The research interests of our group are broad. We work on multiple projects that range from the annotation of genomes (currently birds, tuatara, giant squid and phytophthora) to the (RNA) origin of life. We enjoy benchmarking and improving bioinformatic software, as this is important for the community of bioinformatic software users. We spend a lot of time analysing very large 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
  • MASTR - Multiple Alignment of STructural RNAs
  • Ribo - an RNA alignment game, Candy Crush with a purpose (developed in collaboration with Jérôme Waldispühl)
  • RNIE - an annotation tool for bacterial Rho independent terminators
  • Webserver - online interface for RNIE and RMfam searches 

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.