I'm a bioinforatician currently living in Galway, Ireland. My research interests include genome assembly, pipeline development, comparative genomics, gene regulation, and microbial ecology. Generally speaking, I'm all about finding solution to complex problems. When I'm not working, I like to play music, go rock climbing, and brew beer.

Soil-persistent E. coli

I am working to characterize the strains in a collection of soil-persistent E. coli. The soil from which the strains were isolated had been protected from slurry spreading and other contamination for abut 9 years, providing a unique opportunity to investigate the genomic differences between soil-persistent and non-soil E. coli.

Genome Assembly

riboSeed is a genome assembly pipeline that resolves some of the issues with short-read assembly.

Microbial Ecology

Because riboSeed results in high-quality reconstructions of full-length rDNA operons, we applied it a lots of short read datasets from the SRA database. These sequences were added to existing 16S rRNA databases like SILVA, resulting in increased taxonomic resolution. Find out more at https://github.com/femlab/focusDB.