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Rfam 12.0: updates to the RNA families database
The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy and ontology resources. Expand
Rfam: updates to the RNA families database
Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). Expand
Rfam 11.0: 10 years of RNA families
The Rfam database categorizes non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Expand
A comprehensive comparison of comparative RNA structure prediction approaches
We evaluate a number of RNA folding algorithms using reliable RNA data-sets and compare their relative performance using comparative approaches to structure prediction. Expand
Rfam: Wikipedia, clans and the “decimal” release
The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. Expand
A benchmark of multiple sequence alignment programs upon structural RNAs
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalentsExpand
A comparison of RNA folding measures
We investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Expand
An evaluation of the accuracy and speed of metagenome analysis tools
This paper presents the first large independent benchmark of metagenome analysis tools using complex, realistic simulated data sets. Expand
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the geneticExpand
A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
High-density, strand-specific cDNA sequencing (ssRNA–seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. TyphiExpand