UC SPARK - University of Canterbury - New Zealand

Associate Professor Paul Phillip Gardner

Biological Sciences; Biomolecular Interaction Centre

Phone: +64 3 364 2987 ext. 6742

Office: Biological Sciences 520

Fields of Research

  • Bioinformatics
  • RNA
  • ncRNA

Researcher Summary

My personal research goal is the complete functional classification of all functional RNAs. It is well established that RNAs such as tRNA and rRNA play a vital role in translation. The further discovery of more RNAs that build the translational machinery, such as snoRNAs, RNaseP and MRP along with spliceosomal RNAs, was not too great a shock. What has come as a surprise to RNA researchers in recent years is the importance of RNA in other areas such as regulation. Newly discovered RNAs and RNA-related processes involving regulation include: RNA interference (RNAi), microRNAs, siRNAs, riboswitches, thermosensors, bacterial antisense sRNAs, leader elements, IRES's and frame-shift elements. Further discoveries have shown that RNA is important for defending genomes from invasive elements such as transposons and bacteriophages, for de-activating entire chromosomes, and are essential for DNA replication. Furthermore, the discovery of RNA enzymes, or ribozymes, has lead to the suggestion that early life's genetic and numerous metabolic processes were RNA-based. Yet many groups are discovering thousands of RNAs with no known function. Clearly we are just beginning to appreciate the number of central roles that RNA mediated processes play in biology. What further unrealised roles does this "dark matter" of the cell play?

Subject Area: Disciplines

Research Groups

Key Methodologies

  • Homology search
  • Sequence alignment
  • RNA


  • Rfam (Community Organisation/NGO): Member

Prizes and Awards

  • Rutherford Discovery ( 2010 - 2015)

