The PhD studentship projects listed below are currently available. Please do read our advice for potential PhD students, if you are considering an application.
Project 1: Comprehensive taxonomy, pangenomics and metabolic modelling of Streptomyces.
Supervised by Leighton, and Prof. Paul Hoskisson
Aim 1: Develop a robust taxonomic classification of the Streptomyces genus
Generate an objective and definitive classification scheme for Streptomyces, which is essential for meaningful comparative genomic and pangenome analysis, and for comparison of whole-genome models.
Aim 2: Pangenome analysis of Streptomyces
Produce a definitive pangenome analysis for Streptomyces, using the classification scheme developed in Aim 1, to elucidate the evolutionary history of the genus, and to underpin genome mining of secondary metabolite synthetic clusters. This will link to a BBSRC TRDF proposal (LP, Dr Kate Duncan, Dr Simon Rogers [Glasgow]) to develop the NPLINKER resource for prediction of secondary metabolite structure from genomic sequence. The data generated in this objective can directly inform development of kernel-based methods for associating BGC sequence with the product metabolite mass spectra in NPLINKER.
Aim 3: Whole-genome metabolic modelling of Streptomyces
Generate whole-genome metabolic models for key Streptomyces groups identified in Aims 1 and 2, to support engineering potential and genome mining for BGCs. Extend these models to incorporate gene-protein-reaction rules to incorporate ‘omic datasets for realistic biological constraints. This work will additionally link to a BBSRC proposal (LP, PH, Dr Nick Tucker) that aims to reconstruct whole-genome regulatory networks from Streptomyces.