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Items: 1 to 20 of 45

1.

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Barquist L, Burge SW, Gardner PP.

Curr Protoc Bioinformatics. 2016 Jun 20;54:12.13.1-12.13.25. doi: 10.1002/cpbi.4.

PMID:
27322404
2.

An evaluation of the accuracy and speed of metagenome analysis tools.

Lindgreen S, Adair KL, Gardner PP.

Sci Rep. 2016 Jan 18;6:19233. doi: 10.1038/srep19233.

3.

Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.

PMID:
26282327
4.

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.

5.

Crowdsourcing RNA structural alignments with an online computer game.

Waldispühl J, Kam A, Gardner PP.

Pac Symp Biocomput. 2015:330-41.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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.

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