Research/Scholarly/Creative Works

  • Coray DS., Wheeler NE., Heinemann JA. and Gardner PP. (2017) Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems. RNA Biology 14(3): 275-280. http://dx.doi.org/10.1080/15476286.2016.1272747. (Journal Articles)
  • Mesarich CH., Rees-George J., Gardner PP., Ashari Ghomi F., Gerth ML., Andersen MT., Rikkerink EHA., Fineran PC. and Templeton MD. (2017) Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE 12(3) e0172790 http://dx.doi.org/10.1371/journal.pone.0172790. (Journal Articles)
  • Osborne AJ., Jose BR., Perry J., Smeele Z., Aitken J., Gardner PP. and Slow S. (2017) Complete genome sequences of two geographically distinct Legionella micdadei clinical isolates. American Society for Microbiology 5(e00436-17) http://dx.doi.org/10.1128/genomeA.00436-17. (Journal Articles)
  • Ren X., Eccles DA., Greig GA., Clapham J., Wheeler NE., Lindgreen S., Gardner PP. and MacKichan JK. (2017) Genomic, Transcriptomic, and Phenotypic Analyses ofNeisseria meningitidisIsolates from Disease Patients and Their Household Contacts.. mSystems 2(6) http://dx.doi.org/10.1128/mSystems.00127-17. (Journal Articles)
  • Umu SU. and Gardner PP. (2017) A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Computer applications in the biosciences : CABIOS 33(7): 988-996. http://dx.doi.org/10.1093/bioinformatics/btw728. (Journal Articles)
  • Wu C., Jordan MD., Newcomb RD., Gemmell NJ., Bank S., Meusemann K., Dearden PK., Duncan EJ., Grosser S. and Rutherford K. (2017) Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. BMC Genomics 18(1) http://dx.doi.org/10.1186/s12864-017-4197-1. (Journal Articles)
  • Barquist L., Burge SW. and Gardner PP. (2016) Studying RNA homology and conservation with infernal: From single sequences to RNA families. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2016: 12.13.1-12.13.25. http://dx.doi.org/10.1002/cpbi.4. (Journal Articles)
  • Lindgreen S., Adair KL. and Gardner PP. (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports 6: 19233. http://dx.doi.org/10.1038/srep19233. (Journal Articles)
  • Nawrocki EP., Burge SW., Bateman A., Daub J., Eberhardt RY., Eddy SR., Floden EW., Gardner PP., Jones TA. and Tate J. (2016) Rfam 12.0: updates to the RNA families database. Nucleic Acids Research (early access online) http://dx.doi.org/10.1093/nar/gku1063. (Journal Articles)
  • Umu SU., Poole AM., Dobson RCJ. and Gardner PP. (2016) Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLife 5(September) http://dx.doi.org/10.7554/eLife.13479. (Journal Articles)
  • Wheeler NE., Barquist L., Kingsley RA. and Gardner PP. (2016) A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Computer applications in the biosciences : CABIOS 32(23): 3566-3574. http://dx.doi.org/10.1093/bioinformatics/btw518. (Journal Articles)
  • Barquist L., Burge SW. and Gardner PP. (2015) Building non-coding RNA families. In Mathews D; Turner D (Ed.), Methods in Molecular Biology: RNA Structure Determination New York City: Humana Press. http://arxiv.org/abs/1206.4087. (Chapters)
  • Gardner PP., Fasold M., Burge SW., Ninova M., Hertel J., Kehr S., Steeves TE., Griffiths-Jones S. and Stadler PF. (2015) Conservation and losses of non-coding RNAs in avian genomes. PLOS ONE 10(3) e0121797 http://dx.doi.org/10.1371/journal.pone.0121797. (Journal Articles)
  • Schmid M., Smith J., Burt DW., Aken BL., Antin PB., Archibald AL., Ashwell C., Blackshear PJ., Boschiero C. and Brown CT. (2015) Third Report on Chicken Genes and Chromosomes 2015. Cytogenetic and Genome Research 145(2): 78-179. http://dx.doi.org/10.1159/000430927. (Journal Articles)
  • Waldisp├╝hl J., Kam A. and Gardner PP. (2015) Crowdsourcing RNA structural alignments with an online computer game. Fairmont Orchid, HI, USA: 2015 Pacific Symposium on Biocomputing (PSB 2015), 4-8 Jan 2015. In Pacific Symposium on Biocomputing 20: 330-341. (Conference Contributions - Published)
  • Lindgreen S., Umu SU., Lai ASW., Eldai H., Liu W., McGimpsey S., Wheeler N., Biggs PJ., Thomson NR. and Barquist L. (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Computational Biology 10(10) e1003907 http://dx.doi.org/10.1371/journal.pcbi.1003907. (Journal Articles)
  • Tang Y., Nielsen H., Masquida B., Gardner PP. and Johansen SD. (2014) Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Mobile DNA 5: 25. http://dx.doi.org/10.1186/1759-8753-5-25. (Journal Articles)
