Genomics

Tailed phages contain dsDNA genomes ranging from about 14 kb up to over 600 kb, but most tend to be in the range of 40-300 kb.  Phages are also incredibly diverse, containing a huge amount of sequence with no known function.  Next-generation sequencing platforms like Illumina have allowed us to sequence phage genomes relatively cheaply.  Part of our research focuses on the genomics of phages, as a means to characterize and predict their behavior, and also as an entry point for studying their biology.

Over the past several years, we have helped developed a complete phage annotation pipeline based on the Galaxy platform for analysis and Apollo for visualization.  This is the same system we use for instruction of our Bacteriophage Genomics course, and is available for public use here.  We are also working on getting our tools running on the main EU Galaxy instance, so stay tuned!

Phage therapy

Phages hold great potential as natural antimicrobials.  We are interested right now in phages that infect a number of important pathogens including Salmonella, pathogenic E. coli, Klebsiella pneumoniae, Staphylococcus aureus and Burkholderia.  We are interested in using  genomics to better understand the therapeutic potential of phages, by characterizing the general phage lifestyle, the mutational ability of phages, and identifying novel or interesting phage proteins.