Sen R., and Gutell R.R. (2010).
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 ]
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.
PM | PMC | 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 | PMC | DOI ]
107. Xu W., Ozer S., and Gutell R.R. (2009).
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. June 2-4, 2009. Springer-Verlag. pp. 200-216.
[ pm | PMC | DOI ]
106. Chen Y.P., Evans J.D., Murphy C., Gutell R., Zuker M., Gundersen-Rindal D., and Pettis J.S. (2009).
Morphological, Molecular, and Phylogenetic Characterization of Nosema cerenae, a Microsporidian Parasite Isolated from the European Honey Bee, Apis mellifera.
The Journal of Eukaryotic Microbiology, 56(2):142-147.
PM | PMC | DOI ]
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.
PM | 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.
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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(4):535-548.
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102. Wang S., Gutell R.R., and Miranker D.P. (2007).
Biclustering as a Method for RNA Local Multiple Sequence Alignment.
Bioinformatics, 23(24):3289-3296.
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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(1):564-572.
[ pm | pmc | DOI ]
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 honeybee Apis mellifera.
Nature, 443(7114):931-949.
PM | PMC | DOI ]
Corrigenda: Nature, 444(7118):512. [ pm | pmc | DOI ]
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 | pmc | DOI ]
97. 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 ]
96. Mears J.A., Sharma M.R., Gutell R.R., McCook A.S., Richardson P.E., Caulfield T.R., Agrawal R.K., and Harvey S.C. (2006).
A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome.
Journal of Molecular Biology, 358(1):193-212.
PM | PMC | DOI ]
95. Gillespie J.J., McKenna C.H., Yoder M.J., Gutell R.R., Johnston J.S., Kathirithamby J., and Cognato A.I. (2005).
Assessing the Odd Secondary Structural Properties of Nuclear Small Subunit Ribosomal RNA Sequences (18S) of the Twisted-Wing Parasites (Insecta: Strepsiptera).
Insect Molecular Biology, 14(6):625-643.
PM | pmc | DOI ]
94. 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 ]
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.
[ pm | pmc | 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 | pmc | DOI ]
91. 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 ]
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 ]
89. 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.
 
88. 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 ]
87. 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 ]
86. 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 ]
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 | pmc | DOI ]
84. 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 ]
83. 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 ]
82. Müller K.M., Sherwood A.R., Pueschel C.M., Gutell R.R., and Sheath R.G. (2002).
A proposal for a new red algal order, the Thoreales.
Journal of Phycology, 38(4):807-820.
[ pm | pmc | 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 | pmc | 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. [ pm | PMC | DOI ]
79. Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., and Sampath R. (2001).
RNAMotif, an RNA secondary structure definition and search algorithm.
Nucleic Acids Research, 29(22):4724-4735.
PM | PMC | DOI ]
78. 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 ]
ALT )
77. 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 ]
ALT )
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 | pmc | 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.
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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.
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73. 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.
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72. Chen X., Gutell R.R., and Lambowitz A.M. (2000).
Function of Tyrosyl-tRNA Synthetase in Splicing Group I Introns: An Induced-fit Model for Binding to the P4-P6 Domain Based on Analysis of Mutations at the Junction of the P4-P6 Stacked Helices.
Journal of Molecular Biology, 301(2):265-283.
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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.
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70. 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.
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69. Lydeard C., Holznagel W.E., Schnare M.N., and Gutell R.R. (2000).
Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures.
Molecular Phylogenetics and Evolution, 15(1):83-102.
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68. Babin P., Dolan M., Wollenzien P., and Gutell R.R. (1999).
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.
RNA, 5(11):1430-1439.
PM | PMC | DOI ]
67. Gutell R.R. (1999).
Comparative Analysis of RNA Sequences. Symposium on RNA Biology - North Carolina (October 1999).
Nucleic Acids Research Symposia Series, 41:48-53.
 
66. Conn G.L., Gutell R.R., and Draper D.E. (1998).
A Functional Ribosomal RNA Tertiary Structure Involves a Base Triple Interaction.
Biochemistry, 37(34):11980-11988.
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65. Ortoleva-Donnelly L., Szewczak A.A., Gutell R.R., and Strobel S.A. (1998).
The Chemical Basis of Adenosine Conservation throughout the Tetrahymena Ribozyme.
RNA, 4(5):498-519.
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64. Tanner M.A., Anderson E.M., Gutell R.R., and Cech T.R. (1997).
Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes.
RNA, 3(9):1037-1051.
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63. Li J., Gutell R.R., Damberger S.H., Kissinger J.C., Rogers M.J., Wirtz R.A., Sattabongkot J., and McCutchan T. (1997).
Regulation and trafficking of three distinct 18 S ribosomal RNAs during development of the malaria parasite.
Journal of Molecular Biology, 269(2):203-213.
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62. Huynen M., Gutell R.R. and Konings D. (1997).
Assessing the reliability of RNA folding using statistical mechanics.
Journal of Molecular Biology, 267(5):1104-1112.
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61. Gautheret D. and Gutell R.R. (1997).
Inferring the Conformation of RNA Base Pairs and Triples from Patterns of Sequence Variation.
Nucleic Acids Research, 25(8):1559-1564.
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60. Gutell R.R. and Damberger S.H. (1996).
Comparative Sequence Analysis of Experiments Performed During Evolution.
In: Ribosomal RNA and Group I Introns. pp. 15-33. Green R., and Schroeder R. (eds.) R.G. Landes Company, Austin, Texas.
 
