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Department of Biochemistry profile

Associate Professor Paul Gardner

PositionAssociate Professor
DepartmentDepartment of Biochemistry
QualificationsBSc(Hons) PhD

Research

The three main research strands of our group lie in (1) RNA Biology, particularly the functional characterisation of non-coding RNAs, and more recently in the impact of promiscuous RNA:RNA interactions on translation. (2) the analysis of genome variation, in particular the identification of functionally significant and convergent evolutionary signals that indicate variation of phenotypic importance. We have also used high density transposon mutagenesis and comparative genomics to characterise genomic regions of functional importance. (3) The continual evaluation and improvement of bioinformatic tools is necessary for the field to progress and to help researchers identify the right tools for their questions. We use a range of methods, including benchmarking, curation of positive and negative control datasets and meta-analysis and meta-science based approaches to find where methodological progress can be made.

Research overview figure

For more details, see our Lab’s homepage.

Funding

Our research is funded by generous support from a Rutherford Discovery Fellowship, MBIE Smart Ideas, The Marsden Fund, The Bio-Protection CoRE and The Biomolecular Interaction Centre.

Publications

Gardner, P. P., Paterson, J. M., McGimpsey, S., Ashari-Ghomi, F., Umu, S. U., Pawlik, A., Gavryushkin, A., & Black, M. A. (2022). Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology, 23, 56. doi: 10.1186/s13059-022-02625-x

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461

Smith, L. M., Jackson, S. A., Gardner, P. P., & Fineran, P. C. (2021). SorTn-seq: A high-throughput functional genomics approach to discovering regulators of bacterial gene expression. Nature Protocols. Advance online publication. doi: 10.1038/s41596-021-00582-6

Sitter, T. L., Vaughan, A. L., Schoof, M., Jackson, S. A., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2021). Evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology, 23(9), 5289-5304. doi: 10.1111/1462-2920.15595

Buchka, S., Hapfelmeier, A., Gardner, P. P., Wilson, R., & Boulesteix, A. (2021). On the optimistic performance evaluation of newly introduced bioinformatic methods [Short report]. Genome Biology, 22(1). doi: 10.1186/s13059-021-02365-4

Barquist, L., Burge, S. W., & Gardner, P. P. (2016). Studying RNA homology and conservation with infernal: From single sequences to RNA families. In A. Bateman, S. Draghici, E. Khurana, S. Orchard & W. R. Pearson (Eds.), Current protocols in bioinformatics. (pp. 12.13.1-12.13.25). Wiley. doi: 10.1002/cpbi.4

Chapter in Book - Research

Hertel, J., Fasold, M., Nitsche, A., Erb, I., Prieto, P., Kedra, D., … Gardner, P. P., & Stadler, P. F. (2015). Noncoding RNAs in the chicken genome. In M. Schmid, J. Smith & D. W. Burt (Eds.), Third report on chicken genes and chromosomes 2015. (pp. 89-91). Basel, Switzerland: Karger. doi: 10.1159/isbn.978-3-318-05569-6

Chapter in Book - Research

Bollback, J. P., Gardner, P. P., & Nielsen, R. (2007). Estimating the history of mutations on a phylogeny. In D. A. Liberles (Ed.), Ancestral sequence reconstruction. Oxford University Press. doi: 10.1093/acprof:oso/9780199299188.003.0006

Chapter in Book - Research

Gardner, P. P., Paterson, J. M., McGimpsey, S., Ashari-Ghomi, F., Umu, S. U., Pawlik, A., Gavryushkin, A., & Black, M. A. (2022). Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology, 23, 56. doi: 10.1186/s13059-022-02625-x

Journal - Research Article

Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Nucleic Acids Research, 49, W654-W661. doi: 10.1093/nar/gkab175

Journal - Research Article

Bhandari, B. K., Lim, C. S., Remus, D. M., Chen, A., van Dolleweerd, C., & Gardner, P. P. (2021). Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Computational Biology, 17(10), e1009461. doi: 10.1371/journal.pcbi.1009461

