Dr Massey has been developing methods to assess metabolic flux through a microbial community from shotgun metagenomic data, by reconstructing ‘meta-metabolomic networks’ which show the relative abundance of genes encoding enzymes involved in the different metabolic pathways present. The approach involves large scale Blast searching of millions of individual sequences using grid computing, assignment of metabolic function to the identified sequence homologs, calculation of relative redundancy from the dataset, and calculation of overall flux using the kinetic rate constants of reference enzymes taken from the literature. The overall aim of this project is to assess differences in carbon flux from diverse habitats around the world, with an emphasis on methanogenesis. Data will be obtained from the MG-RAST database and selected for variation in latitude, temperature, and aerobicity. Students will learn a range of command line driven techniques for conducting both local and remote analyses, and will learn how to manage and parse very large data sets.
Dr. Massey is a bioinformatician with a wide range of interests, in genome evolution, metagenomics, organismal complexity, genetic code evolution, evolutionary medicine and ancient DNA.