Research Summary:
The remarkable advances in nucleic acid sequencing and computer technology is transforming how Biology is studied. While I used computational biology and bioinformatics as a graduate student and PostDoc in the 1980s to study the structure and evolution of ribosomal RNA, only within the past five to ten years is computational biology utilized by many more biologists to understand all aspects of biology.  The more recent advances in nucleic acid sequencing and different aspects of computer technology continues to increase the scope and sophistication of the scientific enquiries in my lab's research.

Currently we are addressing the following topics:
(1) STRUCTURE PREDICTION: RNA secondary and tertiary structure prediction with comparative and covariation sequence analysis.
(2) PRINCIPLES OF RNA STRUCTURE: Relationships between RNA sequence and RNA higher order structure.
(3) RNA FOLDING: transforming a single RNA sequence into its biologically correct higher order structure.
(4) PHYLOGENETIC ANALYSIS: Inferring phylogenetic and evolutionary relationships from RNA structures.
(5) DEVELOPMENT OF COMPUTATIONAL METHODS: rCAD - RNA Comparative Analysis Database - SQL-Server, template-based alignment methods, covariation analysis, visualization methods, RNA folding algorithms
(6) Comparative RNA Web (CRW) Site: RNA sequence/structure online web knowledgebase.

The lab seeks an interdisciplinary group of people, with interests in RNA structure, Molecular Biology, Molecular Evolution, Computer Science, and Applied Mathematics.

Publications:

132. 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 ]

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

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

129. 2014 Cannone J.J. and Gutell R.R.  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)

128. 2014 Gutell R.R. Ten Lessons with Carl Woese about RNA and Comparative Analysis.  RNA Biology, 11:254-272. [ PM | pmc | DOI ]

127. 2014 Gutell R.R. Introduction to Special Carl Woese Issue in RNA Biology.  RNA Biology, 11:170-171. [ pm | pmc | DOI ]

126. 2014 Lee J.C. and Gutell R.R.  Helix Capping in RNA Structure.  PLOS One, 9:e93664. [ PM | PMC | DOI ]

125. 2013 Shang L., Gardner D.P., Xu W., Cannone J.J., Miranker D.P., Ozer S., and Gutell R.R. Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems.  BMC Systems Biology, 7(S4):S13. [ pm | pmc | DOI ]

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

123. 2013 McFrederick Q.S., Cannone J.J., Gutell R.R., Kellner K., Plowes R.M., and Mueller U.G.  Specificity between Lactobacilli and Hymenopteran Hosts is the Exception Rather than the Rule.  Applied and Environmental Microbiology, 79:1803-1812. [ PM | PMC | DOI ]

122. 2013 Gutell R.R.  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. 2012 Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. 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. 2012 Feagin J.E., Harrell M.I., Lee J.C., Coe K.J., Sands B., Cannone J.J., Tami G., Schnare M.N., and Gutell R.R. The Fragmented Mitochondrial rRNAs of Plasmodium falciparum, PLoS ONE 7: e38320. [ PM | PMC | DOI ]

119. 2012 Shang L., Xu W., Ozer S., and Gutell R.R. Structural Constraints identified with Covariation Analysis in 16S ribosomal RNA, PLoS ONE 7: e39383. [ PM | PMC | DOI ]

118. 2012 Lee J.C. and Gutell R.R. A Comparison of the Crystal Structures of Eukaryotic and Bacterial SSU Ribosomal RNAs Reveals Common Structural Features in the Hypervariable Regions, PLoS ONE 7: e38203. [ PM | PMC | DOI ]

117. 2011 Ozer S., Doshi K.J., Xu W., and Gutell R.R., rCAD: A Novel Database Schema for the Comparative Analysis of RNA, 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 15-22. [ PM | PMC | DOI ]

116. 2011 Jiang Y., Xu W., Thompson L.P., Gutell R., and Miranker D.   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. 2011 Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R., RNA2DMap: A Visual Exploration Tool of the Information in RNA’s Higher-Order Structure., 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011) November 12-15, 2011 in Atlanta, Georgia, 613-617. [ PM | PMC | DOI ]

114. 2011 Gardner D.P., Ren P., Ozer S., and Gutell R.R., Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure., Journal of Molecular Biology 413: 473-483. [ PM | PMC | DOI ]

