Paul P. Gardner

22 papers Misc 1Journal 21
YearRankTypeTitle / Venue / Authors
2021 J jnl
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.
Bikash K. Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig van Dolleweerd, Paul P. Gardner
2021 J jnl
TISIGNER.com: web services for improving recombinant protein production.
Nucleic Acids Res.
Bikash K. Bhandari, Chun Shen Lim, Paul P. Gardner
2020 J jnl
Solubility-Weighted Index: fast and accurate prediction of protein solubility.
Bioinform.
Bikash K. Bhandari, Paul P. Gardner, Chun Shen Lim
2020 J jnl
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls.
Database J. Biol. Databases Curation
Harry Biggs, Padmini Parthasarathy, Alexandra Gavryushkina, Paul P. Gardner
2017 J jnl
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.
Bioinform.
Sinan Ugur Umu, Paul P. Gardner
2016 J jnl
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.
Bioinform.
Nicole E. Wheeler, Lars Barquist, Robert A. Kingsley, Paul P. Gardner
2015 Misc conf
Crowdsourcing RNA Structural Alignments with an Online Computer Game.
Pacific Symposium on Biocomputing
Jérôme Waldispühl, Arthur Kam, Paul P. Gardner
2015 J jnl
Rfam 12.0: updates to the RNA families database.
Nucleic Acids Res.
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
2014 J jnl
Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling.
PLoS Comput. Biol.
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
2013 J jnl
Rfam 11.0: 10 years of RNA families.
Nucleic Acids Res.
Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman
2012 J jnl
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life.
PLoS Comput. Biol.
Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole
2012 J jnl
Making your database available through Wikipedia: the pros and cons.
Nucleic Acids Res.
Robert D. Finn, Paul P. Gardner, Alex Bateman
2011 J jnl
Rfam: Wikipedia, clans and the "decimal" release.
Nucleic Acids Res.
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
2010 J jnl
Ten Simple Rules for Editing Wikipedia.
PLoS Comput. Biol.
Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman
2009 J jnl
Rfam: updates to the RNA families database.
Nucleic Acids Res.
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
2007 J jnl
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
Bioinform.
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
2007 J jnl
Multiple alignment and structure prediction of non-coding RNA sequences.
BMC Bioinform.
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
2006 J jnl
A hidden Markov model approach for determining expression from genomic tiling micro arrays.
BMC Bioinform.
Kasper Munch, Paul P. Gardner, Peter Arctander, Anders Krogh
2006 J jnl
Measuring covariation in RNA alignments: physical realism improves information measures.
Bioinform.
Stinus Lindgreen, Paul P. Gardner, Anders Krogh
2005 J jnl
A comparison of RNA folding measures.
BMC Bioinform.
Eva Freyhult, Paul P. Gardner, Vincent Moulton
2004 J jnl
A comprehensive comparison of comparative RNA structure prediction approaches.
BMC Bioinform.
Paul P. Gardner, Robert Giegerich
2003 J jnl
A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction.
Bioinform.
Sverker Edvardsson, Paul P. Gardner, Anthony M. Poole, Michael D. Hendy, David Penny, Vincent Moulton