Journal - Research Article

Sitter, T. L., Vaughan, A. L., Schoof, M., Jackson, S. A., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2021). Evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology, 23(9), 5289-5304. doi: 10.1111/1462-2920.15595

Journal - Research Article

Smith, L. M., Jackson, S. A., Malone, L. M., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2021). The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages. Nature Microbiology, 6, 162-172. doi: 10.1038/s41564-020-00822-7

Journal - Research Article

Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Solubility-Weighted Index: Fast and accurate prediction of protein solubility. Bioinformatics, 36(18), 4691-4698. doi: 10.1093/bioinformatics/btaa578

Journal - Research Article

Biggs, H., Parthasarathy, P., Gavryushkina, A., & Gardner, P. P. (2020). ncVarDB: A manually curated database for pathogenic non-coding variants and benign controls. Database, baaa105. doi: 10.1093/database/baaa105

Journal - Research Article

Gemmell, N. J., Rutherford, K., Prost, S., Tollis, M., Winter, D., Macey, J. R., … Gardner, P. P., … Hore, T. A., … Dussex, N., Taylor, H., Abe, H., Bond, D. M., … Ngatiwai Trust Board. (2020). The tuatara genome reveals ancient features of amniote evolution. Nature, 584, 403-409. doi: 10.1038/s41586-020-2561-9

Journal - Research Article

Malone, L. M., Warring, S. L., Jackson, S. A., Warnecke, C., Gardner, P. P., Gumy, L. F., & Fineran, P. C. (2020). A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nature Microbiology, 5, 48-55. doi: 10.1038/s41564-019-0612-5

Journal - Research Article

Gardner, P. P., Watson, R. J., Morgan, X. C., Draper, J. L., Finn, R. D., Morales, S. E., & Stott, M. B. (2019). Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ, 7, e6160 . doi: 10.7717/peerj.6160

Journal - Research Article

Sackton, T. B., Grayson, P., Cloutier, A., Hu, Z., Liu, J. S., Wheeler, N. E., Gardner, P. P., … Edwards, S. V. (2019). Convergent regulatory evolution and loss of flight in paleognathous birds. Science, 364(6435), 74-78. doi: 10.1126/science.aat7244

Journal - Research Article

Wheeler, N. E., Blackmore, T., Reynolds, A. D., Midwinter, A. C., Marshall, J., French, N. P., … Gardner, P. P., & Biggs, P. J. (2019). Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni. Microbial Genomics, 5(2), 1-12. doi: 10.1099/mgen.0.000251

Journal - Research Article

Wheeler, N. E., Gardner, P. P., & Barquist, L. (2018). Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. PLoS Genetics, 14(5), e1007333. doi: 10.1371/journal.pgen.1007333

Journal - Research Article

Umu, S. U., & Gardner, P. P. (2017). A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics, 33(7), 988-996. doi: 10.1093/bioinformatics/btw728

Journal - Research Article

Lindgreen, S., Adair, K. L., & Gardner, P. P. (2016). An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports, 6, 19233 . doi: 10.1038/srep19233

Journal - Research Article

Umu, S. U., Poole, A. M., Dobson, R. C. J., & Gardner, P. P. (2016). Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLIFE, 5, e13479. doi: 10.7554/eLife.13479

Journal - Research Article

Wheeler, N. E., Barquist, L., Kingsley, R. A., & Gardner, P. P. (2016). A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics, 32(23), 3566-3574. doi: 10.1093/bioinformatics/btw518

Journal - Research Article

Gardner, P. P., & Eldai, H. (2015). Annotating RNA motifs in sequences and alignments. Nucleic Acids Research, 43(2), 691-698. doi: 10.1093/nar/gku1327

