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Results: 1 to 20 of 36

1.

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.

PMID:
24639157
[PubMed - in process]
2.

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
3.

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
4.

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
5.

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
6.

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
7.

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
8.

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
9.

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
10.

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
11.

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
12.

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
13.

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
14.

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
15.

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
16.

The use of covariance models to annotate RNAs in whole genomes.

Gardner PP.

Brief Funct Genomic Proteomic. 2009 Nov;8(6):444-50. doi: 10.1093/bfgp/elp042. Review.

PMID:
19833700
[PubMed - indexed for MEDLINE]
Free Article
17.

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.

Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G.

PLoS Genet. 2009 Jul;5(7):e1000569. doi: 10.1371/journal.pgen.1000569. Epub 2009 Jul 17.

PMID:
19609351
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. doi: 10.1093/nar/gkn766. Epub 2008 Oct 25.

PMID:
18953034
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The RNA WikiProject: community annotation of RNA families.

Daub J, Gardner PP, Tate J, Ramsk├Âld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A.

RNA. 2008 Dec;14(12):2462-4. doi: 10.1261/rna.1200508. Epub 2008 Oct 22.

PMID:
18945806
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Mutation of miRNA target sequences during human evolution.

Gardner PP, Vinther J.

Trends Genet. 2008 Jun;24(6):262-5. doi: 10.1016/j.tig.2008.03.009. Epub 2008 May 9.

PMID:
18472179
[PubMed - indexed for MEDLINE]

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