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Otago Medical School staff profiles

Dr Paul Gardner

PositionSenior Lecturer
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

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

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

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

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

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., 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

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

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

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

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

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

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

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

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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

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