Journal - Research Article

Gardner, P. P., Fasold, M., Burge, S. W., Ninova, M., Hertel, J., Kehr, S., … Stadler, P. F. (2015). Conservation and losses of non-coding RNAs in avian genomes. PLoS ONE, 10(3), e0121797. doi: 10.1371/journal.pone.0121797

Journal - Research Article

Nawrocki, E. P., Burge, S. W., Bateman, A., Daub, J., Eberhardt, R. Y., Eddy, S. R., … Gardner, P. P., … Finn, R. D. (2015). Rfam 12.0: Updates to the RNA families database. Nucleic Acids Research, 43(D1), D130-D137. doi: 10.1093/nar/gku1063

Journal - Research Article

Lindgreen, S., Umu, S. U., Lai, A. S.-W., Eldai, H., Liu, W., McGimpsey, S., … Gardner, P. P. (2014). Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Computational Biology, 10(10), e1003907. doi: 10.1371/journal.pcbi.1003907

Journal - Research Article

Tang, Y., Nielsen, H., Masquida, B., Gardner, P. P., & Johansen, S. D. (2014). Molecular characterization of a new member of the lariat capping twin-ribozyme introns. Mobile DNA, 5, 25. doi: 10.1186/1759-8753-5-25

Journal - Research Article

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Avian Genome Consortium, including Gardner, P. P., … Wang, J. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. doi: 10.1126/science.1251385

Journal - Research Article

Barquist, L., Langridge, G. C., Turner, D. J., Phan, M.-D., Turner, A. K., Bateman, A., … 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. doi: 10.1093/nar/gkt148

Journal - Research Article

Burge, S. W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E. P., … Gardner, P. P., & Bateman, A. (2013). Rfam 11.0: 10 years of RNA families. Nucleic Acids Research, 41(D1), D226-D232. doi: 10.1093/nar/gks1005

Journal - Research Article

Kingsley, R. A., Kay, S., Connor, T., Barquist, L., Sait, L., Holt, K. E., … Gardner, P. P., … Dougan, G. (2013). Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. mBio, 4(5), e00565-13. doi: 10.1128/mBio.00565-13

Journal - Research Article

Hoeppner, M. P., Gardner, P. P., & Poole, A. M. (2012). Comparative analysis of RNA families reveals distinct repertoires for each domain of life. PLoS Computational Biology, 8(11), e1002752. doi: 10.1371/journal.pcbi.1002752

Journal - Research Article

Widmann, J., Stombaugh, J., McDonald, D., Chocholousova, J., Gardner, P., Iyer, M. K., … 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. doi: 10.1261/rna.032052.111

Journal - Research Article

Chaudhuri, R. R., Yu, L., Kanji, A., Perkins, T. T., Gardner, P. P., Choudhary, J., … Grant, A. J. (2011). Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome. Microbiology, 157(10), 2922-2932. doi: 10.1099/mic.0.050278-0

Journal - Research Article

Gardner, P. P., Barquist, L., Bateman, A., Nawrocki, E. P., & Weinberg, Z. (2011). RNIE: Genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research, 39(14), 5845-5852. doi: 10.1093/nar/gkr168

Journal - Research Article

Gardner, P. P., Daub, J., Tate, J., Moore, B. L., Osuch, I. H., Griffiths-Jones, S., … Bateman, A. (2011). Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research, 39(Suppl. 1), D141-D145. doi: 10.1093/nar/gkq1129

Journal - Research Article

Nygaard, S., Braunstein, A., Malsen, G., Van Dongen, S., Gardner, P. P., Krogh, A., … Jeffares, D. C. (2010). Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. doi: 10.1371/journal.pgen.1001099

Journal - Research Article

Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., … Bateman, A. (2009). Rfam: Updates to the RNA families database. Nucleic Acids Research, 37(Suppl. 1), D136-D140. doi: 10.1093/nar/gkn766

