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 Fellowship ( 2010 - 2015)

Editorial Work

  • RNA Biology , Associate Editor ( 0 - 2017)

Review and Refereeing

  • Anonymous Reviewer I for the manuscript entitled "Rfam: Wikipedia, clans and the decimal release" ( 2010 )
  • Anonymous Reviewer II for the manuscript entitled "RNIE: genome-wide prediction of bacterial intrinsic terminators". ( 2011 )
  • Anonymous Reviewer II for the manuscript entitled "RNIE: genome-wide prediction of bacterial intrinsic terminators". ( 2011 )
  • Anonymous Reviewer III for the manuscript entitled "Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA" ( 2006 )

Research/Scholarly/Creative Works

  • Wheeler, Nicole E., Barquist, Lars., Kingsley, Robert A. and Gardner, Paul P. (2016) A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.. Bioinformatics (Oxford, England) 32(23): 3566-3574. (Journal articles)
  • Barquist, Lars., Burge, Sarah W. and Gardner, Paul P. (2016) Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.. Current protocols in bioinformatics 54 http://dx.doi.org/10.1002/cpbi.4. (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)
  • Lindgreen, S., Adair, KL. and Gardner, PP. (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports 6 http://dx.doi.org/10.1038/srep19233. (Journal articles)
  • 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 - Published)
  • Barquist, L., Burge, SW. and Gardner, PP. (2015) Building non-coding RNA families. Methods in Molecular Biology: RNA Structure Determination New York City: Humana Press. (Chapters)
  • 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, RPMA., Damas, J., Davis, RVN., 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, MAM., 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. and Sun, L. (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)
  • Nawrocki, EP., Burge, SW., Bateman, A., Daub, J., Eberhardt, RY., Eddy, SR., Floden, EW., Gardner, PP., Jones, TA., Tate, J. and Finn, RD. (2015) Rfam 12.0: Updates to the RNA families database. Nucleic Acids Research 43(D1) http://dx.doi.org/10.1093/nar/gku1063. (Journal articles)
  • 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) http://dx.doi.org/10.1371/journal.pone.0121797. (Journal articles)
  • Zhang, Guojie., Li, Bo., Li, Cai., Gilbert, M Thomas P., Jarvis, Erich D. and Wang, Jun. (2014) Comparative genomic data of the Avian Phylogenomics Project. GigaScience 3(1) http://dx.doi.org/10.1186/2047-217X-3-26. (Journal articles)
  • Gardner, PP. and Pulakanam, V. (2014) Ten suggestions for selecting a research topic. Internet Blog. (Other)
  • Lindgreen, S., Umu, SU., Lai, ASW., Eldai, H., Liu, W., McGimpsey, S., Wheeler, NE., Biggs, PJ., Thomson, NR., Barquist, L., Poole, AM. and Gardner, PP. (2014) Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLoS Computational Biology 10(10) 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(1) http://dx.doi.org/10.1186/1759-8753-5-25. (Journal articles)
  • Correction Zhang, G., Li, C., Li, Q., Li, B., Larkin, DM., Lee, C., Storz, JF., Antunes, A., Greenwold, MJ., Meredith, RW., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., Da Fonseca, RR., Alfaro-Núñez, A., Schubert, M., Orlando, L., Mourier, T., Howard, JT., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, MV., Hara, E., Smith, J., Farré, M., Narayan, J., Slavov, G., Romanov, MN., Borges, R., Machado, JP., Khan, I., Springer, MS., Gatesy, J., Hoffmann, FG., Opazo, JC., Håstad, O., Sawyer, RH., Kim, H., Kim, KW., Kim, HJ., Cho, S., Li, N., Huang, Y., Bruford, MW., Zhan, X., Dixon, A., Bertelsen, MF., Derryberry, E., Warren, W. and Wilson, RK. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346(6215): 1311-1320. http://dx.doi.org/10.1126/science.1251385. (Journal articles)
  • Schroeder, R., Gardner, PP. and Riedmann, EM. (2013) RNA Biology. Letter from the editor.. RNA biology 10(1) (Journal articles)
  • Hoeppner, MP., Barquist, LE. and Gardner, PP. (2013) An introduction to RNA databases. 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., Clare, S., Hale, C., Seshasayee, A., Harris, S., Thomson, NR., Gardner, P., Rabsch, W., Wigley, P., Humphrey, T., Parkhill, J. and Dougan, G. (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 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) http://dx.doi.org/10.1093/nar/gks1005. (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)