113. 2011 Muralidhara C., Gross A.M., Gutell R.R., and Alter O., Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA., PLoS ONE 6: e18768. [ PM | PMC | DOI ]

112. 2010 Xia Z., Gardner D.P., Gutell R.R., and Ren P., Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures, The Journal of Physical Chemistry B, 114: 13497-13506. [ PM | PMC | DOI ]

111. 2010 Milbury C.A., Lee J.C., Cannone J.J., Gaffney P.M., and Gutell R.R., Fragmentation of the Large Subunit Ribosomal RNA Gene in Oyster Mitochondrial Genomes, BMC Genomics 11: 485. PM | PMC | DOI ]

110. 2010 Mueller U.G., Ishak H., Lee J.C., Sen R., and Gutell R.R.  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.  The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.  European Journal of Phycology, 44(3):277-290. [ PM | PMC | DOI ]

108. 2009 Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P.  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. 2009 Xu W., Ozer S., Gutell R.R., 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.conference/book: 200-216. [ pm | PMC | DOI ]

106. 2009 Chen Y.P., Evans J.D., Murphy C., Gutell R., Zuker M., Gundersen-Rindal D., and Pettis J.S.  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. 2009 Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae). Zoologica Scripta, 38:43-62. [ PM | PMC | DOI ]

104. 2008 Smith T.F., Gutell R., Lee J., and Hartman H.  The origin and evolution of the ribosome.  Biology Direct, 3:16. [ PM | PMC | DOI ]

103. 2008 Chandramouli P., Topf M., Ménétret J.-F., Eswar N., Cannone J.J., Gutell R.R., Sali A., and Akey C.W.  Structure of the Mammalian 80S Ribosome at 8.7 Å Resolution.  Structure, 16(4):535-548. PM | PMC | DOI ]

102. 2007 Wang S., Gutell R.R., and Miranker D.P.  Biclustering as a Method for RNA Local Multiple Sequence Alignment.  Bioinformatics, 23(24):3289-3296. [ PM | PMC | DOI ]

101. 2007 Lee C.-Y., Lee J.C., and Gutell R.R. , Networks of interactions in the secondary and tertiary structure of ribosomal RNA., Physica A 386: 564-572. [ pm | pmc | DOI ]

100. 2006 Gillespie J.J., Johnston J.S., Cannone J.J., and Gutell R.R.  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. 2006 Weinstock et al. (81 authors), Gillespie J.J., Cannone J.J., Gutell R.R., et al. (100 authors)  Insights into social insects from the genome of the honeybee Apis mellifera.  Nature, 443(7114):931-949. [PM | PMC | DOI ]

98. 2006 Lee J.C., Gutell R.R., and Russell R., 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: 978-988. [ PM | pmc | DOI ]

97. 2006 Alverson A.J., Cannone J.J., Gutell R.R., and Theriot E.C.  The Evolution of Elongate Shape in Diatoms.  Journal of Phycology, 42(3):655-668. [ pm | pmc | DOI ]

96. 2006 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. A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome.  Journal of Molecular Biology, 358(1):193-212. [ PM | PMC | DOI ]

95. 2005 Gillespie J.J., McKenna C.H., Yoder M.J., Gutell R.R., Johnston J.S., Kathirithamby J., and Cognato A.I.  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. 2005 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.  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. 2005 Muller K.M., Ellenor D.W., Sherwood A.R., Sheath R.G., Cannone J.J., and Gutell R.R., Evidence for Lateral Transfer of an IE Intron Between Fungal and Red Algal Small Subunit rRNA Genes, Journal of Phycology 41: 380-390. [ pm | pmc | DOI ]

92. 2004 Lee J.C. and Gutell R.R., Diversity of Base-pair Conformations and their Occurrence in rRNA Structure and RNA Structural Motifs, Journal of Molecular Biology 344: 1225-1249. [ PM | pmc | DOI ]

91. 2004 Gillespie J., Cannone J., Gutell R., and Cognato A.  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. 2004 Doshi K.J., Cannone J.J., Cobaugh C.W., and Gutell R.R., 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. 2004 Cannone J.J. and Gutell R.R.  Multiple entries in: Dictionary of Bioinformatics and Computational Biology, Hancock J.M. and Zvelebil M.J. (eds.). Wiley. Hoboken, New Jersey. [ pm | pmc | doi ] ( ALT )