Journal - Research Article

Perkins, T. T., Kingsley, R. A., Fookes, M. C., Gardner, P. P., James, K. D., Yu, L., … Dougan, G. (2009). A strand-specific RNA-seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genetics, 5(7), e1000569. doi: 10.1371/journal.pgen.1000569

Journal - Research Article

Mourier, T., Carret, C., Kyes, S., Christodoulou, Z., Gardner, P. P., Jeffares, D. C., … Pain, A. (2008). Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. Genome Research, 18(2), 281-292. doi: 10.1101/gr.6836108

Journal - Research Article

Freyhult, E. K., Bollback, J. P., & Gardner, P. P. (2007). Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA. Genome Research, 17(1), 117-125. doi: 10.1101/gr.5890907

Journal - Research Article

Lindgreen, S., Gardner, P. P., & Krogh, A. (2007). MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics, 23(24), 3304-3311. doi: 10.1093/bioinformatics/btm525

Journal - Research Article

Weiler, C., Gardner, P. P., Hedegaard, M. M., & Vinther, J. (2007). Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes. BMC Genomics, 8, 244. doi: 10.1186/1471-2164-8-244

Journal - Research Article

Lindgreen, S., Gardner, P. P., & Krogh, A. (2006). Measuring covariation in RNA alignments: Physical realism improves information measures. Bioinformatics, 22(24), 2988-2995. doi: 10.1093/bioinformatics/btl514

Journal - Research Article

Freyhult, E., Gardner, P. P., & Moulton, V. (2005). A comparison of RNA folding measures. BMC Bioinformatics, 6, 241. doi: 10.1186/1471-2105-6-241

Journal - Research Article

Freyhult, E., Moulton, V., & Gardner, P. (2005). Predicting RNA structure using mutual information. Applied Bioinformatics, 4(1), 53-59. doi: 10.2165/00822942-200504010-00006

Journal - Research Article

Gardner, P. P., Wilm, A., & Washietl, S. (2005). A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research, 33(8), 2433-2439. doi: 10.1093/nar/gki541

Journal - Research Article

Gardner, P. P., & Giegerich, R. (2004). A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics, 5, 140. doi: 10.1186/1471-2105-5-140

Journal - Research Article

Edvardsson, S., Gardner, P. P., Poole, A. M., Hendy, M. D., Penny, D., & Moulton, V. (2003). A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics, 19(7), 865-873. doi: 10.1093/bioinformatics/btg080

Journal - Research Article

Gardner, P. P., Holland, B. R., Moulton, V., Hendy, M., & Penny, D. (2003). Optimal alphabets for an RNA world. Proceedings of the Royal Society of London: Series B, 270(1520), 1177-1182. doi: 10.1098/rspb.2003.2355

Journal - Research Article

Rakonjac, J., Ward, L. J. H., Schiemann, A. H., Gardner, P. P., Lubbers, M. W., & O'Toole, P. W. (2003). Sequence diversity and functional conservation of the origin of replication in lactococcal prolate phages. Applied & Environmental Microbiology, 69(9), 5104-5114. doi: 10.1128/AEM.69.9.5104-5114.2003

Journal - Research Article

Buchka, S., Hapfelmeier, A., Gardner, P. P., Wilson, R., & Boulesteix, A. (2021). On the optimistic performance evaluation of newly introduced bioinformatic methods [Short report]. Genome Biology, 22(1). doi: 10.1186/s13059-021-02365-4

Journal - Research Other

Smith, L. M., Jackson, S. A., Gardner, P. P., & Fineran, P. C. (2021). SorTn-seq: A high-throughput functional genomics approach to discovering regulators of bacterial gene expression. Nature Protocols. Advance online publication. doi: 10.1038/s41596-021-00582-6

Journal - Research Other

da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., … Gilbert, M. T. P. (2020). A draft genome sequence of the elusive giant squid, Architeuthis dux [Data note]. GigaScience, 9(1), giz152. doi: 10.1093/gigascience/giz152

