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Results: 1 to 20 of 41

1.

Crowdsourcing RNA structural alignments with an online computer game.

WaldispĆ¼hl J, Kam A, Gardner PP.

Pac Symp Biocomput. 2015;20:330-41.

PMID:
25592593
[PubMed - in process]
Free Article
2.

Annotating RNA motifs in sequences and alignments.

Gardner PP, Eldai H.

Nucleic Acids Res. 2014 Dec 17. pii: gku1327. [Epub ahead of print]

PMID:
25520192
[PubMed - as supplied by publisher]
Free Article
3.

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 28;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.

PMID:
25392425
[PubMed - in process]
Free Article
4.

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.

PMID:
25357249
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
25342998
[PubMed]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23470992
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23392241
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23133357
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23125362
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22366418
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22144683
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
21940779
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21881407
[PubMed - indexed for MEDLINE]
Free Article
15.

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.

PMID:
21816880
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21478170
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21062808
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
20941386
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
20838588
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

SnoPatrol: how many snoRNA genes are there?

Gardner PP, Bateman A, Poole AM.

J Biol. 2010;9(1):4. doi: 10.1186/jbiol211. Epub 2010 Jan 25.

PMID:
20122292
[PubMed - indexed for MEDLINE]
Free PMC Article
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