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Results: 1 to 20 of 42

1.

Conservation and Losses of Non-Coding RNAs in Avian Genomes.

Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF.

PLoS One. 2015 Mar 30;10(3):e0121797. doi: 10.1371/journal.pone.0121797. eCollection 2015.

PMID:
25822729
2.

Crowdsourcing RNA structural alignments with an online computer game.

Waldisp├╝hl J, Kam A, Gardner PP.

Pac Symp Biocomput. 2015:330-41.

3.

Annotating RNA motifs in sequences and alignments.

Gardner PP, Eldai H.

Nucleic Acids Res. 2015 Jan;43(2):691-8. doi: 10.1093/nar/gku1327. Epub 2014 Dec 17.

4.

Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.

5.

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003907. doi: 10.1371/journal.pcbi.1003907. eCollection 2014 Oct.

6.

Molecular characterization of a new member of the lariat capping twin-ribozyme introns.

Tang Y, Nielsen H, Masquida B, Gardner PP, Johansen SD.

Mob DNA. 2014 Sep 15;5:25. doi: 10.1186/1759-8753-5-25. eCollection 2014.

7.

An introduction to RNA databases.

Hoeppner MP, Barquist LE, Gardner PP.

Methods Mol Biol. 2014;1097:107-23. doi: 10.1007/978-1-62703-709-9_6. Review.

PMID:
24639157
8.

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP.

Nucleic Acids Res. 2013 Apr;41(8):4549-64. doi: 10.1093/nar/gkt148. Epub 2013 Mar 6.

9.

RNA Biology. Letter from the editor.

Schroeder R, Gardner PP, Riedmann EM.

RNA Biol. 2013 Jan;10(1):1. doi: 10.4161/rna.23502. Epub 2013 Jan 1. No abstract available.

10.

Comparative analysis of RNA families reveals distinct repertoires for each domain of life.

Hoeppner MP, Gardner PP, Poole AM.

PLoS Comput Biol. 2012;8(11):e1002752. doi: 10.1371/journal.pcbi.1002752. Epub 2012 Nov 1.

11.

Rfam 11.0: 10 years of RNA families.

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32. doi: 10.1093/nar/gks1005. Epub 2012 Nov 3.

12.

A VapBC toxin-antitoxin module is a posttranscriptional regulator of metabolic flux in mycobacteria.

McKenzie JL, Robson J, Berney M, Smith TC, Ruthe A, Gardner PP, Arcus VL, Cook GM.

J Bacteriol. 2012 May;194(9):2189-204. doi: 10.1128/JB.06790-11. Epub 2012 Feb 24.

13.

Making your database available through Wikipedia: the pros and cons.

Finn RD, Gardner PP, Bateman A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D9-12. doi: 10.1093/nar/gkr1195. Epub 2011 Dec 5.

14.

RNAcentral: A vision for an international database of RNA sequences.

Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.

RNA. 2011 Nov;17(11):1941-6. doi: 10.1261/rna.2750811. Epub 2011 Sep 22.

15.

Two covariance models for iron-responsive elements.

Stevens SG, Gardner PP, Brown C.

RNA Biol. 2011 Sep-Oct;8(5):792-801. doi: 10.4161/rna.8.5.16037. Epub 2011 Sep 1.

16.

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.

Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP, Choudhary J, Maskell DJ, Grant AJ.

Microbiology. 2011 Oct;157(Pt 10):2922-32. doi: 10.1099/mic.0.050278-0. Epub 2011 Aug 4.

17.

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z.

Nucleic Acids Res. 2011 Aug;39(14):5845-52. doi: 10.1093/nar/gkr168. Epub 2011 Apr 7.

18.

Rfam: Wikipedia, clans and the "decimal" release.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D141-5. doi: 10.1093/nar/gkq1129. Epub 2010 Nov 9.

19.

Ten simple rules for editing Wikipedia.

Logan DW, Sandal M, Gardner PP, Manske M, Bateman A.

PLoS Comput Biol. 2010 Sep 30;6(9). pii: e1000941. doi: 10.1371/journal.pcbi.1000941. No abstract available.

20.

Long- and short-term selective forces on malaria parasite genomes.

Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC.

PLoS Genet. 2010 Sep 9;6(9):e1001099. doi: 10.1371/journal.pgen.1001099.

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