Associate Professor Paul Gardner

2026

Journal - Research Article

Adey, B. N., Maddock, D. J., Hermann-Le Denmat, S., Dinger, M. E., Gardner, P. P., Poole, A. M., & Ganley, A. R. D. (2026). Pervasive transcription in the human genome exceeds background noise. Genome Biology & Evolution. Advance online publication. doi: 10.1093/gbe/evag042

Conference Contribution - Verbal presentation and other Conference outputs

Wang, X., Jowsey, W. J., Cheung, C.-Y., Dickerhof, N., Taka, J. R. H., Hampton, M. B., … Gardner, P., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2026, February). Genetic vulnerabilities in rifampicin resistant strains of Mycobacterium tuberculosis [Invited]. Verbal presentation at the Genetics Otago (GO) Annual Symposium, Dunedin, New Zealand.

2025

Journal - Research Article

Champion, D. J., Chen, T.-H., Thomson, S., Black, M. A., & Gardner, P. P. (2025). Evaluating computational tools for protein-coding sequence detection: Are they up to the task? RNA. Advance online publication. doi: 10.1261/rna.080416.125

Gardner, P. P. (2025). A bioinformatician, computer scientist, and geneticist lead bioinformatic tool development: Which one is better? Bioinformatics Advances, vbaf011. Advance online publication. doi: 10.1093/bioadv/vbaf011

Journal - Research Other

Lim, C. S., Mace, P., Fineran, P. C., & Gardner, P. P. (2025). Towards a phylogenetically informed approach to solving protein-protein interactions [Perspective]. Biochemical Society Transactions, 53, 1457-1467. doi: 10.1042/bst20253031

Conference Contribution - Published proceedings: Abstract

Schiavinato, D., Rojas Lopez, K. E., Cooper, H. B., Black, M. A., & Gardner, P. P. (2025). Predicting functional genomic features. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

Gardner, P. P. (2025). What really drives bioinformatic tool accuracy? Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go

2024

Journal - Research Article

Ghomi, F. A., Jung, J. J., Langridge, G. C., Cain, A. K., Boinett, C. J., El Ghany, M. A., … Gardner, P. P., & Barquist, L. (2024). High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality. mBio, 15(10). doi: 10.1128/mbio.01798-24

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

Conference Contribution - Published proceedings: Abstract

Champion, D. J., Chen, T.-H., Thomson, S., Black, M., & Gardner, P. P. (2024). Flawed machine learning and protein coding sequence annotation. Proceedings of the 17th GeneMappers Conference. Retrieved from https://www.genemappersconference.org

Schiavinato, D., Rojas Lopez, K. E., Cooper, H., Black, M., & Gardner, P. (2024). Predicting functional genomic features. Proceedings of the 17th GeneMappers Conference. Retrieved from https://www.genemappersconference.org

Rojas Lopez, K. E., Schiavinato, D., Cooper, H. B., Gardner, P. P., & Black, M. (2024). Statistics of functional genomic features. Proceedings of the 17th GeneMappers Conference. Retrieved from https://www.genemappersconference.org

Mayo-Muñoz, D., Hampton, H. G., Sharma, S., Wakelin, H., Vallabhjee, D., Yevstigneyeva, M. S., … Gardner, P. P., & Fineran, P. C. (2024). Hfq and small RNA regulation of anti-phage systems in Serratia. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/

Conference Contribution - Poster Presentation (not in published proceedings)

Hermann-Le Denmat, S., Adey, B. N., Poole, A. M., Gardner, P. P., Maddock, D. J., & Ganley, A. R. D. (2024, September). Studying alien DNA in human cell lines. Poster session presented at the Queenstown Research Week (QRW) Synthetic Biology Meeting, Queenstown, New Zealand.

Conference Contribution - Verbal presentation and other Conference outputs

Maddock, D. J., Adey, B. N., Hermann-Le Denmat, S., Poole, A. M., Paulsen, I. T., Gardner, P. P., & Ganley, A. R. D. (2024, September). Building synthetic chromosomes to separate junk from function in eukaryotic genomes. Verbal presentation at the Queenstown Research Week (QRW) Synthetic Biology Meeting, Queenstown, New Zealand.

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

Conference Contribution - Published proceedings: Abstract

Cooper, H. B., & Gardner, P. P. (2020). Features of functional human genes. Proceedings of the Genetics Otago (GO) Zoom Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

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