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Essential guidelines for computational method benchmarking.

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD.

Genome Biol. 2019 Jun 20;20(1):125. doi: 10.1186/s13059-019-1738-8. Review.


Convergent regulatory evolution and loss of flight in paleognathous birds.

Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV.

Science. 2019 Apr 5;364(6435):74-78. doi: 10.1126/science.aat7244.


Transcriptional noise and exaptation as sources for bacterial sRNAs.

Jose BR, Gardner PP, Barquist L.

Biochem Soc Trans. 2019 Apr 30;47(2):527-539. doi: 10.1042/BST20180171. Epub 2019 Mar 5. Review.


Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.

Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP, Biggs PJ.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000251. Epub 2019 Feb 19.


Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.

Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB.

PeerJ. 2019 Jan 4;7:e6160. doi: 10.7717/peerj.6160. eCollection 2019.


Towards robust and repeatable sampling methods in eDNA-based studies.

Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L.

Mol Ecol Resour. 2018 May 26. doi: 10.1111/1755-0998.12907. [Epub ahead of print] Review.


Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Wheeler NE, Gardner PP, Barquist L.

PLoS Genet. 2018 May 8;14(5):e1007333. doi: 10.1371/journal.pgen.1007333. eCollection 2018 May.


An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.

Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM.

Mol Biol Evol. 2018 Jun 1;35(6):1451-1462. doi: 10.1093/molbev/msy046.


Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts.

Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP, MacKichan JK.

mSystems. 2017 Nov 14;2(6). pii: e00127-17. doi: 10.1128/mSystems.00127-17. eCollection 2017 Nov-Dec.


Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR.

BMC Genomics. 2017 Oct 17;18(1):795. doi: 10.1186/s12864-017-4197-1.


Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates.

Osborne AJ, Jose BR, Perry J, Smeele Z, Aitken J, Gardner PP, Slow S.

Genome Announc. 2017 Jun 1;5(22). pii: e00436-17. doi: 10.1128/genomeA.00436-17.


Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae.

Mesarich CH, Rees-George J, Gardner PP, Ghomi FA, Gerth ML, Andersen MT, Rikkerink EH, Fineran PC, Templeton MD.

PLoS One. 2017 Mar 1;12(3):e0172790. doi: 10.1371/journal.pone.0172790. eCollection 2017.


Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.

Coray DS, Wheeler NE, Heinemann JA, Gardner PP.

RNA Biol. 2017 Mar 4;14(3):275-280. doi: 10.1080/15476286.2016.1272747. Epub 2017 Jan 9. Review.


A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.

Umu SU, Gardner PP.

Bioinformatics. 2017 Apr 1;33(7):988-996. doi: 10.1093/bioinformatics/btw728.


Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.

Umu SU, Poole AM, Dobson RC, Gardner PP.

Elife. 2016 Sep 20;5. pii: e13479. doi: 10.7554/eLife.13479.


A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Wheeler NE, Barquist L, Kingsley RA, Gardner PP.

Bioinformatics. 2016 Dec 1;32(23):3566-3574. doi: 10.1093/bioinformatics/btw518. Epub 2016 Aug 8.


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.


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.


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.


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.


Crowdsourcing RNA structural alignments with an online computer game.

Waldispühl J, Kam A, Gardner PP.

Pac Symp Biocomput. 2015:330-41.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


The RNA WikiProject: community annotation of RNA families.

Daub J, Gardner PP, Tate J, Ramsköld 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.


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.


Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum.

Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A.

Genome Res. 2008 Feb;18(2):281-92. Epub 2007 Dec 20.


MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

Lindgreen S, Gardner PP, Krogh A.

Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.


Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes.

Weile C, Gardner PP, Hedegaard MM, Vinther J.

BMC Genomics. 2007 Jul 23;8:244.


Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA.

Freyhult EK, Bollback JP, Gardner PP.

Genome Res. 2007 Jan;17(1):117-25. Epub 2006 Dec 6.


Measuring covariation in RNA alignments: physical realism improves information measures.

Lindgreen S, Gardner PP, Krogh A.

Bioinformatics. 2006 Dec 15;22(24):2988-95. Epub 2006 Oct 12.


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