We work on projects that involve RNA analysis, the analysis of genome variation or the benchmarking of bioinformatic software tools. We spend a lot of resources analysing large and complex datasets that have been generated with next-generation sequencing technology. We are involved with comparative analyses of genomic, transcriptomic and recently whole-genome transposon mutagenesis screens. We are very interested in predicting the phenotypic consequences of genetic variation and are developing tools to do this. We are looking at the relationship between mRNA abundance and protein abundance and ways to infer the mechanisms for when these are not related.
Databases 
  • Rfam - the RNA families database
  • RMfam - the RNA motif families database

Datasets

  • AREBA - RNAseq datasets and analysis tools for bacteria and archaea
  • Bird ncRNAs -  annotations and analysis results for 48 bird genomes
  • BRalibase - datasets for benchmarking bioinformatic tools for RNA analysis 
  • Metabenchmark - datasets for benchmarking metagenome analysis tools (alternative link)

 

Software

  • TIsigner & SoDope design optimised mRNA sequences for expression and solubility
  • RNIE - an annotation tool for bacterial Rho independent terminators
  • RMfam - annotate RNA structure motifs in alignments and genomes
  • Ribo - an RNA alignment game, Candy Crush with a purpose (developed in collaboration with Jérôme Waldispühl)
  • MASTR - Multiple Alignment of STructural RNA

Crowd-sourcing science


Funding

Our research is funded by generous support from a Rutherford Discovery Fellowship, MBIE Smart Ideas, The Marsden Fund, The Bio-Protection CoRE and The Biomolecular Interaction Centre.