A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction. - Sverker Edvardsson; Paul P. Gardner; Anthony M. Poole; Michael D. Hendy; David Penny; Vincent Moulton (Bioinform., 2003)

A comprehensive comparison of comparative RNA structure prediction approaches. - Paul P. Gardner; Robert Giegerich (BMC Bioinform., 2004)

A comparison of RNA folding measures. - Eva Freyhult; Paul P. Gardner; Vincent Moulton (BMC Bioinform., 2005)

Measuring covariation in RNA alignments: physical realism improves information measures. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (Bioinform., 2006)

A hidden Markov model approach for determining expression from genomic tiling micro arrays. - Kasper Munch; Paul P. Gardner; Peter Arctander; Anders Krogh (BMC Bioinform., 2006)

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (Bioinform., 2007)

Multiple alignment and structure prediction of non-coding RNA sequences. - Stinus Lindgreen; Paul P. Gardner; Anders Krogh (BMC Bioinform., 2007)

Rfam: updates to the RNA families database. - Paul P. Gardner; Jennifer Daub; John G. Tate; Eric P. Nawrocki; Diana L. Kolbe; Stinus Lindgreen; Adam C. Wilkinson; Robert D. Finn; Sam Griffiths-Jones; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2009)

Ten Simple Rules for Editing Wikipedia. - Darren W. Logan; Massimo Sandal; Paul P. Gardner; Magnus Manske; Alex Bateman (PLoS Comput. Biol., 2010)

Rfam: Wikipedia, clans and the "decimal" release. - Paul P. Gardner; Jennifer Daub; John G. Tate; Benjamin L. Moore; Isabelle H. Osuch; Sam Griffiths-Jones; Robert D. Finn; Eric P. Nawrocki; Diana L. Kolbe; Sean R. Eddy; Alex Bateman (Nucleic Acids Res., 2011)

Making your database available through Wikipedia: the pros and cons. - Robert D. Finn; Paul P. Gardner; Alex Bateman (Nucleic Acids Res., 2012)

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life. - Marc P. Hoeppner; Paul P. Gardner; Anthony M. Poole (PLoS Comput. Biol., 2012)

Rfam 11.0: 10 years of RNA families. - Sarah W. Burge; Jennifer Daub; Ruth Y. Eberhardt; John G. Tate; Lars Barquist; Eric P. Nawrocki; Sean R. Eddy; Paul P. Gardner; Alex Bateman (Nucleic Acids Res., 2013)

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. - Stinus Lindgreen; Sinan Ugur Umu; Alicia Sook-Wei Lai; Hisham Eldai; Wenting Liu; Stephanie McGimpsey; Nicole E. Wheeler; Patrick J. Biggs; Nick R. Thomson; Lars Barquist; Anthony M. Poole; Paul P. Gardner (PLoS Comput. Biol., 2014)

Crowdsourcing RNA Structural Alignments with an Online Computer Game. - Jérôme Waldispühl; Arthur Kam; Paul P. Gardner (Pacific Symposium on Biocomputing, 2015)

Rfam 12.0: updates to the RNA families database. - Eric P. Nawrocki; Sarah W. Burge; Alex Bateman; Jennifer Daub; Ruth Y. Eberhardt; Sean R. Eddy; Evan W. Floden; Paul P. Gardner; Thomas A. Jones; John G. Tate; Robert D. Finn (Nucleic Acids Res., 2015)

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. - Nicole E. Wheeler; Lars Barquist; Robert A. Kingsley; Paul P. Gardner (Bioinform., 2016)

A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. - Sinan Ugur Umu; Paul P. Gardner (Bioinform., 2017)

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. - Harry Biggs; Padmini Parthasarathy; Alexandra Gavryushkina; Paul P. Gardner (Database J. Biol. Databases Curation, 2020)

Solubility-Weighted Index: fast and accurate prediction of protein solubility. - Bikash K. Bhandari; Paul P. Gardner; Chun Shen Lim (Bioinform., 2020)

TISIGNER.com: web services for improving recombinant protein production. - Bikash K. Bhandari; Chun Shen Lim; Paul P. Gardner (Nucleic Acids Res., 2021)

Analysis of 11, 430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. - Bikash K. Bhandari; Chun Shen Lim; Daniela M. Remus; Augustine Chen; Craig van Dolleweerd; Paul P. Gardner (PLoS Comput. Biol., 2021)