Paul P. Gardner

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Alex BatemanHead of Protein Sequence Resources, EMBL-EBIVerified email at ebi.ac.uk
Lars BarquistUniversity of Toronto; Helmholtz Institute for RNA-based Infection ResearchVerified email at helmholtz-hiri.de
Eric P NawrockiNational Center for Biotechnology Information (NCBI), NLM, NIHVerified email at ncbi.nlm.nih.gov
Jennifer DaubUniversity of EdinburghVerified email at ed.ac.uk
Sarah BurgeDepartment of Oncology, University of CambridgeVerified email at cam.ac.uk
Stinus LindgreenCurrent Member of ParliamentVerified email at ft.dk
Robert D. FinnMicrobiome Informatics Team Leader, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambs, CB10 1SDVerified email at ebi.ac.uk
Sean R. EddyHHMI & Harvard UniversityVerified email at fas.harvard.edu
Sam Griffiths-JonesFaculty of Biology, Medicine and Health. University of ManchesterVerified email at manchester.ac.uk
Nicole E WheelerResearch Fellow, University of BirminghamVerified email at bham.ac.uk
Anthony M PooleSchool of Biological Sciences, University of Auckland, New ZealandVerified email at auckland.ac.nz
Chun Shen LimDepartment of Biochemistry, University of Otago, Dunedin, New ZealandVerified email at otago.ac.nz
Bikash Kumar BhandariEMBL-EBIVerified email at ebi.ac.uk
Diana L KolbeResearch Scientist, IIHG, University of IowaVerified email at uiowa.edu
Julian ParkhillUniversity of CambridgeVerified email at cam.ac.uk
Peter FineranProfessor, Head of Phage-host interactions (Phi) laboratory,University of Otago, New ZealandVerified email at otago.ac.nz
Nick ThomsonProfessor of Bacterial Evolution and GenomicsVerified email at sanger.ac.uk
Robert A KingsleyGroup Leader at the Quadram Institute Bioscience, UKVerified email at quadram.ac.uk
Anders KroghDepartment of Computer Science and Center for Health Data Science, University of CopenhagenVerified email at di.ku.dk
Eva FreyhultUppsala UniversityVerified email at nbis.se

Paul P. Gardner

University of Otago, New Zealand

Verified email at otago.ac.nz

ncRNA Bioinformatics Genome variation Benchmarking


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Rfam 12.0: updates to the RNA families database EP Nawrocki, SW Burge, A Bateman, J Daub, RY Eberhardt, SR Eddy, ... Nucleic acids research 43 (D1), D130-D137, 2015	1107	2015
Comparative genomics reveals insights into avian genome evolution and adaptation G Zhang, C Li, Q Li, B Li, DM Larkin, C Lee, JF Storz, A Antunes, ... Science 346 (6215), 1311-1320, 2014	1087	2014
Rfam: updates to the RNA families database PP Gardner, J Daub, JG Tate, EP Nawrocki, DL Kolbe, S Lindgreen, ... Nucleic acids research 37 (suppl 1), D136-D140, 2009	1010	2009
Rfam 11.0: 10 years of RNA families SW Burge, J Daub, R Eberhardt, J Tate, L Barquist, EP Nawrocki, ... Nucleic acids research 41 (D1), D226-D232, 2013	927	2013
A comprehensive comparison of comparative RNA structure prediction approaches PP Gardner, R Giegerich BMC bioinformatics 5 (1), 140, 2004	487	2004
Rfam: Wikipedia, clans and the “decimal” release PP Gardner, J Daub, J Tate, BL Moore, IH Osuch, S Griffiths-Jones, ... Nucleic acids research 39 (suppl 1), D141-D145, 2011	480	2011
A benchmark of multiple sequence alignment programs upon structural RNAs PP Gardner, A Wilm, S Washietl Nucleic acids research 33 (8), 2433-2439, 2005	369	2005
An evaluation of the accuracy and speed of metagenome analysis tools S Lindgreen, KL Adair, P Gardner Scientific Reports 6 (19), doi:10.1038/srep19233, 2016	363	2016
A strand-specific RNA–Seq analysis of the transcriptome of the typhoid bacillus salmonella typhi TT Perkins, RA Kingsley, MC Fookes, PP Gardner, KD James, L Yu, ... PLoS genetics 5 (7), 2009	284	2009
Convergent regulatory evolution and loss of flight in paleognathous birds TB Sackton, P Grayson, A Cloutier, Z Hu, JS Liu, NE Wheeler, PP Gardner, ... Science 364 (6435), 74-78, 2019	263	2019
Towards robust and repeatable sampling methods in eDNA based studies IA Dickie, S Boyer, H Buckley, RP Duncan, P Gardner, ID Hogg, ... Molecular Ecology Resources, 2018	198	2018
Identification of miRNA targets with stable isotope labeling by amino acids in cell culture J Vinther, MM Hedegaard, PP Gardner, JS Andersen, P Arctander Nucleic acids research 34 (16), e107-e107, 2006	166	2006
Essential guidelines for computational method benchmarking LM Weber, W Saelens, R Cannoodt, C Soneson, A Hapfelmeier, ... Genome Biology 20 (1), 125, 2019	159	2019
Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA EK Freyhult, JP Bollback, PP Gardner Genome research 17 (1), 117-125, 2007	158	2007
A comparison of RNA folding measures E Freyhult, PP Gardner, V Moulton BMC bioinformatics 6 (1), 241, 2005	148	2005
The tuatara genome reveals ancient features of amniote evolution NJ Gemmell, K Rutherford, S Prost, M Tollis, D Winter, JR Macey, ... Nature, doi.org/10.1038/s41586-020-2561-9, 2020	144	2020
Comparative genomic data of the Avian Phylogenomics Project G Zhang, B Li, C Li, MTP Gilbert, ED Jarvis, J Wang, TAG Consortium GigaScience 3 (26), doi:10.1186/2047-217X-3-26, 2014	144	2014
A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity LM Malone, SL Warring, SA Jackson, C Warnecke, PP Gardner, LF Gumy, ... Nature Microbiology 5 (1), 48-55, 2020	143	2020
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium L Barquist, GC Langridge, DJ Turner, MD Phan, AK Turner, A Bateman, ... Nucleic acids research 41 (8), 4549-4564, 2013	139	2013
A VapBC Toxin-Antitoxin Module is a Post-Transcriptional Regulator of Metabolic Flux in Mycobacteria JL McKenzie, J Robson, M Berney, TC Smith, A Ruthe, PP Gardner, ... Journal of Bacteriology, 2012	118	2012

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