88. 2003 Hewitt E.A., Müller K.M., Cannone J., Hogan D.J., Gutell R., and Prescott D.M.  Phylogenetic Relationships Among 28 Spirotrichous Ciliates Defined by rDNA.  Molecular Phylogenetics and Evolution, 29(2):258-267. [ PM | pmc | DOI ]

87. 2003 Goertzen L.R., Cannone J.J., Gutell R.R., and Jansen R.K. 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. 2003 Bhattacharya D, Simon D., Huang J., Cannone J.J., and Gutell R.R.  The Exon Context and Distribution of Euascomycetes rRNA Spliceosomal Introns.  BioMed Central Evolutionary Biology, 3:7. [ PM | PMC | DOI ]

85. 2003 Lee J.C., Cannone J.J., and Gutell R.R., The Lonepair Triloop: A New Motif in RNA Structure, Journal of Molecular Biology 325: 65-83. [ PM | pmc | DOI ]

84. 2002 Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R., and Woodson S.A.  Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome.  Journal of Molecular Biology, 323(1):35-52. [ PM | pmc | DOI ]

83. 2002 Mears J.A., Cannone J.J., Stagg S.M., Gutell R.R., Agrawal R.K., and Harvey S.C. Modeling a Minimal Ribosome Based on Comparative Sequence Analysis.  Journal of Molecular Biology, 321(2):215-234. [ PM | pmc | DOI ]

82. 2002 Müller K.M., Sherwood A.R., Pueschel C.M., Gutell R.R., and Sheath R.G. A proposal for a new red algal order, the Thoreales.  Journal of Phycology, 38(4):807-820. [ pm | pmc | DOI ]

81. 2002 Gutell R.R., Lee J.C., and Cannone J.J., The Accuracy of Ribosomal RNA Comparative Structure Models, Current Opinion in Structural Biology 12: 301-310. [ PM | pmc | DOI ]

80. 2002 Cannone J.J, Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N.,Shang Z., Yu N., and Gutell R.R. , 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 (and 15). [ PM | PMC | DOI ]

79. 2001 Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., and Sampath R. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Research, 29(22):4724-4735. [ PM | PMC | DOI ]

78. 2001 Vernon D., Gutell R.R., Cannone J.J., Rumpf R.W., and Birky C.W. Jr.  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. 2001 Müller K.M., Cannone J.J., Gutell R.R., and Sheath R.G. 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. 2001 Bhattacharya D., Cannone J.J., and Gutell R.R.  Group I Intron Lateral Transfer Between Red and Brown Algae Ribosomal RNA.  Current Genetics, 40(1):82-90. [ PM | pmc | DOI ]

75. 2001 Elgavish T., Cannone J.J., Lee J.C., Harvey S.C., and Gutell R.R., 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: 735-753.  [ PM | pmc | DOI ]

74. 2000 Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J., A Story: Unpaired Adenosine Bases in Ribosomal RNA. , Journal of Molecular Biology, 304: 335-354. [ PM | pmc | DOI ]

73. 2000 Ragan M.A., MacCallum G.S., Murphy C.A., Cannone J.J., Gutell R.R., and McGladdery S.E.
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 ]

72. 2000 Chen X., Gutell R.R., and Lambowitz A.M.  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. [ PM | pmc | DOI ]

71. 2000 Gutell R.R., Cannone J.J., Konings D., and Gautheret D., Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis. , Journal of Molecular Biology 300: 791-803. [ PM | pmc | DOI ]

70. 2000 Rand T.G., White K., Cannone J.J., Gutell R.R., Murphy C.A., and Ragan M.A.  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 ]

69. 2000 Lydeard C., Holznagel W.E., Schnare M.N., and Gutell R.R.  Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures.  Molecular Phylogenetics and Evolution, 15(1):83-102. [ PM | pmc | DOI ]

68. 1999 Babin P., Dolan M., Wollenzien P., and Gutell R.R.  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. 1999 Gutell R.R.  Comparative Analysis of RNA Sequences. Symposium on RNA Biology - North Carolina (October 1999).  Nucleic Acids Research Symposia Series, 41:48-53.

66. 1998 Conn G.L., Gutell R.R., and Draper D.E.  A Functional Ribosomal RNA Tertiary Structure Involves a Base Triple Interaction.  Biochemistry, 37(34):11980-11988. [ PM | PMC | DOI ]

65. 1998 Ortoleva-Donnelly L., Szewczak A.A., Gutell R.R., and Strobel S.A.  The Chemical Basis of Adenosine Conservation throughout the Tetrahymena Ribozyme.  RNA, 4(5):498-519. [ PM | PMC | DOI ]

64. 1997 Tanner M.A., Anderson E.M., Gutell R.R., and Cech T.R.  Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes.  RNA, 3(9):1037-1051. [ PM | PMC | doi ]

63. 1997 Li J., Gutell R.R., Damberger S.H., Kissinger J.C., Rogers M.J., Wirtz R.A., Sattabongkot J., and McCutchan T..  Regulation and trafficking of three distinct 18 S ribosomal RNAs during development of the malaria parasite.  Journal of Molecular Biology, 269(2):203-213. [ PM | pmc | DOI ]

62. 1997 Huynen M., Gutell R.R. and Konings D.  Assessing the reliability of RNA folding using statistical mechanics.  Journal of Molecular Biology, 267(5):1104-1112. [ PM | pmc | DOI ]

61. 1997 Gautheret D. and Gutell R.R, Inferring the Conformation of RNA Base Pairs and Triples from Patterns of Sequence Variation, Nucleic Acids Research 25: 1559-1564. [ PM | PMC | DOI ]

60. 1996 Gutell R.R. and Damberger S.H.  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. 1996 Fields D.S. and Gutell R.R., An Analysis of Large rRNA Sequences Folded by a Thermodynamic Method, Folding and Design 1: 419-430. [ PM | pmc | DOI ]

58. 1996 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.  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. 1996 Picon M., Gutell R.R., Ehrlich R., Zaha A.  Characterization of a flatworm ribosomal RNA-encoding gene: promoter sequence and small subunit rRNA secondary structure.  Gene, 171(2):215-220. [ PM | pmc | DOI ]

56. 1996 Buchheim M.A., Lemieux C., Otis C., Gutell R.R., Chapman R.L., and Turmel M. 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. [ PM | pmc | DOI ]

55. 1996 Rogers M.J., Gutell R.R., Damberger S.H., Li J., McConkey G.A., Waters A.P., and McCutchan T.
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. [ PM | PMC | doi ]

54. 1996 Schnare M.N., Damberger S.H., Gray M.W., and Gutell R.R. , Comprehensive Comparison of Structural Characteristics in Eukaryotic Cytoplasmic Large Subunit (23S-like) Ribosomal RNA, Journal of Molecular Biology 256: 701-719. [ PM | pmc | DOI ]

53. 1996 Gutell R.R. 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. 1995 Turmel M., Boudreau E., Gutell R.R., Otis C., and Lemieux C.  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. 1995 Gautheret D., Konings D., and Gutell R.R., G.U Base pairing Motifs in Ribosomal RNAs, RNA 1: 807-814. [ PM | PMC | doi ]

50. 1995 Lodmell J.S., Gutell R.R., and Dahlberg A.E.  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. [ PM | PMC | DOI ]

49. 1995 Kim N.W., Gutell R.R., and Chan V.L.  Complete sequences and organization of the rrnA operon from Campylobacter jejuni TGH9011 (ATCC 43431).  Gene, 164(1):101-106. [ PM | pmc | DOI ]

48. 1995 Ragan M.A. and Gutell R.R., Are red algae plants? , Botanical Journal of the Linnean Society 118: 81-105. [ pm | pmc | DOI ]

47. 1995 Fan M., Chen L-C., Ragan M.A., Gutell R.R., Warner J.R., Currie B.P., and Casadevall A.  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. [ PM | pmc | DOI ]

46. 1995 Konings D.A.M. and Gutell R.R., A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs, RNA 1: 559-574. [ PM | PMC | doi ]

45. 1995 Oliveira M.C., Kurniawan J., Bird C.J., Rice E.L., Murphy C.A., Singh R.K., Gutell R.R., and Ragan M.A.
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. 1995 Gautheret D., Damberger S.H., and Gutell R.R., Identification of Base Triples in RNA Using Comparative Sequence Analysis, Journal of Molecular Biology 248: 27-43. [ PM | pmc | DOI ]

