Works by Gardner, Paul P.

Results: 48

Essential guidelines for computational method benchmarking.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1738-8

By:

Weber, Lukas M.;
Saelens, Wouter;
Cannoodt, Robrecht;
Soneson, Charlotte;
Hapfelmeier, Alexander;
Gardner, Paul P.;
Boulesteix, Anne-Laure;
Saeys, Yvan;
Robinson, Mark D.

Publication type:

Article

RNA Folding Argues Against a Hot-Start Origin of Life.

Published in:

Journal of Molecular Evolution, 2000, v. 51, n. 4, p. 416, doi. 10.1007/s002390010104

By:

Moulton, Vincent;
Gardner, Paul P.;
Pointon, Robert F.;
Creamer, Lawrence K.;
Jameson, Geoffrey B.;
Penny, David

Publication type:

Article

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

Published in:

Bioinformatics, 2020, v. 36, n. 18, p. 4691, doi. 10.1093/bioinformatics/btaa578

By:

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

Publication type:

Article

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 8, p. 4549, doi. 10.1093/nar/gkt148

By:

Barquist, Lars;
Langridge, Gemma C.;
Turner, Daniel J.;
Phan, Minh-Duy;
Turner, A. Keith;
Bateman, Alex;
Parkhill, Julian;
Wain, John;
Gardner, Paul P.

Publication type:

Article

Rfam 11.0: 10 years of RNA families.

Published in:

Nucleic Acids Research, 2013, v. 41, p. D226, doi. 10.1093/nar/gks1005

By:

Burge, Sarah W.;
Daub, Jennifer;
Eberhardt, Ruth;
Tate, John;
Barquist, Lars;
Nawrocki, Eric P.;
Eddy, Sean R.;
Gardner, Paul P.;
Bateman, Alex

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2012, p. D9, doi. 10.1093/nar/gkr1195

By:

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

Publication type:

Article

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 14, p. 5845, doi. 10.1093/nar/gkr168

By:

Gardner, Paul P.;
Barquist, Lars;
Bateman, Alex;
Nawrocki, Eric P.;
Weinberg, Zasha

Publication type:

Article

Rfam: Wikipedia, clans and the “decimal” release.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D141, doi. 10.1093/nar/gkq1129

By:

Gardner, Paul P.;
Daub, Jennifer;
Tate, John;
Moore, Benjamin L.;
Osuch, Isabelle H.;
Griffiths-Jones, Sam;
Finn, Robert D.;
Nawrocki, Eric P.;
Kolbe, Diana L.;
Eddy, Sean R.;
Bateman, Alex

Publication type:

Article

Rfam: updates to the RNA families database.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D136, doi. 10.1093/nar/gkn766

By:

Gardner, Paul P.;
Daub, Jennifer;
Tate, John G.;
Nawrocki, Eric P.;
Kolbe, Diana L.;
Lindgreen, Stinus;
Wilkinson, Adam C.;
Finn, Robert D.;
Griffiths-Jones, Sam;
Eddy, Sean R.;
Bateman, Alex

Publication type:

Article

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 16, p. e107, doi. 10.1093/nar/gkl590

By:

Vinther, Jeppe;
Hedegaard, Mads M.;
Gardner, Paul P.;
Andersen, Jens S.;
Arctander, Peter

Publication type:

Article

A benchmark of multiple sequence alignment programs upon structural RNAs.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 8, p. 2433, doi. 10.1093/nar/gki541

By:

Gardner, Paul P.;
Wilm, Andreas;
Washietl, Stefan

Publication type:

Article

Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems.

Published in:

RNA Biology, 2017, v. 14, n. 3, p. 275, doi. 10.1080/15476286.2016.1272747

By:

Coray, Dorien S.;
Wheeler, Nicole E.;
Heinemann, Jack A.;
Gardner, Paul P.

Publication type:

Article

A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi.

Published in:

PLoS Genetics, 2009, v. 5, n. 7, p. 1, doi. 10.1371/journal.pgen.1000569

By:

Perkins, Timothy T.;
Kingsley, Robert A.;
Fookes, Maria C.;
Gardner, Paul P.;
James, Keith D.;
Lu Yu;
Assefa, Samuel A.;
Miao He;
Croucher, Nicholas J.;
Pickard, Derek J.;
Maskell, Duncan J.;
Parkhill, Julian;
Choudhary, Jyoti;
Thomson, Nicholas R.;
Dougan, Gordon

Publication type:

Article

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

Published in:

Bioinformatics, 2007, v. 23, n. 24, p. 3304, doi. 10.1093/bioinformatics/btm525

By:

Stinus Lindgreen;
Paul P. Gardner;
Anders Krogh

Publication type:

Article

Evolution of virulence in a novel family of transmissible mega‐plasmids.

Published in:

Environmental Microbiology, 2021, v. 23, n. 9, p. 5289, doi. 10.1111/1462-2920.15595

By:

Sitter, Thomas L.;
Vaughan, Amy L.;
Schoof, Marion;
Jackson, Simon A.;
Glare, Travis R.;
Cox, Murray P.;
Fineran, Peter C.;
Gardner, Paul P.;
Hurst, Mark R. H.

