Don't miss our weekly PhD newsletter | Sign up now Don't miss our weekly PhD newsletter | Sign up now

  Combining genome-scale metabolic models and multi-omics data for a system level understanding of bacteria

   Institute of Systems, Molecular and Integrative Biology

This project is no longer listed on and may not be available.

Click here to search for PhD studentship opportunities
  Dr Francesco Del Carratore, Prof R Goodacre, Prof Steve Paterson  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Understanding microbial metabolism is essential for the exploitation of bacteria in a number of different biotechnological applications, the members of the Streptomyces genus being a particularly biotechnologically interesting example (Del Carratore et al., 2022).

Genome-scale metabolic models (GSMMs) are mathematical models designed to represent the whole metabolic network of a given organism. They are used to predict growth rates and metabolic fluxes under different conditions, and they can be exploited to identify genetic engineering strategies (Gu et al., 2019).

Multi-omics data refers to the data generated by different omics such as genomics, transcriptomics and metabolomics. The data obtained through these molecular profiling experiments provide extremely useful information on dynamic cellular processes governing an organism and can be used to validate and refine GSMMs. At the same time, well-curated GSMMs provide the perfect framework for the integration and interpretation of multi-omics datasets (Del Carratore et al., 2021).

This project aims to develop the computational methods needed to gain a system-level understanding of the metabolism of specific bacterial strains, by combining GSMMs with multi-omics data.

You will be based in Liverpool in the Institute of Systems, Molecular and Integrative Biology, host of some of the world’s best facilities for metabolomics, genomics, proteomics and computational biology (

This research project comes with a multi-disciplinary training revolving around computational biology and data analysis of big biological data. This will provide you highly transferrable skills and a wide choice of career options.

You will have at least a good B.Sc. 2:1 in Biological or Life Sciences, Computer Science or Engineering. Previous experience in programming is an advantage. Informal enquiries to [Email Address Removed] are welcome.


Biological Sciences (4) Mathematics (25)

Funding Notes

The project is open to both European/UK and International students. It is UNFUNDED and applicants are encouraged to contact the Principal Supervisor directly to discuss their application and the project.
Assistance will be given to those who are applying to international funding schemes.
The successful applicant will be expected to provide the funding for tuition fees and living expenses.
A £2000 ISMIB Travel and Training Support Grant may be available to new self-funded applicants who are paying for their own tuition fees
Details of costs can be found on the University website:


Del Carratore, et al. "Biotechnological application of Streptomyces for the production of clinical drugs and other bioactive molecules." Current Opinion in Biotechnology 77 (2022): 102762.
Del Carratore, et al. "Multi-omics study of Planobispora rosea, producer of the thiopeptide antibiotic GE2270A." MSystems 6.3 (2021): e00341-21.
Gu, et al. "Current status and applications of genome-scale metabolic models." Genome Biology 20 (2019): 1-18.

Where will I study?

Search Suggestions
Search suggestions

Based on your current searches we recommend the following search filters.