59. Fields D.S. and Gutell R.R. (1996).
An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method.
Folding and Design, 1(6):419-430.
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58. Ragan M.A., Goggin C.L., Cawthorn R.J., Cerenius L., Jamieson A.V.C., Plourde S.M., Rand T.G., Soederhaell K., and Gutell R.R. (1996).
A novel clade of protistan parasites near the animal-fungal divergence.
Proceedings of the National Academy of Sciences (USA), 93(21):11907-11912.
PM | PMC | DOI ]
57. Picon M., Gutell R.R., Ehrlich R., Zaha A. (1996).
Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure.
Gene, 171(2):215-220.
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56. Buchheim M.A., Lemieux C., Otis C., Gutell R.R., Chapman R.L., and Turmel M. (1996)
Phylogeny of the Chlamydomonales (Chlorophyceae): A comparison of ribosomal RNA gene sequences from the nucleus and the chloroplast.
Molecular Phylogenetics and Evolution, 5(2):391-402.
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55. Rogers M.J., Gutell R.R., Damberger S.H., Li J., McConkey G.A., Waters A.P., and McCutchan T. (1996).
Structural features of the large subunit rRNA expressed in Plasmodium falciparum sporozoites that distinguish it from the asexually expressed large subunit rRNA.
RNA, 2(2):134-145.
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54. Schnare M.N., Damberger S.H., Gray M.W., and Gutell R.R. (1996).
Comprehensive Comparison of Structural Characteristics in Eukaryotic Cytoplasmic Large Subunit (23S-like) Ribosomal RNA.
Journal of Molecular Biology, 256(4):701-719.
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53. Gutell R.R. (1996).
Comparative Sequence Analysis and the Structure of 16S and 23S rRNA.
In: Ribosomal RNA. Structure, Evolution, Processing, and Function in Protein Biosynthesis. pp. 111-128. Dahlberg A.E. and Zimmermann R.A.. (eds.) CRC Press. Boca Raton.
 
52. Turmel M., Boudreau E., Gutell R.R., Otis C., and Lemieux C. (1995).
Chloroplast gene organization and phylogenetic relationships in green algae.
In: Plant Genome and Plastome: Their Structure and Evolution. Tsunewaki K. (ed.) pp. 147-156.
 