  • Widmann, J., Stombaugh, J., Mcdonald, D., Chocholousova, J., Gardner, P., Iyer, MK., Liu, Z., Lozupone, CA., Quinn, J., Smit, S., Wikman, S., Zaneveld, JRR. and Knight, R. (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)
  • Finn, RD., Gardner, PP. and Bateman, A. (2012) Making your database available through Wikipedia: The pros and cons. Nucleic Acids Research 40(D1) http://dx.doi.org/10.1093/nar/gkr1195. (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 posttranscriptional regulator of metabolic flux in mycobacteria. Journal of Bacteriology 194(9): 2189-2204. http://dx.doi.org/10.1128/JB.06790-11. (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(11) http://dx.doi.org/10.1371/journal.pcbi.1002752. (Journal articles)
  • Stevens, SG., Gardner, PP. and Brown, CM. (2011) Two covariance models for iron-responsive elements. RNA Biology 8(5) (Journal articles)
  • 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, HDA., Kelly, KA., Kersey, P., Kozomara, ANA., Lowe, TM., Marz, M., Moxon, S., Pruitt, KD., Samuelsson, T., Stadler, PF., Vilella, AJ., Vogel, JH., Williams, KP., Wright, MW. and Zwieb, C. (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 articles)
  • Stevens, SG., Gardner, PP. and Brown, C. (2011) Two covariance models for iron-responsive elements.. RNA biology 8(5): 792-801. (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 campylobacter jejuni transcriptome. Microbiology 157(10): 2922-2932. http://dx.doi.org/10.1099/mic.0.050278-0. (Journal articles)
  • Gardner, PP., Daub, J., Tate, J., Moore, BL., Osuch, IH., Griffiths-Jones, S., Finn, RD., Nawrocki, EP., Kolbe, DL., Eddy, SR. and Bateman, A. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research 39(SUPPL. 1) http://dx.doi.org/10.1093/nar/gkq1129. (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)
  • Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, PP., Krogh, A., Otto, TD., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, ET. and Jeffares, DC. (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 articles)
  • Gardner, PP., Bateman, A. and Poole, AM. (2010) SnoPatrol: How many snoRNA genes are there? Journal of Biology 9(1) http://dx.doi.org/10.1186/jbiol211. (Journal articles)
  • Gardner, PP. and Bateman, AG. (2009) A home for RNA families at RNA Biology. RNA Biology 6(1) (Journal articles)
  • Gardner, PP., Daub, J., Tate, JG., Nawrocki, EP., Kolbe, DL., Lindgreen, S., Wilkinson, AC., Finn, RD., Griffiths-Jones, S., Eddy, SR. and Bateman, A. (2009) Rfam: Updates to the RNA families database. Nucleic Acids Research 37(SUPPL. 1) http://dx.doi.org/10.1093/nar/gkn766. (Journal articles)
  • 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 articles)
  • 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. and Dougan, G. (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 articles)
  • 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 articles)
  • 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. and Pain, A. (2008) 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)
  • 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 - Published)
  • Lindgreen, Stinus., Gardner, Paul P. and Krogh, Anders. (2007) Multiple alignment and structure prediction of non-coding RNA sequences.. In BMC Bioinformatics 8 (Conference - Other)
  • 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)
  • 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 articles)
  • 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. Genome Research 17(1): 117-125. http://dx.doi.org/10.1101/gr.5890907. (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)
  • 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 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 http://dx.doi.org/10.1186/1471-2105-7-239. (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)
  • 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)
  • 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 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)
  • 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)