43. 1994 Srikantha T., Gutell R.R., Morrow B., and Soll D.R. 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. [ PM | pmc | DOI ]

42. 1994 Damberger S.H. and Gutell R.R.  A Comparative Database of Group I Intron Structures.  Nucleic Acids Research, 22(17):3508-3510. [ PM | PMC | DOI ]

41. 1994 Gutell R.R. Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures: 1994.  Nucleic Acids Research, 22(17):3502-3507. [ PM | PMC | DOI ]

40. 1994 Gautheret D., Konings D., and Gutell R.R., A Major Family of Motifs Involving G-A Mismatches in Ribosomal RNA, Journal of Molecular Biology 242: 1-8. [ PM | pmc | DOI ]

39. 1994 Bird C.J., Ragan M.A., Critchley A.T., Rice E.L., and Gutell R.R. Molecular relationships among the Gracilariaceae (Rhodophyta): further observations on some undetermined species.  European Journal of Phycology, 29:195-202. [ pm | pmc | DOI ]

38. 1994 Fan M., Currie B.P., Gutell R.R., Ragan M.A., and Casadevall A.  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. 1994 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., 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: 4597-4609. [ PM | PMC | doi ]

36. 1994 Ragan M.A., Bird C.J., Rice E.L., Gutell R.R., Murphy C.A., and Singh R.K.  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. 1994 Cech T.R., Damberger S.H., and Gutell R.R.  Representation of the Secondary and Tertiary Structure of Group I Introns.  Nature Structural Biology, 1(5):273-280. [ PM | pmc | DOI ]

34. 1994 Gutell R.R., Larsen N., and Woese C.R., Lessons from an Evolving Ribosomal RNA: 16S and 23S rRNA Structure from a Comparative Perspective, Microbiological Reviews 58: 10-26. [ PM | PMC | doi ]

33. 1993 Gutell R.R.  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. 1993 Ree H.K., Larsen N., Gutell R.R., and Zimmermann R.A.  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. 1993 Turmel M., Gutell R.R., Mercier J-P., Otis C., and Lemieux C.  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. 1993 Gutell R.R. Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures.  Nucleic Acids Research, 21(13):3051-3054. [ PM | PMC | DOI ]

29. 1993 Gutell R.R., Gray M.W., and Schnare M.N.  A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures: 1993.  Nucleic Acids Research, 21(13):3055-3074. [ PM | PMC | DOI ]

28. 1993 Gutell R.R.  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. 1993 van Keulen H., Gutell R.R., Gates M.A., Campbell S.R., Erlandsen S.L., Jarroll E.L., Kulda J., and Meyer E.A.  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. [ PM | pmc | doi ]
( ALT )

26. 1992 Gutell R.R.   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. 1992 Gutell R.R., Power A., Hertz G., Putz E., and Stormo G., Identifying Constraints on the Higher-Order Structure of RNA: Continued Development and Application of Comparative Sequence Analysis Methods. , Nucleic Acids Research, 20: 5785-5795. [ PM | PMC | DOI ]

24. 1992 van Keulen H., Gutell R.R., Campbell S.R., Erlandsen S.L, and Jarroll E.L.  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. [ PM | pmc | DOI ]

23. 1992 Gutell R.R., Schnare M.N., and Gray M.W. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures.  Nucleic Acids Research, 20(Supplement):2095-2109. [ PM | PMC | doi ]

22. 1992 Chakrabarti D., Dame J.B., Gutell R.R., and Yowell C.A.  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. [ PM | pmc | DOI ]

21. 1991 Pan T., Gutell R.R., and Uhlenbeck O.  Folding of Circularly Permuted Transfer RNAs.  Science, 254(5036):1361-1364. [ PM | pmc | DOI ]

20. 1990 Woese C.R., Winker S. and Gutell R.R., Architecture of Ribosomal RNA: Constraints on the sequence of Tetra-loops, Proceedings of the National Academy of Sciences (USA) 87: 8467-8471. [ PM | PMC | DOI ]

19. 1990 Gutell R.R., Schnare M., and Gray M. 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. 1990 Gutell, R.R. and C.R. Woese, 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: 663-667. [ PM | PMC | DOI ]

