Paul P Gardner
Affiliation: Wellcome Trust Genome Campus
- Rfam: updates to the RNA families databasePaul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Nucleic Acids Res 37:D136-40. 2009..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
- The use of covariance models to annotate RNAs in whole genomesPaul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Brief Funct Genomic Proteomic 8:444-50. 2009..Some recent innovations for improving the speed and accuracy of covariance models is discussed...
- SnoPatrol: how many snoRNA genes are there?Paul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK
J Biol 9:4. 2010..Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found...
- Rfam: Wikipedia, clans and the "decimal" releasePaul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
Nucleic Acids Res 39:D141-5. 2011..We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk...
- RNIE: genome-wide prediction of bacterial intrinsic terminatorsPaul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, UK
Nucleic Acids Res 39:5845-52. 2011..tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE...
- Rfam 11.0: 10 years of RNA familiesSarah W Burge
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Nucleic Acids Res 41:D226-32. 2013..0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license...
- A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and TyphimuriumLars Barquist
Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
Nucleic Acids Res 41:4549-64. 2013..We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks...
- Making your database available through Wikipedia: the pros and consRobert D Finn
HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA, USA
Nucleic Acids Res 40:D9-12. 2012..Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis...
- A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhiTimothy T Perkins
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
PLoS Genet 5:e1000569. 2009..Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome...