Tim specialises in systems biology and metabolic modelling

​My research centres around the development and application of modelling techniques to study the metabolism of various organisms, with a particular interest in industrial biotechnology. In particular, I use a combination of multi-'omics data and metabolic models to deeply characterise the phenotypes of organisms to understand how they are functioning and why, and importantly, how they can be modified to achieve a more desirable phenotype (for example, produce more of a product of interest). Currently I am working on a project which seeks to use cyanobacteria, a photosynthetic bacteria that uses carbon dioxide as a carbon source and light as an energy source,  to produce commercially valuable products.

​Tim completed his PhD under the supervision of Prof. Lars Nielsen and Assoc. Prof. Esteban Marcellin in 2018, where he applied systems biology and metabolic modelling to study propionic acid production in Propionibacteria in an ARC Linkage Project with Dow. After his PhD, Tim worked in the Queensland-Metabolomics and Proteomics facility at AIBN where he provided a service analysing and integrating 'omics data with metabolic models. As part of this role, Tim worked on a project with Amyris where he utilised kinetic models to rationally guide the design of yeast strains to be built at the Amyris genome foundry, characterising around 250 strains in total. In 2022, Tim transitioned to a new appointment in the Centre of Excellence for Synthetic Biology at the AIBN where he is currently working with BondiBio to engineering cyanobacteria, as well as leading a modelling team for IDEAbio, a synthetic biology service which helps guide strain design for the enhanced production of bio-based products

Key Publications

McCubbin T, Gonzalez Garcia R, Palfreyman R, Stowers C, Nielsen L, Marcellin E: A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversity. BMC Genomics. 2020

Navone L, McCubbin T, Gonzalez-Garcia R, Nielsen, L, Marcellin E: Genome-scale model guided design of Propionibacterium for enhanced propionic acid production. Met. Eng. Comm. 2018

Mahamkali V, McCubbin T, Beber M, Noor E, Marcellin E, Nielsen L: multiTFA: a Python package for multi-variate thermodynamics-based flux analysis. Bioinformatics. 2021


Featured projects Duration
Queensland Strain Factory