Dr Paul Phillip Gardner

Biological Sciences

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
  • RNA Biology (Journal & Publication): Assistant Editor-in-Chief

Publications

  • Barquist, L., Burge, S.W. and Gardner, P.P. (2014) Building non-coding RNA families. In D. Mathews and D. Turner (Ed.), Methods in Molecular Biology: RNA Structure Determination: http://arxiv.org/abs/1206.4087. New York City: Humana Press. (Chapters in Books)
  • Gardner, P.P., Fasold, M., Burge, S.W., Ninova, M., Hertel, J., Kehr, S., Steeves, T.E., Griffiths-Jones, S. and Stadler, P.F. (2014) Conservation and losses of avian non-coding RNA loci. Quantitative Biology (early access online) arXiv.org > q-bio > arXiv:1406.7140. (Journal Articles)
  • Tang, Y., Nielsen, H., Masquida, B., Gardner, P.P. and Johansen, S.D. (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)
  • Lindgreen, S., Umu, S.U., Lai, A.S-W., Eldai, H., Liu, W., McGimpsey, S., Wheeler, N., Biggs, P.J., Thomson, N.R., Barquist, L., Poole, A.M. and Gardner, P.P. (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. Quantitative Biology (early access online) http://arxiv.org/abs/1406.7133. (Journal Articles)
  • Barquist, L., Langridge, G.C., Turner, D.J., Phan, M.D., Turner, A.K., Bateman, A., Parkhill, J., Wain, J. and Gardner, P.P. (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. Access via UC Research Repository. (Journal Articles)
  • Kingsley, R.A., Kay, S., Connor, T., Barquist, L., Sait, L., Holt, K.E., Sivaraman, K., Wileman, T., Goulding, D., Clare, S., Hale, C., Seshasayee, A., Harris, S., Thomson, N.R., Gardner, P.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. American Society for Microbiology 4(5): e00565-13. http://dx.doi.org/10.1128/mBio.00565-13. Access via UC Research Repository. (Journal Articles)
  • McKenzie, J.L., Robson, J., Berney, M., Smith, T.C., Ruthe, A., Gardner, P.P., Arcus, V.L. and Cook, G.M. (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, M.K., Liu, Z., Lozupone, C.A., Quinn, J., Smit, S., Wikman, S., Zaneveld, J.R. 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)
  • Chaudhuri, R.R., Yu, L., Kanji, A., Perkins, T.T., Gardner, P.P., Choudhary, J., Maskell, D.J. and Grant, A.J. (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, P.P., Daub, J., Tate, J., Moore, B.L., Osuch, I.H., Griffiths-Jones, S., Finn, R.D., Nawrocki, E.P., Kolbe, D.L., Eddy, S.R. and Bateman, A. (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)
  • Bateman, A., Agrawal, S., Birney, E., Bruford, E.A., Bujnicki, J.M., Cochrane, G., Cole, J.R., Dinger, M.E., Enright, A.J., Gardner, P.P., Gautheret, D., Griffiths-Jones, S., Harrow, J., Herrero, J., Holmes, I.H., Huang, H-D., Kelly, K.A., Kersey, P., Kozomara, A., Lowe, T.M., Marz, M., Moxon, S., Pruitt, K.D., Samuelsson, T., Stadler, P.F., Vilella, A.J., Vogel, J-H., Williams, K.P., Wright, M.W. and Zwieb, C. (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)
  • Gardner, P.P., Barquist, L., Bateman, A., Nawrocki, E.P. 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, P.P., Krogh, A., Otto, T.D., Pain, A., Berriman, M., McAuliffe, J., Dermitzakis, E.T. and Jeffares, D.C. (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, P.P., Bateman, A. and Poole, A.M. (2010) SnoPatrol: how many snoRNA genes are there? Journal of Biology 9(1): 4pp. http://jbiol.com/content/9/1/4. (Journal Articles)
  • Perkins, T.T., Kingsley, R.A., Fookes, M.C., Gardner, P.P., James, K.D., Yu, L., Assefa, S.A., He, M., Croucher, N.J., Pickard, D.J., Maskell, D.J., Parkhill, J., Choudhary, J., Thomson, N.R. and Dougan, G. (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)
  • Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. and Bateman, A. (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)
  • Gardner, P.P. (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, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. and Bateman, A. (2008) Rfam: updates to the RNA families database. Nucleic Acids Research 37(Database issue): D136-D140. http://dx.doi.org/10.1093/nar/gkn766. (Journal Articles)
  • Daub, J., Gardner, P.P., Tate, J., Ramsköld, D., Manske, M., Scott, W.G., 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, E.K., Bollback, J.P. and Gardner, P.P. (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)
  • Mourier, T., Carret, C., Kyes, S., Christodoulou, Z., Gardner, P.P., Jeffares, D.C., Pinches, R., Barrell, B., Berriman, M., Griffiths-Jones, S., Ivens, A., Newbold, C. and Pain, A. (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)
  • Lindgreen, S., Gardner, P.P. 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, P.P. 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, P.P. 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), 21-25 Jul 2007. In BMC Bioinformatics 8(Suppl 8) 8. (Conference Contributions - Abstracts)
  • Weile, C., Gardner, P.P., Hedegaard, M.M. 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)
  • Munch, K., Gardner, P.P., 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, M.M., Gardner, P.P., Andersen, J.S. 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)
  • Lindgreen, S., Gardner, P.P. 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)
  • Lindgreen, S., Gardner, P.P. 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)
  • Gardner, P.P., 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)
  • Freyhult, E., Gardner, P.P. and Moulton, V. (2005) Predicting RNA structure using mutual information. Applied Bioinformatics 4(1): 53-59. (Journal Articles)
  • Gardner, P.P. 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, P.P., Poole, A.M., Hendy, M.D., 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, P.P., 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, L.J.H., Schiemann, A.H., Gardner, P.P., Lubbers, M.W. and O'Toole, P.W. (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, P.P., Pointon, R.F., Creamer, L.K., Jameson, G.B. and Penny, D. (2000) RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution 51(4): 416-421. (Journal Articles)