1. Jose BR, Gardner PP, Barquist L (2019) Transcriptional noise and exaptation as sources for bacterial sRNAs Biochemical Society Transactions.
  2. Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, Edwards SV (2019) Convergent regulatory evolution and loss of flight in paleognathous birds Science.
  3. Wheeler NE, Blackmore T, Reynolds AD, Midwinter AC, Marshall J, French NP, Savoian MS, Gardner PP, Biggs PJ (2019) Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni Microbial Genomics.
  4. Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB (2019) Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies PeerJ.
  5. Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD (2018) Essential guidelines for computational method benchmarking arViv.
  6. Wheeler NE, Gardner PP, Barquist L (2018) Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica PLOS GENETICS.
  7. Hoeppner MP, Denisenko E, Gardner PP, Schmeier, Poole AM (2018) Evolutionary, structural and functional explorations of non-coding RNA and protein genetic robustness bioRxiv. 
  8. Coray DS, Sibaeva N, McGimpsey S, Gardner PP (2018) Evolutionary, structural and functional explorations of non-coding RNA and protein genetic robustness bioRxiv.
  9. Dickie IA, Boyer S, Buckley H, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L (2018) Towards robust and repeatable sampling methods in eDNA based studies Molecular Ecology Resources.
  10. Ren X, Eccles DA, Greig GA, Clapham J, Wheeler NE, Lindgreen S, Gardner PP, MacKichan JK (2017) Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts mSystems.
  11. Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR (2017) Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution BMC Genomics. 
  12. Osborne AJ, Jose BR, Perry J, Smeele Z, Aitken J, Garner PP, Slow S (2017) Complete Genome Sequences of Two Geographically Distinct Legionella micdadei Clinical Isolates Genome announcements.
  13. Umu SU, Gardner PP (2017) A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life Bioinformatics.
  14. Mesarich CH, Rees-George J, Gardner PP, Ghomi FA, Gerth ML, Andersen MT, Rikkerink EHA, Fineran PC, Templeton MD (2017) Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae PLOS ONE.
  15. Coray DS, Wheeler NE, Heinemann JA, Gardner PP (2017) Why so narrow: distribution of anti-sense regulated, type I toxin-antitoxin systems compared to type II and type III systems. RNA biology.
  16. Umu SU, Gardner PP (2017) A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of lifeBioinformatics.
  17. Umu SU, Poole AM, Dobson RCJ, Gardner PP (2016) Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLife.
  18. Wheeler NE, Barquist L, Kingsley RA, Gardner PP (2016) A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinformatics. 
  19. Lindgreen S, Adair KL, Gardner PP (2016) An evaluation of the accuracy and speed of metagenome analysis tools. Scientific Reports.
  20. Waldispühl J, Kam A, Gardner PP (2015) Crowdsourcing RNA structural alignments with an online computer game. Pacific Symposium on Biocomputing.
  21. Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF(2015) Conservation and Losses of Non-Coding RNAs in Avian GenomesPLOS ONE.
  22. Gardner PP, Eldai H(2014) Annotating RNA motifs in sequences and alignments.Nucleic Acids Research. 
  23. Lindgreen SUmu SU, Lai AS, Eldai H, Liu W, McGimpsey SWheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Comput Biol.
  24. Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee A, Harris S, Thomson NR, Gardner P, Rabsch W, Wigley P, Humphrey T, Parkhill J, Dougan G (2013Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. MBio.
  25. Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP (2013) A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.Nucleic Acids Research. 
  26. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013Rfam 11.0: 10 years of RNA families. Nucleic Acids Research.
  27. Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z (2011RNIE: genome-wide prediction of bacterial intrinsic terminators. Nucleic Acids Research.
  28. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. (2011Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Research.
  29. Gardner PP, Bateman A, Poole AM. (2010SnoPatrol: how many snoRNA genes are there? Journal of Biology.
  30. Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ, Maskell DJ, Parkhill J, Choudhary J, Thomson NR, Dougan G (2009A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genetics.
  31. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A (2009Rfam: updates to the RNA families database. Nucleic Acids Research.
  32. Gardner PP, Vinther J. (2008Mutation of miRNA target sequences during human evolution. Trends in Genetics.
  33. Freyhult EK, Bollback JP, Gardner PP (2007Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA. Genome Research.
  34. Lindgreen S, Gardner PP, Krogh A (2007MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics.
  35. Lindgreen S, Gardner PP, Krogh A (2006Measuring covariation in RNA alignments: physical realism improves information measures. Bioinformatics.
  36. Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P (2006Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Research.
  37. Gardner PP, Wilm A, Washietl S (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Research.
  38. Gardner PP, Giegerich R (2004) A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 
  39. Gardner PP, Holland BR, Moulton V, Hendy M, Penny D (2003) Optimal alphabets for an RNA world. Proceedings of the Royal Society B (Biological Sciences).