51. Gautheret D., Konings D., and Gutell R.R. (1995).
G.U Base pairing Motifs in Ribosomal RNAs.
RNA, 1(8):807-814.
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50. Lodmell J.S., Gutell R.R., and Dahlberg A.E. (1995).
Genetic and comparative analyses reveal an alternative secondary structure in the region of nt 912 of 16S ribosomal RNA.
Proceedings of the National Academy of Sciences (USA), 92(23):10555-10559.
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49. Kim N.W., Gutell R.R., and Chan V.L. (1995).
Complete sequences and organization of the rrnA operon from Campylobacter jejuni TGH9011 (ATCC 43431).
Gene, 164(1):101-106.
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48. Ragan M.A. and Gutell R.R. (1995).
Are red algae plants?
Botanical Journal of the Linnean Society, 118:81-105.
[ pm | pmc | DOI ]
47. Fan M., Chen L-C., Ragan M.A., Gutell R.R., Warner J.R., Currie B.P., and Casadevall A. (1995).
The 5S rRNA and the rRNA intergenic spacer of the two varieties of Cryptococcus neoformans.
Journal of Medical and Veterinary Mycology, 33(4):215-221.
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46. Konings D.A.M. and Gutell R.R. (1995).
A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.
RNA, 1(6):559-574.
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45. Oliveira M.C., Kurniawan J., Bird C.J., Rice E.L., Murphy C.A., Singh R.K., Gutell R.R., and Ragan M.A. (1995).
A preliminary investigation of the order Bangiales (Bangiophycidae, Rhodophyta) based on sequences of nuclear small-subunit ribosomal RNA genes.
Phycological Research, 43(2):71-79.
[ pm | pmc | DOI ]
44. Gautheret D., Damberger S.H., and Gutell R.R. (1995).
Identification of Base Triples in RNA Using Comparative Sequence Analysis.
Journal of Molecular Biology, 248(1):27-43.
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43. Srikantha T., Gutell R.R., Morrow B., and Soll D.R. (1994).
Partial nucleotide sequence of a single ribosomal RNA coding region and secondary structure of the large subunit 25S rRNA of Candida albicans.
Current Genetics, 26(4):321-328.
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42. Damberger S.H. and Gutell R.R. (1994).
A Comparative Database of Group I Intron Structures.
Nucleic Acids Research, 22(17):3508-3510.
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41. Gutell R.R. (1994)
Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures: 1994.
Nucleic Acids Research, 22(17):3502-3507.
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40. Gautheret D., Konings D., and Gutell R.R. (1994).
A Major Family of Motifs Involving G-A Mismatches in Ribosomal RNA.
Journal of Molecular Biology, 242(1):1-8.
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39. Bird C.J., Ragan M.A., Critchley A.T., Rice E.L., and Gutell R.R. (1994).
Molecular relationships among the Gracilariaceae (Rhodophyta): further observations on some undetermined species.
European Journal of Phycology, 29:195-202.
[ pm | pmc | DOI ]
38. Fan M., Currie B.P., Gutell R.R., Ragan M.A., and Casadevall A. (1994).
The 16S-like, 5.8S, and 23S-like rRNA of the two varieties of Cryptococcus neoformans: Sequence, Secondary Structure, Phylogenetic Analysis, and restriction fragment polymorphisms.
Journal of Medical and Veterinary Mycology, 32(3):163-180.
PM | pmc | DOI ]
37. 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. (1994).
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(15):4597-4609.
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36. Ragan M.A., Bird C.J., Rice E.L., Gutell R.R., Murphy C.A., and Singh R.K. (1994).
A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene.
Proceedings of the National Academy of Sciences (USA), 91(15):7276-7280.
PM | PMC | DOI ]
35. Cech T.R., Damberger S.H., and Gutell R.R. (1994).
Representation of the Secondary and Tertiary Structure of Group I Introns.
Nature Structural Biology, 1(5):273-280.
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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.
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33. Gutell R.R. (1993).
The Simplicity Behind the Elucidation of Complex Structure in Ribosomal RNA.
in: The Translational Apparatus, Nierhaus K.H., Subramanian A.R., Erdmann V.A., Franceschi F., and Wittman-Liebold B. (eds). pp. 477-488. Plenum Publishing Corporation. New York, New York.
 
32. Ree H.K., Larsen N., Gutell R.R., and Zimmermann R.A. (1993).
The Primary and Secondary Structures of the 23S Ribosomal RNA from Thermoplasma acidophilum define an Ancient Archaeal Divergence.
Systematic and Applied Microbiology, 16:333-341.
 
31. Turmel M., Gutell R.R., Mercier J-P., Otis C., and Lemieux C. (1993)
Analysis of the Chloroplast Large Subunit Ribosomal RNA Gene from 17 Chlamydomonas Taxa. Three Internal Transcribed Spacers and 12 Group I Intron Insertion Sites.
Journal of Molecular Biology, 232(2):446-467.
PM | pmc | DOI ]
30. Gutell R.R. (1993)
Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures.
Nucleic Acids Research, 21(13):3051-3054.
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29. Gutell R.R., Gray M.W., and Schnare M.N. (1993).
A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures: 1993.
Nucleic Acids Research, 21(13):3055-3074.
PM | PMC | DOI ]
28. Gutell R.R. (1993).
COMPARATIVE STUDIES OF RNA: Inferring Higher-Order Structure from Patterns of Sequence Variation.
Current Opinion in Structural Biology, 3(3):313-322.
[ pm | pmc | DOI ]
27. van Keulen H., Gutell R.R., Gates M.A., Campbell S.R., Erlandsen S.L., Jarroll E.L., Kulda J., and Meyer E.A. (1993).
Unique phylogenetic position of Diplomonadida based on the complete small subunit ribosomal RNA sequence of Giardia ardeae, G.muris, G.duodenalis and Hexamita sp.
FASEB J., 7(1):223-231.
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ALT )
26. Gutell R.R. (1992).
Evolutionary Characteristics of 16S and 23S rRNA Structures.
pp. 243-309. PRESENTED AT: The Symposium -- The Origin and Evolution of Prokaryotic and Eukaryotic Cells. Shimoda, Japan. April 22-25, 1992. Hyman Hartman and Koichiro Matsuno (eds.). World Scientific Publishing Co., New Jersey. USA.
 