Publication type:

Article

Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae.

Published in:

PLoS ONE, 2017, v. 12, n. 3, p. 1, doi. 10.1371/journal.pone.0172790

By:

Mesarich, Carl H.;
Rees-George, Jonathan;
Gardner, Paul P.;
Ghomi, Fatemeh Ashari;
Gerth, Monica L.;
Andersen, Mark T.;
Rikkerink, Erik H. A.;
Fineran, Peter C.;
Templeton, Matthew D.

Publication type:

Article

SorTn-seq: a high-throughput functional genomics approach to discovering regulators of bacterial gene expression.

Published in:

Nature Protocols, 2021, v. 16, n. 9, p. 4382, doi. 10.1038/s41596-021-00582-6

By:

Smith, Leah M.;
Jackson, Simon A.;
Gardner, Paul P.;
Fineran, Peter C.

Publication type:

Article

An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics.

Published in:

Molecular Biology & Evolution, 2018, v. 35, n. 6, p. 1451, doi. 10.1093/molbev/msy046

By:

Hoeppner, Marc P;
Denisenko, Elena;
Gardner, Paul P;
Schmeier, Sebastian;
Poole, Anthony M

Publication type:

Article

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

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 988, doi. 10.1093/bioinformatics/btw728

By:

Umu, Sinan Uğur;
Gardner, Paul P.

Publication type:

Article

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Published in:

Bioinformatics, 2016, v. 32, n. 23, p. 3566, doi. 10.1093/bioinformatics/btw518

By:

Wheeler, Nicole E.;
Barquist, Lars;
Kingsley, Robert A.;
Gardner, Paul P.

Publication type:

Article

Serratia‐based toxin cluster elements are associated with a type I fimbria.

Published in:

MicrobiologyOpen, 2024, v. 13, n. 1, p. 1, doi. 10.1002/mbo3.1395

By:

Sitter, Lesley;
Schoof, Marion;
Glare, Travis R.;
Cox, Murray P.;
Fineran, Peter C.;
Gardner, Paul P.;
Hurst, Mark R. H.

Publication type:

Article

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02625-x

By:

Gardner, Paul P.;
Paterson, James M.;
McGimpsey, Stephanie;
Ashari-Ghomi, Fatemeh;
Umu, Sinan U.;
Pawlik, Aleksandra;
Gavryushkin, Alex;
Black, Michael A.

Publication type:

Article

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.

Published in:

Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02625-x

By:

Gardner, Paul P.;
Paterson, James M.;
McGimpsey, Stephanie;
Ashari-Ghomi, Fatemeh;
Umu, Sinan U.;
Pawlik, Aleksandra;
Gavryushkin, Alex;
Black, Michael A.

Publication type:

Article

On the optimistic performance evaluation of newly introduced bioinformatic methods.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02365-4

By:

Buchka, Stefan;
Hapfelmeier, Alexander;
Gardner, Paul P.;
Wilson, Rory;
Boulesteix, Anne-Laure

Publication type:

Article

Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 10, p. 1, doi. 10.1371/journal.pcbi.1009461

By:

Bhandari, Bikash K.;
Lim, Chun Shen;
Remus, Daniela M.;
Chen, Augustine;
van Dolleweerd, Craig;
Gardner, Paul P.

Publication type:

Article

Towards robust and repeatable sampling methods in eDNA‐based studies.

Published in:

Molecular Ecology Resources, 2018, v. 18, n. 5, p. 940, doi. 10.1111/1755-0998.12907

By:

Makiola, Andreas;
Dickie, Ian A.;
Lear, Gavin;
Morales, Sergio E.;
Powell, Jeff R.;
Weaver, Louise;
Gardner, Paul P.;
Boyer, Stephane;
Buckley, Hannah L.;
Duncan, Richard P.;
Hogg, Ian D.;
Holdaway, Robert J.

Publication type:

Article

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4197-1

By:

Chen Wu;
Jordan, Melissa D.;
Newcomb, Richard D.;
Gemmell, Neil J.;
Bank, Sarah;
Meusemann, Karen;
Dearden, Peter K.;
Duncan, Elizabeth J.;
Grosser, Sefanie;
Rutherford, Kim;
Gardner, Paul P.;
Crowhurst, Ross N.;
Steinwender, Bernd;
Tooman, Leah K.;
Stevens, Mark I.;
Buckley, Thomas R.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2007, v. 8, p. 1, doi. 10.1186/1471-2105-8-S8-P8

By:

Lindgreen, Stinus;
Gardner, Paul P.;
Krogh, Anders

Publication type:

Article

A comprehensive comparison of comparative RNA structure prediction approaches.

