Contact Details
- Phone
- +64 3 479 7264
- paul.gardner@otago.ac.nz
University Links
- Position
- Associate Professor
- Department
- Department of Biochemistry
- Qualifications
- BSc(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.
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
Sitter, L., Schoof, M., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2024). Serratia-based toxin cluster elements are associated with a type I fimbria. MicrobiologyOpen, 13, e1395. doi: 10.1002/mbo3.1395 Journal - Research Article
Gardner, P., Coray, D. S., Sibaeva, N., McGimpsey, S., Smith, L., Chen, A., & Fineran, P. (2023). The mutational robustness of RNA and protein. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference Conference Contribution - Published proceedings: Abstract
Adey, B. N., Maddock, D. J., Gardner, P. P., & Ganley, A. R. D. (2023). Using machine learning approaches to resolve the junk DNA-dark matter DNA debate. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference Conference Contribution - Published proceedings: Abstract
Erdmann, M. B., Gardner, P. P., & Lamont, I. L. (2023). The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa. PLoS ONE, 18(10), e0292818. doi: 10.1371/journal.pone.0292818 Journal - Research Article
Cooper, H. B., Krause, K. L., & Gardner, P. P. (2023). Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis. PeerJ, 11, e14969. doi: 10.7717/peerj.14969 Journal - Research Article
2024
Journal - Research Article
Sitter, L., Schoof, M., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2024). Serratia-based toxin cluster elements are associated with a type I fimbria. MicrobiologyOpen, 13, e1395. doi: 10.1002/mbo3.1395
2023
Journal - Research Article
Erdmann, M. B., Gardner, P. P., & Lamont, I. L. (2023). The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa. PLoS ONE, 18(10), e0292818. doi: 10.1371/journal.pone.0292818
Cooper, H. B., Krause, K. L., & Gardner, P. P. (2023). Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis. PeerJ, 11, e14969. doi: 10.7717/peerj.14969
Conference Contribution - Published proceedings: Abstract
Gardner, P., Coray, D. S., Sibaeva, N., McGimpsey, S., Smith, L., Chen, A., & Fineran, P. (2023). The mutational robustness of RNA and protein. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference
Adey, B. N., Maddock, D. J., Gardner, P. P., & Ganley, A. R. D. (2023). Using machine learning approaches to resolve the junk DNA-dark matter DNA debate. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference
2022
Journal - Research Article
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
Conference Contribution - Published proceedings: Abstract
Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2022). Fast and scalable prediction of protein-protein interactions. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Conference Contribution - Verbal presentation and other Conference outputs
Smith, L. M., Jackson, S. A., Malone, L. M., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2022, August). Inverse regulation of CRISPR-Cas and surface-based immunity discriminates plasmids versus phages. Verbal presentation at the CRISPR Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
2021
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
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
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
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 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, 16, 4382-4418. doi: 10.1038/s41596-021-00582-6
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
Conference Contribution - Published proceedings: Abstract
Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021). TISIGNER.com: Web services for improving recombinant protein production. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 2). Retrieved from https://www.faobmb2021.org
Smith, L. M., Jackson, S. A., Malone, L., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2021). Inverse control of surface and CRISPR-Cas adaptive immunity discriminates plasmids and phages. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 120). Retrieved from https://www.faobmb2021.org
Gardner, P. (2021). Features of functional human genes. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 80). Retrieved from https://www.faobmb2021.org
2020
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
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
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
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 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
Working Paper; Discussion Paper; Technical Report
Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2020). Improving recombinant protein production using TISIGNER.com. bioRxiv. doi: 10.1101/2020.07.09.196469
Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020). Protein solubility is controlled by global structural flexibility. bioRxiv. doi: 10.1101/2020.02.15.951012
2019
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
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
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 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
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
Conference Contribution - Published proceedings: Abstract
Bhandari, B. K., Lim, C. S., & Gardner, P. (2019). Protein expression is controlled by the accessibility of translation initiation sites. Proceedings of the 16th Asian Conference on Transcription. (pp. 43). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02
Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019). Highly accessible translation initiation sites are predictive of successful heterologous protein expression. Proceedings of the 16th Asian Conference on Transcription. (pp. 75-76). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/
Bhandari, B., Lim, C. S., & Gardner, P. (2019). SoDoPE: Soluble domain for protein expression. Proceedings of the 16th Asian Conference on Transcription. (pp. 66). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/
Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019). Improving the expression and solubility of recombitant proteins by smart sequence design algorithms. Proceedings of the 16th Asian Conference on Transcription. (pp. 52). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/
Erdmann, M. B., Gardner, P., & Lamont, I. (2019). Colistin resistance in Pseudomonas aeruginosa. Proceedings of the New Zealand Microbiological Society (NZMS) Annual Conference. 645. Retrieved from https://www.nzmscoference.org.nz
Templeton, M. D., McAtee, P. A., Nieuwenhuizen, N. J., Chen, X., Jose, B., Jayaraman, J., … Gardner, P. P., & Allan, A. C. (2019). Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit. Molecular Plant-Microbe Interactions, 32(10 Suppl.), (pp. 187-188). doi: 10.1094/MPMI-32- 10-S1.1
Conference Contribution - Poster Presentation (not in published proceedings)
Cooper, H., Biggs, H., & Gardner, P. (2019, August-September). Using machine learning algorithms to identify suitable traits for predicting non-coding RNA functionality. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2019, August-September). TIsigner: Controlling protein expression with designer translation initiation regions. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Lim, C. S., Bhandari, B. K., & Gardner, P. P. (2019, August-September). Highly accessible translation initiation sites are predictive of successful heterologous protein expression. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Pinkney, H. R., Xiong, H., Gardner, P. P., & Diermeier, S. D. (2019, August-September). Investigating the RNA interactome in colorectal cancer. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2019, August-September). Protein expression is controlled by the accessibility of translation initiation sites. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Other Research Output
Gardner, P. (2019, September). Meta-benchmarking: What can we learn by comparing benchmarks? Mathematics Seminar Series, Department of Mathematics & Statistics, University of Otago, Dunedin, New Zealand. [Department Seminar].