17. 1989 Haselman T., Gutell R.R., Jurka J., and Fox G.E. Additional Watson-Crick interactions suggest a structural core in large subunit rRNA.  Journal of Biomolecular Structure and Dynamics, 7(1):181-186. [ PM | pmc | doi ]

16. 1989 Woese C.R. and Gutell R.R., Evidence for several higher order structural elements in ribosomal RNA., Proceedings of the National Academy of Sciences (USA) 86: 3119-3122. [ PM | PMC | DOI ]

15. 1988 Gutell R.R. and Fox G.E.  A compilation of large subunit RNA sequences presented in a structural format.  Nucleic Acids Research, 16(Supplement):r175-r269. [ PM | PMC | doi ]

14. 1986 Gutell R.R., Noller H.F., and Woese C.R., Higher order structure in ribosomal RNA, The EMBO Journal 5: 1111-1113. [ PM | PMC | doi ]

13. 1985 Noller H.F., Van Stolk B.J., Moazed D., Douthwaite S., and Gutell R.R.  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. 1985 Gutell R.R., Weiser B., Woese C.R., and Noller H.F. , Comparative anatomy of 16S-like ribosomal RNA., Progress in Nucleic Acid Research and Molecular Biology 32: 155-216. [ PM | pmc | DOI ]

11. 1985 Sloof P., Van den Burg J., Voogd A., Benne R., Agostinellia M., Borst P., Gutell R., and Noller H.  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. [ PM | PMC | DOI ]

10. 1984 Seilhamer J.J., Gutell R.R., and Cummings D.J.  Paramecium mitochondrial genes: II.large subunit rRNA gene sequence and microevolution.  Journal of Biological Chemistry, 259(8):5173-5181. [ PM | pmc | doi ]  ( ALT )

9. 1984 Hogan J.J., Gutell R.R., and Noller H.F.  Probing the conformation of 26S rRNA in yeast 60S ribosomal subunits with kethoxal.  Biochemistry, 23(14):3330-3335. [ PM | pmc | DOI ]

8. 1984 Hogan J.J., Gutell R.R., and Noller H.F.  Probing the conformation of 18S rRNA in yeast 40S ribosomal subunits with kethoxal.  Biochemistry, 23(14):3322-3330. [ PM | pmc | DOI ]

7. 1984 Chan Y.-L., Gutell R., Noller H.F., and Wool I.G. 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. [ PM | pmc | doi ]  ( ALT )

6. 1983 Prince J.B., Gutell R.R., and Garrett R.A.  A consensus model of the Escherichia coli ribosome.  Trends in Biochemical Sciences, 8:359-363. [ pm | pmc | DOI ]

5. 1983 Woese C.R., Gutell R., Gupta R., and Noller H.F.  Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids.  Microbiological Reviews, 47(4):621-669. [ PM | PMC | doi ]

4. 1981 Brosius J., Ullrich A., Raker M.A., Gray A., Dull T.J., Gutell R.R., and Noller H.F.  Construction and fine mapping of recombinant plasmids containing the rrnB ribosomal RNA operon of E. coli.  Plasmid, 6(1):112-118. [ PM | pmc | DOI ]

3. 1981 Kingston, R.E., Gutell R.R., Taylor A.R., and Chamberlin M.J.  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. [ PM | pmc | DOI ]

2. 1981 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. Secondary structure model for 23S ribosomal RNA.  Nucleic Acids Research, 9(22):6167-6189. [ PM | PMC | DOI ]

1. 1980 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.  Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence.  Nucleic Acids Research, 8(10):2275-2293. [ PM | PMC | DOI ]

2014 Fall      BIO321G      Introduction to Computational Biology (53524), Undergraduate

2014 Spring BIO321G      Introduction to Computational Biology (49870), Undergraduate

2013 Fall      BIO384K      Comparative Analysis of RNA Sequences (51495), Graduate (RNA Folding)

2013 Spring BIO337J/      Computational Biology lab(49875,49880), Undergraduate

                   BIO384K.20 Recent Advances in Computational Biology(50960), Graduate

2012 Fall      BIO384K      Comparative Analysis of RNA Sequences (50720), Graduate (RNA Folding)

2012 Spring BIO337J/      Computational Biology lab (49570, 49575) Undergraduate

                   BIO384K.20 Recent Advances in Computational Biology(50615), Graduate