UC SPARK - University of Canterbury - New Zealand

Associate Professor Paul Phillip Gardner

Biological Sciences; Biomolecular Interaction Centre

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

Affiliations

  • 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 Article)
  • Mesarich CH., Rees-George J., Gardner PP., Ghomi FA., 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) http://dx.doi.org/10.1371/journal.pone.0172790. (Journal Article)
  • 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 Article)
  • 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.] 54: 12.13.1-12.13.25. http://dx.doi.org/10.1002/cpbi.4. (Journal Article)
  • Lindgreen S., Adair KL. and Gardner PP. (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports 6 ARTN 19233: 14. http://dx.doi.org/10.1038/srep19233. (Journal Article)
  • 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 ARTN e13479: 16. http://dx.doi.org/10.7554/eLife.13479. (Journal Article)
  • 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 Article)
  • 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. (Chapter)
  • 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) ARTN e0121797: 19. http://dx.doi.org/10.1371/journal.pone.0121797. (Journal Article)
  • Nawrocki EP., Burge SW., Bateman A., Daub J., Eberhardt RY., Eddy SR., Floden EW., Gardner PP., Jones TA. and Tate J. (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Research 43(D1): D130-D137. http://dx.doi.org/10.1093/nar/gku1063. (Journal Article)
  • 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. Cytogenetics and Cell Genetics 145(2): 78-179. http://dx.doi.org/10.1159/000430927. (Journal Article)
  • Waldispühl J., Kam A. and Gardner PP. (2015) Crowdsourcing RNA structural alignments with an online computer game. In 20th Pacific Symposium on Biocomputing, PSB 2015: 330-341. (Conference Contribution - Published)
  • Lindgreen S., Umu SU., Lai AS-W., Eldai H., Liu W., McGimpsey S., Wheeler NE., Biggs PJ., Thomson NR. and Barquist L. (2014) Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLoS Computational Biology 10(10) ARTN e1003907: 10. http://dx.doi.org/10.1371/journal.pcbi.1003907. (Journal Article)
  • 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 ARTN 25: 13. http://dx.doi.org/10.1186/1759-8753-5-25. (Journal Article)
  • Zhang G., Li B., Li C., Gilbert MTP., Jarvis ED. and Wang J. (2014) Comparative genomic data of the Avian Phylogenomics Project. GigaScience 3(1) http://dx.doi.org/10.1186/2047-217X-3-26. (Journal Article)
  • 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 Article)
  • 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 Article)
  • 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 Article)
  • 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. http://10.0.3.239/978-1-62703-709-9_6. (Chapter)
  • 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) http://dx.doi.org/10.1128/mBio.00565-13. (Journal Article)
  • Schroeder R., Gardner PP. and Riedmann EM. (2013) RNA Biology. Letter from the editor.. RNA Biology 10(1): 1. (Journal Article)
  • Finn RD., Gardner PP. and Bateman A. (2012) Making your database available through Wikipedia: the pros and cons. Nucleic Acids Research 40(D1): D9-D12. http://dx.doi.org/10.1093/nar/gkr1195. (Journal Article)
  • 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(11) ARTN e1002752: 8. http://dx.doi.org/10.1371/journal.pcbi.1002752. (Journal Article)
  • 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 Posttranscriptional Regulator of Metabolic Flux in Mycobacteria. Journal of Bacteriology 194(9): 2189-2204. http://dx.doi.org/10.1128/JB.06790-11. (Journal Article)
  • 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 Article)
  • 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 17(11): 1941-1946. http://dx.doi.org/10.1261/rna.2750811. (Journal Article)
  • Chaudhuri RR., Yu L., Kanji A., Perkins TT., Gardner PP., Choudhary J., Maskell DJ. and Grant AJ. (2011) Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome. Microbiology 157(10): 2922-2932. http://dx.doi.org/10.1099/mic.0.050278-0. (Journal Article)
  • 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 Article)
  • 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(SUPPL. 1) http://dx.doi.org/10.1093/nar/gkq1129. (Journal Article)
  • Stevens SG., Gardner PP. and Brown C. (2011) Two covariance models for iron-responsive elements.. RNA Biology 8(5): 792-801. (Journal Article)
  • Stevens SG., Gardner PP. and Brown CM. (2011) Two covariance models for iron-responsive elements. RNA Biology 8(5) (Journal Article)
  • 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 Genetics 6(9) http://dx.doi.org/10.1371/journal.pgen.1001099. (Journal Article)
  • Gardner PP. (2009) The use of covariance models to annotate RNAs in whole genomes. Briefings in Functional Genomics and Proteomics 8(6): 444-450. http://dx.doi.org/10.1093/bfgp/elp042. (Journal Article)
  • Gardner PP. and Bateman AG. (2009) A home for RNA families at RNA Biology. RNA Biology 6(1): 2. (Journal Article)
  • 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) http://dx.doi.org/10.1093/nar/gkn766. (Journal Article)
  • 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) http://dx.doi.org/10.1371/journal.pgen.1000569. (Journal Article)
  • Daub J., Gardner PP., Tate J., Ramsköl 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 Article)
  • Mourier T., Carret C., Kyes S., Christodoulou Z., Gardner PP., Jeffares DC., Pinches R., Barrell B., Berriman M. and Griffiths-Jones S. (2008) Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. PCR methods and applications 18(2): 281-292. http://dx.doi.org/10.1101/gr.6836108. (Journal Article)
  • Freyhult EK., Bollback JP. and Gardner PP. (2007) Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. PCR methods and applications 17(1): 117-125. http://dx.doi.org/10.1101/gr.5890907. (Journal Article)
  • 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 Article)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Computer applications in the biosciences : CABIOS 23(24): 3304-3311. http://dx.doi.org/10.1093/bioinformatics/btm525. (Journal Article)
  • 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 Contribution - Published)
  • Lindgreen S., Gardner PP. and Krogh A. (2007) Multiple alignment and structure prediction of non-coding RNA sequences.. (Conference Contribution - Other)
  • 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 http://dx.doi.org/10.1186/1471-2164-8-244. (Journal Article)
  • Lindgreen S., Gardner PP. and Krogh A. (2006) Measuring covariation in RNA alignments: Physical realism improves information measures. Computer applications in the biosciences : CABIOS 22(24): 2988-2995. http://dx.doi.org/10.1093/bioinformatics/btl514. (Journal Article)
  • 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 http://dx.doi.org/10.1186/1471-2105-7-239. (Journal Article)
  • 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) http://dx.doi.org/10.1093/nar/gkl590. (Journal Article)
  • 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 Article)
  • 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. Computer applications in the biosciences : CABIOS 19(7): 865-873. http://dx.doi.org/10.1093/bioinformatics/btg080. (Journal Article)
  • Gardner PP., Holland BR., 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 Article)
  • 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 Article)
  • 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 Article)