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RNAcentral: a comprehensive database of non-coding RNA sequences.

The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME.

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28.


R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N.

Nucleic Acids Res. 2015 Jul 1;43(W1):W15-23. doi: 10.1093/nar/gkv543. Epub 2015 Jun 5.


rRNA--the evolution of that magic molecule.

Gutell RR.

RNA. 2015 Apr;21(4):627-9. doi: 10.1261/rna.050211.115. No abstract available.


RNAcentral: an international database of ncRNA sequences.

RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, Pruitt KD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991. Epub 2014 Oct 28.


Introduction to special Carl Woese issue in RNA Biology.

Gutell RR.

RNA Biol. 2014;11(3):170-1. doi: 10.4161/rna.28393. Epub 2014 Mar 17. No abstract available.


Ten lessons with Carl Woese about RNA and comparative analysis.

Gutell RR.

RNA Biol. 2014;11(3):254-72. doi: 10.4161/rna.28718. Epub 2014 Apr 2. Review.


Helix capping in RNA structure.

Lee JC, Gutell RR.

PLoS One. 2014 Apr 1;9(4):e93664. doi: 10.1371/journal.pone.0093664. eCollection 2014.


Two accurate sequence, structure, and phylogenetic template-based RNA alignment systems.

Shang L, Gardner DP, Xu W, Cannone JJ, Miranker DP, Ozer S, Gutell RR.

BMC Syst Biol. 2013;7 Suppl 4:S13. doi: 10.1186/1752-0509-7-S4-S13. Epub 2013 Oct 23.


Specificity between lactobacilli and hymenopteran hosts is the exception rather than the rule.

McFrederick QS, Cannone JJ, Gutell RR, Kellner K, Plowes RM, Mueller UG.

Appl Environ Microbiol. 2013 Mar;79(6):1803-12. doi: 10.1128/AEM.03681-12. Epub 2013 Jan 4.


An Accurate Scalable Template-based Alignment Algorithm.

Gardner DP, Xu W, Miranker DP, Ozer S, Cannone JJ, Gutell RR.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2012 Dec 31;2012:1-7.


The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum.

Feagin JE, Harrell MI, Lee JC, Coe KJ, Sands BH, Cannone JJ, Tami G, Schnare MN, Gutell RR.

PLoS One. 2012;7(6):e38320. doi: 10.1371/journal.pone.0038320. Epub 2012 Jun 22.


Structural constraints identified with covariation analysis in ribosomal RNA.

Shang L, Xu W, Ozer S, Gutell RR.

PLoS One. 2012;7(6):e39383. doi: 10.1371/journal.pone.0039383. Epub 2012 Jun 19.


rCAD: A Novel Database Schema for the Comparative Analysis of RNA.

Ozer S, Doshi KJ, Xu W, Gutell RR.

Proc IEEE Int Conf Escience. 2011 Dec 31;2011:15-22.


R-PASS: A Fast Structure-based RNA Sequence Alignment Algorithm.

Jiang Y, Xu W, Thompson LP, Gutell RR, Miranker DP.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011 Dec 31;2011:618-622.


Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure.

Gardner DP, Ren P, Ozer S, Gutell RR.

J Mol Biol. 2011 Oct 21;413(2):473-83. doi: 10.1016/j.jmb.2011.08.033. Epub 2011 Aug 23.


Tensor decomposition reveals concurrent evolutionary convergences and divergences and correlations with structural motifs in ribosomal RNA.

Muralidhara C, Gross AM, Gutell RR, Alter O.

PLoS One. 2011;6(4):e18768. doi: 10.1371/journal.pone.0018768. Epub 2011 Apr 29.


RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.

Xu W, Wongsa A, Lee J, Shang L, Cannone JJ, Gutell RR.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011:613-617.


Coarse-grained model for simulation of RNA three-dimensional structures.

Xia Z, Gardner DP, Gutell RR, Ren P.

J Phys Chem B. 2010 Oct 28;114(42):13497-506. doi: 10.1021/jp104926t.


Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes.

Milbury CA, Lee JC, Cannone JJ, Gaffney PM, Gutell RR.

BMC Genomics. 2010 Sep 2;11:485. doi: 10.1186/1471-2164-11-485.


Placement of attine ant-associated Pseudonocardia in a global Pseudonocardia phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.

Mueller UG, Ishak H, Lee JC, Sen R, Gutell RR.

Antonie Van Leeuwenhoek. 2010 Aug;98(2):195-212. doi: 10.1007/s10482-010-9427-3. Epub 2010 Mar 24. Review.


The limits of nuclear encoded SSU rDNA for resolving the diatom phylogeny.

Theriot EC, Cannone JJ, Gutell RR, Alverson AJ.