2018
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 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
Conference Contribution - Published proceedings: Abstract
Gardner, P. (2018). Exploring the genetic robustness of ncRNA and protein. Proceedings of the Computational Approaches to RNA Structure and Function Workshop. Retrieved from http://benasque.org/2018rna
Smith, L. M., Gardner, P. P., Jackson, S. A., Ussher, J. E., & Fineran, P. C. (2018). Developing SorTn-Seq: A state-of-the-art method to study CRISPR-Cas regulation. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 109). Retrieved from https://www.nzmsconference.org.nz
McGimpsey, S., & Gardner, P. (2018). The twilight zone of homology. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 75). Retrieved from https://www.nzmsconference.org.nz
Gavryushkina, A. S., Parthasarathy, P., & Gardner, P. (2018). Delta bit scores for non-coding DNA variation. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 67). Retrieved from https://www.nzmsconference.org.nz
Jose, B. R., Barquist, L., & Gardner, P. P. (2018). The evolutionary origins of bacterial sRNAs. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 52). Retrieved from https://www.nzmsconference.org.nz
Lim, C. S., & Gardner, P. (2018). How can we increase the success rate of recombinant protein expression in Escherichia coli? Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 38-39). Retrieved from https://www.nzmsconference.org.nz
Conference Contribution - Poster Presentation (not in published proceedings)
McGimpsey, S., & Gardner, P. P. (2018, August). The Twilight Zone of homology. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Coray, D. S., Sibaeva, N., McGimpsey, S., & Gardner, P. P. (2018, August). Exploring the genetic robustness of ncRNA and protein. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Lim, C. S., & Gardner, P. P. (2018, August). Avoidance of stochastic mRNA:ncRNA interactions in successful recombinant protein expression in Escherichia coli. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Wheeler, N. E., Gardner, P. P., & Barquist, L. (2018, August). AI in healthcare: Identifying and understanding superbugs. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
2017
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 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
2016
Chapter in Book - Research
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
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
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
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
Conference Contribution - Verbal presentation and other Conference outputs
Gardner, P. (2016, November). A meta-analysis of computational biology benchmarks reveals influences on software performance. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Ghomi, F. A., Gardner, P., & Barquist, L. (2016, November). Are essential genes conserved? Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Gardner, P. (2016, November). Random RNA interactions control protein expression in prokaryotes [NZSBMS Custom Science Award Speaker]. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Osborne, A., Umu, S., Lindgreen, S., Hoeppner, M., Poole, A., & Gardner, P. (2016, November). Can RNA evolve from one form to another? Illuminating the genomic 'dark matter'. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Wheeler, N. E., & Gardner, P. P. (2016, November). Functional divergence of orthologous proteins associated with invasiveness in Salmonella enterica. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
2015
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
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
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
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
Conference Contribution - Published proceedings: Full paper
Waldispühl, J., Kam, A., & Gardner, P. P. (2015). Crowdsourcing RNA structural alignments with an online computer game. Proceedings of the Pacific Symposium on Biocomputing (PSB). 20, (pp. 330-341). Retrieved from https://psb.stanford.edu
2014
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
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
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
2013
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
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
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 - Professional & Other Non-Research Articles
Schroeder, R., Gardner, P. P., & Riedmann, E. M. (2013). Letter from the Editor. RNA Biology, 10(1), 1. doi: 10.4161/rna.23502
2012
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
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 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
Gardner, P. P. (2012). Three years of RNA families. RNA Biology, 9(1), 2-3. doi: 10.4161/rna.9.1.18979
2011
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
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
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 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
2010
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 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
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
2009
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
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 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
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
2008
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 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
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
2007
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
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
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
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
Conference Contribution - Published proceedings: Abstract
Lindgreen, S., Gardner, P. P., & Krogh, A. (2007). Multiple alignment and structure prediction of non-coding RNA sequences. BMC Bioinformatics, 8(Suppl. 8), P8. doi: 10.1186/1471-2105-8-S8-P8
2006
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 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
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
2005
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
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
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
2004
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
2003
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
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
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
2000
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