Paul P. Gardner
Paul P. Gardner
University of Otago, New Zealand
Verified email at otago.ac.nz - Homepage
TitleCited byYear
A benchmark of multiple sequence alignment programs upon structural RNAs
PP Gardner, A Wilm, S Washietl
Nucleic acids research 33 (8), 2433-2439, 2005
3052005
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
L Barquist, GC Langridge, DJ Turner, MD Phan, AK Turner, A Bateman, ...
Nucleic acids research 41 (8), 4549-4564, 2013
762013
A comparison of RNA folding measures
E Freyhult, PP Gardner, V Moulton
BMC bioinformatics 6 (1), 241, 2005
1212005
A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life
SU Umu, PP Gardner
Bioinformatics 33 (7), 988-996, 2017
242017
A comprehensive comparison of comparative RNA structure prediction approaches
PP Gardner, R Giegerich
BMC bioinformatics 5 (1), 140, 2004
4102004
A hidden Markov model approach for determining expression from genomic tiling micro arrays
K Munch, PP Gardner, P Arctander, A Krogh
BMC bioinformatics 7 (1), 239, 2006
412006
A home for RNA families at RNA Biology
PP Gardner, AG Bateman
RNA Biology 6 (1), 2-4, 2009
102009
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity
LM Malone, SL Warring, SA Jackson, C Warnecke, PP Gardner, LF Gumy, ...
Nature Microbiology, 1-8, 2019
2019
A meta-analysis of bioinformatics software benchmarks reveals that publication-bias unduly influences software accuracy
PP Gardner, JM Paterson, FA Ghomi, SUU Umu, S McGimpsey, A Pawlik
bioRxiv, 092205, 2017
22017
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
NE Wheeler, L Barquist, RA Kingsley, PP Gardner
Bioinformatics, 10.1093/bioinformatics/btw518, 2016
142016
A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction
S Edvardsson, PP Gardner, AM Poole, MD Hendy, D Penny, V Moulton
Bioinformatics 19 (7), 865-873, 2003
632003
A strand-specific RNA–Seq analysis of the transcriptome of the typhoid bacillus salmonella typhi
TT Perkins, RA Kingsley, MC Fookes, PP Gardner, KD James, L Yu, ...
PLoS genetics 5 (7), e1000569, 2009
2442009
A VapBC Toxin-Antitoxin Module is a Post-Transcriptional Regulator of Metabolic Flux in Mycobacteria
JL McKenzie, J Robson, M Berney, TC Smith, A Ruthe, PP Gardner, ...
Journal of Bacteriology, 2012
812012
An evaluation of function of multicopy non-coding RNAs in mammals using ENCODE/FANTOM data and comparative genomics
MP Hoeppner, E Denisenko, PP Gardner, S Schmeier, AM Poole
Molecular Biology and Evolution, 2018
32018
An evaluation of the accuracy and speed of metagenome analysis tools
S Lindgreen, KL Adair, P Gardner
Scientific Reports 6 (19), doi:10.1038/srep19233, 2016
1942016
An introduction to RNA databases
MP Hoeppner, LE Barquist, PP Gardner
RNA Sequence, Structure, and Function: Computational and Bioinformatic …, 2014
82014
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution
C Wu, MD Jordan, RD Newcomb, NJ Gemmell, S Bank, K Meusemann, ...
BMC Genomics 18 (1), 795, 2017
192017
Annotating RNA motifs in sequences and alignments
PP Gardner, H Eldai
Nucl. Acids Res., doi: 10.1093/nar/gku1327, 2014
142014
Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea
SU Umu, AM Poole, RCJ Dobson, PP Gardner
eLive 5 (http://dx.doi.org/10.7554/eLife.13479), e13479, 2016
192016
Building non-coding RNA families
L Barquist, SW Burge, PP Gardner
Methods in Molecular Biology, 2012
42012
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Articles 1–20