25. Gutell R.R., Power A., Hertz G., Putz E., and Stormo G. (1992).
Identifying Constraints on the Higher-Order Structure of RNA: Continued Development and Application of Comparative Sequence Analysis Methods.
Nucleic Acids Research, 20:5785-5795.
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24. van Keulen H., Gutell R.R., Campbell S.R., Erlandsen S.L, and Jarroll E.L. (1992).
The nucleotide sequence of the entire ribosomal DNA operon and the structure of the large subunit rRNA of Giardia muris.
Journal of Molecular Evolution, 35(4):318-328.
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23. Gutell R.R., Schnare M.N., and Gray M.W. (1992)
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures.
Nucleic Acids Research, 20(Supplement):2095-2109.
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22. Chakrabarti D., Dame J.B., Gutell R.R., and Yowell C.A. (1992).
Characterization of the rDNA unit and sequence analysis of the Small Subunit rRNA and 5.8S rRNA genes from Tritrichomonas foetus.
Molecular and Biochemical Parasitology, 52(1):75-84.
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21. Pan T., Gutell R.R., and Uhlenbeck O. (1991).
Folding of Circularly Permuted Transfer RNAs.
Science, 254(5036):1361-1364.
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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.
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19. Gutell R.R., Schnare M., and Gray M. (1990)
A compilation of large subunit (23S-like) ribosomal RNA sequences presented in a secondary structure format.
Nucleic Acids Research, 18(Supplement):2319-2330.
PM | PMC | doi ]
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.
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17. Haselman T., Gutell R.R., Jurka J., and Fox G.E. (1989)
Additional Watson-Crick interactions suggest a structural core in large subunit rRNA.
Journal of Biomolecular Structure and Dynamics, 7(1):181-186.
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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.
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15. Gutell R.R. and Fox G.E. (1988).
A compilation of large subunit RNA sequences presented in a structural format.
Nucleic Acids Research, 16(Supplement):r175-r269.
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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.
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13. Noller H.F., Van Stolk B.J., Moazed D., Douthwaite S., and Gutell R.R.(1985).
Studies on the structure and function of 16S ribosomal RNA using structure-specific chemical probes.
Proc. Int. Symp. Biomol. Struct. Interactions, Suppl. J. Biosci., 8:747-755.
[ pm | pmc | DOI ]
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.
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11. Sloof P., Van den Burg J., Voogd A., Benne R., Agostinellia M., Borst P., Gutell R., and Noller H. (1985).
Further characterization of the extremely small mitochondrial RNAs from trypanosomes: a detailed comparison of the 9S and 12S RNAs from Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms.
Nucleic Acids Research, 13(11):4171-4190.
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10. Seilhamer J.J., Gutell R.R., and Cummings D.J. (1984).
Paramecium mitochondrial genes: II.large subunit rRNA gene sequence and microevolution.
Journal of Biological Chemistry, 259(8):5173-5181.
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ALT )
9. Hogan J.J., Gutell R.R., and Noller H.F. (1984).
Probing the conformation of 26S rRNA in yeast 60S ribosomal subunits with kethoxal.
Biochemistry, 23(14):3330-3335.
PM | pmc | DOI ]
8. Hogan J.J., Gutell R.R., and Noller H.F. (1984).
Probing the conformation of 18S rRNA in yeast 40S ribosomal subunits with kethoxal.
Biochemistry, 23(14):3322-3330.
PM | pmc | DOI ]
7. Chan Y.-L., Gutell R., Noller H.F., and Wool I.G. (1984).
The nucleotide sequence of a rat 18S ribosomal ribonucleic acid gene and a proposal for the secondary structure of 18S ribosomal ribonucleic acid.
Journal of Biological Chemistry, 259(1):224-230.
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ALT )
6. Prince J.B., Gutell R.R., and Garrett R.A. (1983).
A consensus model of the Escherichia coli ribosome.
Trends in Biochemical Sciences, 8:359-363.
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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.
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4. Brosius J., Ullrich A., Raker M.A., Gray A., Dull T.J., Gutell R.R., and Noller H.F. (1981).
Construction and fine mapping of recombinant plasmids containing the rrnB ribosomal RNA operon of E. coli.
Plasmid, 6(1):112-118.
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3. Kingston, R.E., Gutell R.R., Taylor A.R., and Chamberlin M.J. (1981).
Transcriptional mapping of plasmid pKK3535, quantitation of the effect of guanosine tetraphosphate on binding to the rrnB promotors and a lambda promotor with sequence homologies to the CII binding region.
Journal of Molecular Biology, 146(4):433-449.
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2. Noller H.F., Kop J., Wheaton V., Brosius J., Gutell R.R., Kopylov A.M., Dohme F., Herr W., Stahl D.A., Gupta R., and Woese C.R. (1981).
Secondary structure model for 23S ribosomal RNA.
Nucleic Acids Research, 9(22):6167-6189.
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1. Woese C.R., Magrum L.J., Gupta R., Siegel R.B., Stahl D.A., Kop J., Crawford N., Brosius J., Gutell R., Hogan J.J., and Noller H.F. (1980)
Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.
Nucleic Acids Research, 8(10):2275-2293.
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*

(Robin Gutell)