Journal - Research Other

Jose, B. R., Gardner, P. P., & Barquist, L. (2019). Transcriptional noise and exaptation as sources for bacterial sRNAs. Biochemical Society Transactions, 47(2), 527-539. doi: 10.1042/bst20180171

Journal - Research Other

Weber, L. M., Saelens, W., Cannoodt, R., Soneson, C., Hapfelmeier, A., Gardner, P. P., … Robinson, M. D. (2019). Essential guidelines for computational method benchmarking. Genome Biology, 20(1), 125. doi: 10.1186/s13059-019-1738-8

Journal - Research Other

Dickie, I. A., Boyer, S., Buckley, H., Duncan, R. P., Gardner, P., Hogg, I. D., … Morales, S. E., … Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA based studies. Molecular Ecology Resources, 18(5), 940-952. doi: 10.1111/1755-0998.12907

Journal - Research Other

Coray, D., Wheeler, N. E., Heinemann, J. A., & Gardner, P. P. (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. doi: 10.1080/15476286.2016.1272747

Journal - Research Other

Finn, R. D., Gardner, P. P., & Bateman, A. (2012). Making your database available through Wikipedia: The pros and cons. Nucleic Acids Research, 40(D1), D9-D12. doi: 10.1093/nar/gkr1195

Journal - Research Other

Gardner, P. P. (2012). Three years of RNA families. RNA Biology, 9(1), 2-3. doi: 10.4161/rna.9.1.18979

Journal - Research Other

Bateman, A., Agrawal, S., Birney, E., Bruford, E. A., Bujnicki, J. M., Cochrane, G., … Gardner, P. P., … Zwieb, C. (2011). RNAcentral: A vision for an international database of RNA sequences. RNA, 17(11), 1941-1946. doi: 10.1261/rna.2750811

Journal - Research Other

Gardner, P. P., Bateman, A., & Poole, A. M. (2010). SnoPatrol: How many snoRNA genes are there? Journal of Biology, 9(1), 4. doi: 10.1186/jbiol211

Journal - Research Other

Logan, D. W., Sandal, M., Gardner, P. P., Manske, M., & Bateman, A. (2010). Ten simple rules for editing wikipedia. PLoS Computational Biology, 6(9), e1000941. doi: 10.1371/journal.pcbi.1000941

Journal - Research Other

Gardner, P. P. (2009). The use of covariance models to annotate RNAs in whole genomes. Briefings in Functional Genomics, 8(6), 444-450. doi: 10.1093/bfgp/elp042

Journal - Research Other

Gardner, P. P., & Bateman, A. G. (2009). A home for RNA families at RNA Biology. RNA Biology, 6(1), 2-4. doi: 10.4161/rna.6.1.7635

Journal - Research Other

Daub, J., Gardner, P. P., Tate, J., Ramsköld, D., Manske, M., Scott, W. G., … Bateman, A. (2008). The RNA WikiProject: Community annotation of RNA families. RNA, 14(12), 2462-2464. doi: 10.1261/rna.1200508

Journal - Research Other

Gardner, P. P., & Vinther, J. (2008). Mutation of miRNA target sequences during human evolution. Trends in Genetics, 24(6), 262-265. doi: 10.1016/j.tig.2008.03.009

Journal - Research Other

Munch, K., Gardner, P. P., Arctander, P., & Krogh, A. (2006). A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics, 7, 239. doi: 10.1186/1471-2105-7-239

Journal - Research Other

Vinther, J., Hedegaard, M. M., Gardner, P. P., Andersen, J. S., & Arctander, P. (2006). Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Research, 34(16), e107. doi: 10.1093/nar/gkl590

Journal - Research Other

Moulton, V., Gardner, P. P., Pointon, R. F., Creamer, L. K., & Jameson, G. B. (2000). RNA folding argues against a hot-start origin of life. Journal of Molecular Evolution, 51(4), 416-421. doi: 10.1007/s002390010104

Journal - Research Other

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