  • Zhang G., Li C., Li Q., Li B., Larkin DM., Lee C., Storz JF., Antunes A., Greenwold MJ. and Meredith RW. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. The Scientific monthly 346(6215): 1311-1320. http://dx.doi.org/10.1126/science.1251385. (Journal Articles)
  • Zhang., G., Li., B., Li., C., Gilbert., P MT., Jarvis. and D E. (2014) Comparative genomic data of the Avian Phylogenomics Projects. GigaScience 3: 26. http://dx.doi.org/10.1186/2047-217X-3-26. (Journal Articles)
  • Barquist L., Langridge GC., Turner DJ., Phan MD., Turner AK., Bateman A., Parkhill J., Wain J. and Gardner PP. (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium. Nucleic Acids Research 41(8): 4549-4564. http://dx.doi.org/10.1093/nar/gkt148. (Journal Articles)
  • Burge SW., Daub J., Eberhardt R., Tate J., Barquist L., Nawrocki EP., Eddy SR., Gardner PP. and Bateman A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Research 41(D1) D226-D232 http://dx.doi.org/10.1093/nar/gks1005. (Journal Articles)
  • Hoeppner MP., Barquist LE. and Gardner PP. (2013) An introduction to RNA databases. In Gorodkin J; Ruzzo WL (Ed.), RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods: 107-123. Methods in Molecular Biology: Springer. (Chapters)
  • Kingsley RA., Kay S., Connor T., Barquist L., Sait L., Holt KE., Sivaraman K., Wileman T., Goulding D. and Clare S. (2013) Genome and transcriptome adaptation accompanying emergence of the definitive Type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. mBio 4(5) e00565-13 http://dx.doi.org/10.1128/mBio.00565-13. (Journal Articles)
  • Schroeder R., Gardner PP. and Riedmann EM. (2013) RNA Biology. Letter from the editor.. RNA Biology 10(1): 1. (Journal Articles)
  • Finn RD., Gardner PP. and Bateman A. (2012) Making your database available through Wikipedia: the pros and cons. Nucleic Acids Research 40(Database Issue) D9-D12 http://dx.doi.org/10.1093/nar/gkr1195. (Journal Articles)
  • Hoeppner MP., Gardner PP. and Poole AM. (2012) Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life. PLoS Computational Biology 8 e1002752 http://dx.doi.org/10.1371/journal.pcbi.1002752. (Journal Articles)
  • McKenzie JL., Robson J., Berney M., Smith TC., Ruthe A., Gardner PP., Arcus VL. and Cook GM. (2012) A VapBC Toxin-Antitoxin Module is a Post-Transcriptional Regulator of Metabolic Flux in Mycobacteria. Journal of Bacteriology 194(9): 2189-2204. http://dx.doi.org/10.1128/JB.06790-11. (Journal Articles)
  • Widmann J., Stombaugh J., McDonald D., Chocholousova J., Gardner P., Iyer MK., Liu Z., Lozupone CA., Quinn J. and Smit S. (2012) RNASTAR: An RNA Structural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA 18(7): 1319-1327. http://dx.doi.org/10.1261/rna.032052.111. (Journal Articles)
  • Bateman A., Agrawal S., Birney E., Bruford EA., Bujnicki JM., Cochrane G., Cole JR., Dinger ME., Enright AJ. and Gardner PP. (2011) RNAcentral: A vision for an international database of RNA sequences. RNA 2011(17): 1941-1946. http://dx.doi.org/10.1261/rna.2750811. (Journal Articles)
  • Chaudhuri RR., Yu L., Kanji A., Perkins TT., Gardner PP., Choudhary J., Maskell DJ. and Grant AJ. (2011) Quantitative RNA-seq analysis of the transcriptome of Campylobacter jejuni. Microbiology 157(10): 2922-2932. http://dx.doi.org/10.1099/mic.0.050278-0. (Journal Articles)
  • Gardner PP., Barquist L., Bateman A., Nawrocki EP. and Weinberg Z. (2011) RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research 39(14): 5845-5852. http://dx.doi.org/10.1093/nar/gkr168. (Journal Articles)
  • Gardner PP., Daub J., Tate J., Moore BL., Osuch IH., Griffiths-Jones S., Finn RD., Nawrocki EP., Kolbe DL. and Eddy SR. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research 39(Database issue) D141-D145 http://dx.doi.org/10.1093/nar/gkq1129. (Journal Articles)
  • Stevens SG., Gardner PP. and Brown CM. (2011) Two covariance models for iron-responsive elements. RNA Biology 8(5) (Journal Articles)
  • Gardner PP., Bateman A. and Poole AM. (2010) SnoPatrol: how many snoRNA genes are there? Journal of Biology 9(1): 4pp. http://jbiol.com/content/9/1/4. (Journal Articles)
  • Nygaard S., Braunstein A., Malsen G., Van Dongen S., Gardner PP., Krogh A., Otto TD., Pain A., Berriman M. and McAuliffe J. (2010) Long-and Short-Term Selective Forces on Malaria Parasite Genomes. PLoS Genet 9(6) e1001099 http://dx.doi.org/10.1371/journal.pgen.1001099. (Journal Articles)
  • Gardner PP. (2009) The use of covariance models to annotate RNAs in whole genomes. Briefings in Functional Genomics 8(6): 444-450. http://dx.doi.org/10.1093/bfgp/elp042. (Journal Articles)