Eur J Phycol. 2009 Aug 1;44(3):277-290.


Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).

Maddison DR, Moore W, Baker MD, Ellis TM, Ober KA, Cannone JJ, Gutell RR.

Zool Scr. 2009;38(1):43-62.


Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

Wu JC, Gardner DP, Ozer S, Gutell RR, Ren P.

J Mol Biol. 2009 Aug 28;391(4):769-83. doi: 10.1016/j.jmb.2009.06.036. Epub 2009 Jun 18.


Morphological, molecular, and phylogenetic characterization of Nosema ceranae, a microsporidian parasite isolated from the European honey bee, Apis mellifera.

Chen YP, Evans JD, Murphy C, Gutell R, Zuker M, Gundensen-Rindal D, Pettis JS.

J Eukaryot Microbiol. 2009 Mar-Apr;56(2):142-7. doi: 10.1111/j.1550-7408.2008.00374.x.


The origin and evolution of the ribosome.

Smith TF, Lee JC, Gutell RR, Hartman H.

Biol Direct. 2008 Apr 22;3:16. doi: 10.1186/1745-6150-3-16. Review.


Structure of the mammalian 80S ribosome at 8.7 A resolution.

Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW.

Structure. 2008 Apr;16(4):535-48. doi: 10.1016/j.str.2008.01.007.


Biclustering as a method for RNA local multiple sequence alignment.

Wang S, Gutell RR, Miranker DP.

Bioinformatics. 2007 Dec 15;23(24):3289-96. Epub 2007 Oct 6.


The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions.

Lee JC, Gutell RR, Russell R.

J Mol Biol. 2006 Jul 28;360(5):978-88. Epub 2006 Jun 16.


A structural model for the large subunit of the mammalian mitochondrial ribosome.

Mears JA, Sharma MR, Gutell RR, McCook AS, Richardson PE, Caulfield TR, Agrawal RK, Harvey SC.

J Mol Biol. 2006 Apr 21;358(1):193-212. Epub 2006 Feb 10.


Assessing the odd secondary structural properties of nuclear small subunit ribosomal RNA sequences (18S) of the twisted-wing parasites (Insecta: Strepsiptera).

Gillespie JJ, McKenna CH, Yoder MJ, Gutell RR, Johnston JS, Kathirithamby J, Cognato AI.

Insect Mol Biol. 2005 Dec;14(6):625-43.


Phylogenetic relationships among 28 spirotrichous ciliates documented by rDNA.

Hewitt EA, Müller KM, Cannone J, Hogan DJ, Gutell R, Prescott DM.

Mol Phylogenet Evol. 2003 Nov;29(2):258-67.


ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae.

Goertzen LR, Cannone JJ, Gutell RR, Jansen RK.

Mol Phylogenet Evol. 2003 Nov;29(2):216-34.


The exon context and distribution of Euascomycetes rRNA spliceosomal introns.

Bhattacharya D, Simon D, Huang J, Cannone JJ, Gutell RR.

BMC Evol Biol. 2003 Apr 25;3:7. Epub 2003 Apr 25.


The lonepair triloop: a new motif in RNA structure.

Lee JC, Cannone JJ, Gutell RR.

J Mol Biol. 2003 Jan 3;325(1):65-83.


Distribution of rRNA introns in the three-dimensional structure of the ribosome.

Jackson S, Cannone J, Lee J, Gutell R, Woodson S.

J Mol Biol. 2002 Oct 11;323(1):35-52.


Modeling a minimal ribosome based on comparative sequence analysis.

Mears JA, Cannone JJ, Stagg SM, Gutell RR, Agrawal RK, Harvey SC.

J Mol Biol. 2002 Aug 9;321(2):215-34.


The accuracy of ribosomal RNA comparative structure models.

Gutell RR, Lee JC, Cannone JJ.

Curr Opin Struct Biol. 2002 Jun;12(3):301-10. Review.


The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs.

Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR.

BMC Bioinformatics. 2002;3:2. Epub 2002 Jan 17. Erratum in: BMC Bioinformatics. 2002 Jul;3(1):15.


RNAMotif, an RNA secondary structure definition and search algorithm.

Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R.

Nucleic Acids Res. 2001 Nov 15;29(22):4724-35.


Group I intron lateral transfer between red and brown algal ribosomal RNA.

Bhattacarya D, Cannone JJ, Gutell RR.

Curr Genet. 2001 Aug;40(1):82-90.


A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta).

Müller KM, Cannone JJ, Gutell RR, Sheath RG.

Mol Biol Evol. 2001 Sep;18(9):1654-67.


AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices.

Elgavish T, Cannone JJ, Lee JC, Harvey SC, Gutell RR.

J Mol Biol. 2001 Jul 20;310(4):735-53.


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