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Items: 27

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

13.
14.

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.

PMID:
13678678
15.

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.

16.

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.

PMID:
12473452
17.

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.

PMID:
12144780
18.

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.

PMID:
12127448
19.

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.

20.

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.

PMID:
11570520
21.
22.

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.

PMID:
11504846
23.

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.

PMID:
11453684
24.

Protistan parasite QPX of hard-shell clam Mercenaria mercenaria is a member of Labyrinthulomycota.

Ragan MA, MacCallum GS, Murphy CA, Cannone JJ, Gutell RR, McGladdery SE.

Dis Aquat Organ. 2000 Sep 28;42(3):185-90.

25.

A story: unpaired adenosine bases in ribosomal RNAs.

Gutell RR, Cannone JJ, Shang Z, Du Y, Serra MJ.

J Mol Biol. 2000 Dec 1;304(3):335-54.

PMID:
11090278
26.

Ichthyophonus irregularis sp. nov. from the yellowtail flounder Limanda ferruginea from the Nova Scotia shelf.

Rand TG, White K, Cannone JJ, Gutell RR, Murphy CA, Ragan MA.

Dis Aquat Organ. 2000 May 25;41(1):31-6.

27.

Predicting U-turns in ribosomal RNA with comparative sequence analysis.

Gutell RR, Cannone JJ, Konings D, Gautheret D.

J Mol Biol. 2000 Jul 21;300(4):791-803.

PMID:
10891269

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