Paul P. Gardner

According to our database, Paul P. Gardner authored at least 22 papers between 2003 and 2021.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

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

TISIGNER.com: web services for improving recombinant protein production.

Bikash K. Bhandari, Chun Shen Lim, Paul P. Gardner

Nucleic Acids Res., 2021

2020

Solubility-Weighted Index: fast and accurate prediction of protein solubility.

Bikash K. Bhandari, Paul P. Gardner, Chun Shen Lim

Bioinform., 2020

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

2017

A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.

Sinan Ugur Umu, Paul P. Gardner

Bioinform., 2017

2016

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

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

Crowdsourcing RNA Structural Alignments with an Online Computer Game.

Jérôme Waldispühl, Arthur Kam, Paul P. Gardner

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

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

2013

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

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

Making your database available through Wikipedia: the pros and cons.

Robert D. Finn, Paul P. Gardner, Alex Bateman

Nucleic Acids Res., 2012

2011

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

2010

Ten Simple Rules for Editing Wikipedia.

Darren W. Logan, Massimo Sandal, Paul P. Gardner, Magnus Manske, Alex Bateman

PLoS Comput. Biol., 2010

2009

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

2007

Multiple alignment and structure prediction of non-coding RNA sequences.

Stinus Lindgreen, Paul P. Gardner, Anders Krogh

BMC Bioinform., 2007

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

Stinus Lindgreen, Paul P. Gardner, Anders Krogh

Bioinform., 2007

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

Measuring covariation in RNA alignments: physical realism improves information measures.

Stinus Lindgreen, Paul P. Gardner, Anders Krogh

Bioinform., 2006

2005

A comparison of RNA folding measures.

Eva Freyhult, Paul P. Gardner, Vincent Moulton

BMC Bioinform., 2005

2004

A comprehensive comparison of comparative RNA structure prediction approaches.

Paul P. Gardner, Robert Giegerich

BMC Bioinform., 2004

2003

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