  • Gardner PP. and Bateman AG. (2009) A home for RNA families at RNA Biology. RNA Biology 6(1): 2. (Journal Articles)
  • Gardner PP., Daub J., Tate JG., Nawrocki EP., Kolbe DL., Lindgreen S., Wilkinson AC., Finn RD., Griffiths-Jones S. and Eddy SR. (2009) Rfam: updates to the RNA families database. Nucleic Acids Research 37(Suppl 1) D136-D140 http://dx.doi.org/10.1093/nar/gkn766. (Journal Articles)
  • Perkins TT., Kingsley RA., Fookes MC., Gardner PP., James KD., Yu L., Assefa SA., He M., Croucher NJ. and Pickard DJ. (2009) A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. PLoS Genetics 5(7) e1000569 http://dx.doi.org/10.1371/journal.pgen.1000569. (Journal Articles)
  • Daub J., Gardner PP., Tate J., Ramsk├Âld D., Manske M., Scott WG., Weinberg Z., Griffiths-Jones S. and Bateman A. (2008) The RNA WikiProject: Community annotation of RNA families. RNA 14(12): 2462-2464. http://dx.doi.org/10.1261/rna.1200508. (Journal Articles)
  • Freyhult EK., Bollback JP. and Gardner PP. (2007) Exploring genomic dark matter: a critical assessment of the performance of homology search methods on non-coding RNA. Genome Research 17(1): 117-125. http://dx.doi.org/10.1101/gr.5890907. (Journal Articles)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics 23(24): 3304-3311. http://dx.doi.org/10.1093/bioinformatics/btm525. (Journal Articles)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics 23(24): 3304-3311. http://dx.doi.org/10.1093/bioinformatics/btm525. (Journal Articles)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) Multiple alignment and structure prediction of non-coding RNA sequences. In BMC Bioinformatics 8(SUPPL. 8) http://dx.doi.org/10.1186/1471-2105-8-S8-P8. (Conference Contributions - Published)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) Multiple alignment and structure prediction of non-coding RNA sequences. Vienna, Austria: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computional Biology (ECCB), 21-26 Jul 2007 (Conference Contributions - Other)
  • Mourier T., Carret C., Kyes S., Christodoulou Z., Gardner PP., Jeffares DC., Pinches R., Barrell B., Berriman M. and Griffiths-Jones S. (2007) Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Research 18(2): 281-292. http://dx.doi.org/10.1101/gr.6836108. (Journal Articles)
  • Weile C., Gardner PP., Hedegaard MM. and Vinther J. (2007) Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes. BMC Genomics 8(244): 11pp. http://dx.doi.org/10.1186/1471-2164-8-244. (Journal Articles)
  • Lindgreen S., Gardner PP. and Krogh A. (2006) Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics 22(24): 2988-2995. http://dx.doi.org/10.1093/bioinformatics/btl514. (Journal Articles)
  • Munch K., Gardner PP., Arctander P. and Krogh A. (2006) A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics 7(239): 11pp. http://dx.doi.org/10.1186/1471-2105-7-239. (Journal Articles)
  • Vinther J., Hedegaard MM., Gardner PP., Andersen JS. and Arctander P. (2006) Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Research 34(16) e107 http://dx.doi.org/10.1093/nar/gkl590. (Journal Articles)
  • Freyhult E., Gardner PP. and Moulton V. (2005) Predicting RNA structure using mutual information. Applied Bioinformatics 4(1): 53-59. (Journal Articles)
  • Gardner PP., Wilm A. and Washietl S. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research 33(8): 2433-2439. http://dx.doi.org/10.1093/nar/gki541. (Journal Articles)
  • Gardner PP. and Giegerich R. (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 5: 140. http://dx.doi.org/10.1186/1471-2105-5-140. (Journal Articles)
  • Edvardsson S., Gardner PP., Poole AM., Hendy MD., Penny D. and Moulton V. (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19(7): 865-873. http://dx.doi.org/10.1093/bioinformatics/btg080. (Journal Articles)
  • Gardner PP., Holland B., Moulton V., Hendy M. and Penny D. (2003) Optimal alphabets for an RNA-world. Proceedings of the Royal Society B: Biological Sciences 270(1520): 1177-1182. http://dx.doi.org/10.1098/rspb.2003.2355. (Journal Articles)
  • Rakonjac J., Ward LJH., Schiemann AH., Gardner PP., Lubbers MW. and O'Toole PW. (2003) Sequence Diversity and Functional Conservation of the Origin of Replication in Lactococcal Prolate Phages. Applied and Environmental Microbiology 69(9): 5104-5114. http://dx.doi.org/10.1128/AEM.69.9.5104-5114.2003. (Journal Articles)
  • Moulton V., Gardner PP., Pointon RF., Creamer LK., Jameson GB. and Penny D. (2000) RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution 51(4): 416-421. (Journal Articles)