Published in:

BMC Bioinformatics, 2004, v. 5, p. 140, doi. 10.1186/1471-2105-5-140

By:

Gardner, Paul P.;
Giegerich, Robert

Publication type:

Article

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003907

By:

Lindgreen, Stinus;
Umu, Sinan Uğur;
Lai, Alicia Sook-Wei;
Eldai, Hisham;
Liu, Wenting;
McGimpsey, Stephanie;
Wheeler, Nicole E.;
Biggs, Patrick J.;
Thomson, Nick R.;
Barquist, Lars;
Poole, Anthony M.;
Gardner, Paul P.

Publication type:

Article

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.pcbi.1002752

By:

Hoeppner, Marc P.;
Gardner, Paul P.;
Poole, Anthony M.

Publication type:

Article

Ten Simple Rules for Editing Wikipedia.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000941

By:

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

Publication type:

Article

The use of covariance models to annotate RNAs in whole genomes.

Published in:

Briefings in Functional Genomics & Proteomics, 2009, v. 8, n. 6, p. 444, doi. 10.1093/bfgp/elp042

By:

Gardner, Paul P.

Publication type:

Article

Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis.

Published in:

PeerJ, 2023, p. 1, doi. 10.7717/peerj.14969

By:

Cooper, Helena B.;
Krause, Kurt L.;
Gardner, Paul P.

Publication type:

Article

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies.

Published in:

PeerJ, 2019, p. 1, doi. 10.7717/peerj.6160

By:

Gardner, Paul P.;
Watson, Renee J.;
Morgan, Xochitl C.;
Draper, Jenny L.;
Finn, Robert D.;
Morales, Sergio E.;
Stott, Matthew B.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2021, v. 49, n. W1, p. W654, doi. 10.1093/nar/gkab175

By:

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

Publication type:

Article

Annotating RNA motifs in sequences and alignments.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 2, p. 691, doi. 10.1093/nar/gku1327

By:

Gardner, Paul P.;
Eldai, Hisham

Publication type:

Article

Rfam 12.0: updates to the RNA families database.

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D130, doi. 10.1093/nar/gku1063

By:

Nawrocki, Eric P.;
Burge, Sarah W.;
Bateman, Alex;
Daub, Jennifer;
Eberhardt, Ruth Y.;
Eddy, Sean R.;
Floden, Evan W.;
Gardner, Paul P.;
Jones, Thomas A.;
Tate, John;
Finn, Robert D.

Publication type:

Article

The PitA protein contributes to colistin susceptibility in Pseudomonas aeruginosa.

Published in:

PLoS ONE, 2023, v. 18, n. 10, p. 1, doi. 10.1371/journal.pone.0292818

By:

Erdmann, Mareike B.;
Gardner, Paul P.;
Lamont, Iain L.

Publication type:

Article

Author Correction: An evaluation of the accuracy and speed of metagenome analysis tools.

Published in:

2020

By:

Lindgreen, Stinus;
Adair, Karen L.;
Gardner, Paul P.

Publication type:

Correction Notice

Author Correction: An evaluation of the accuracy and speed of metagenome analysis tools.

Published in:

2020

By:

Lindgreen, Stinus;
Adair, Karen L.;
Gardner, Paul P.

Publication type:

Correction Notice

ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baaa105

By:

Biggs, Harry;
Parthasarathy, Padmini;
Gavryushkina, Alexandra;
Gardner, Paul P

Publication type:

Article

Conservation and Losses of Non-Coding RNAs in Avian Genomes.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0121797

By:

Gardner, Paul P.;
Fasold, Mario;
Burge, Sarah W.;
Ninova, Maria;
Hertel, Jana;
Kehr, Stephanie;
Steeves, Tammy E.;
Griffiths-Jones, Sam;
Stadler, Peter F.

Publication type:

Article

Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.

Published in:

eLife, 2016, p. 1, doi. 10.7554/eLife.13479

By:

Umu, Sinan Uğur;
Poole, Anthony M.;
Dobson, Renwick C. J.;
Gardner, Paul P.

Publication type:

Article

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Published in:

PLoS Genetics, 2018, v. 14, n. 5, p. 1, doi. 10.1371/journal.pgen.1007333

By:

Wheeler, Nicole E.;
Gardner, Paul P.;
Barquist, Lars

Publication type:

Article

An evaluation of the accuracy and speed of metagenome analysis tools.

Published in:

Scientific Reports, 2016, p. 19233, doi. 10.1038/srep19233

By:

Lindgreen, Stinus;
Adair, Karen L.;
Gardner, Paul P.

Publication type:

Article

Transcriptional noise and exaptation as sources for bacterial sRNAs.

Published in:

Biochemical Society Transactions, 2019, v. 47, n. 2, p. 527, doi. 10.1042/BST20180171

By:

Jose, Bethany R.;
Gardner, Paul P.;
Barquist, Lars

Publication type:

Article

Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes.

Published in:

BMC Genomics, 2007, v. 8, p. 244, doi. 10.1186/1471-2164-8-244

By:

Weile, Christian;
Gardner, Paul P;
Hedegaard, Mads M;
Vinther, Jeppe

Publication type:

Article