Paul P. Gardner

Publication Activity (10 Years)

Years Active: 2003-2021
Publications (10 Years): 6

Top Topics

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Database J. Biol. Databases Curation

Publications

Bikash K. Bhandari, Chun Shen Lim, Paul P. Gardner
TISIGNER.com: web services for improving recombinant protein production. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Bikash K. Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig van Dolleweerd, Paul P. Gardner
Analysis of 11, 430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput. Biol. 17 (10) (2021)
Bikash K. Bhandari, Paul P. Gardner, Chun Shen Lim
Solubility-Weighted Index: fast and accurate prediction of protein solubility. Bioinform. 36 (18) (2020)
Harry Biggs, Padmini Parthasarathy, Alexandra Gavryushkina, Paul P. Gardner
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls. Database J. Biol. Databases Curation 2020 (2020)
Sinan Ugur Umu, Paul P. Gardner
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinform. 33 (7) (2017)
Nicole E. Wheeler, Lars Barquist, Robert A. Kingsley, Paul P. Gardner
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. Bioinform. 32 (23) (2016)
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
Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43 (Database-Issue) (2015)
Jérôme Waldispühl, Arthur Kam, Paul P. Gardner
Crowdsourcing RNA Structural Alignments with an Online Computer Game. Pacific Symposium on Biocomputing (2015)
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
Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLoS Comput. Biol. 10 (10) (2014)
Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman
Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41 (Database-Issue) (2013)
Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life. PLoS Comput. Biol. 8 (11) (2012)
Robert D. Finn, Paul P. Gardner, Alex Bateman
Making your database available through Wikipedia: the pros and cons. Nucleic Acids Res. 40 (Database-Issue) (2012)
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
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res. 39 (Database-Issue) (2011)
Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman
Ten Simple Rules for Editing Wikipedia. PLoS Comput. Biol. 6 (9) (2010)
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
Rfam: updates to the RNA families database. Nucleic Acids Res. 37 (Database-Issue) (2009)
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinform. 23 (24) (2007)
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
Multiple alignment and structure prediction of non-coding RNA sequences. BMC Bioinform. 8 (S-8) (2007)
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
Measuring covariation in RNA alignments: physical realism improves information measures. Bioinform. 22 (24) (2006)
Kasper Munch, Paul P. Gardner, Peter Arctander, Anders Krogh
A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinform. 7 (2006)
Eva Freyhult, Paul P. Gardner, Vincent Moulton
A comparison of RNA folding measures. BMC Bioinform. 6 (2005)
Paul P. Gardner, Robert Giegerich
A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinform. 5 (2004)
Sverker Edvardsson, Paul P. Gardner, Anthony M. Poole, Michael D. Hendy, David Penny, Vincent Moulton
A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction. Bioinform. 19 (7) (2003)