Debugging Lung Disease: Applying mathematical modelling for a precision medicine approach to the Pulmonary Microbiome Ref: 3053

About the award


Professor Krasimira Tsaneva-Atanasova,College of Engineering, Mathematics and Physical Sciences, University of Exeter.

Assistant Professor Sanjay Chotirmall, Nanyang Technological University, Singapore

About the programme

The University of Exeter (UoE) and Nanyang Technological University (NTU), Singapore are offering six fully funded postgraduate studentships to undertake collaborative research projects at the two institutions, leading to PhD degrees (split-site) to be conferred either by the UoE or NTU.

Students pursuing these postgraduate research projects will benefit from the unique opportunity to conduct their research at both institutions.  Students will be registered at one or other institution, where they will be based for the majority of their time, but will spend at least 12 and not more than 18 months at the partner institution over the duration of the programme.  The frequency and length of stays at each institution will be agreed with successful candidates prior to offers being made.

All six projects are advertised concurrently at both institutions and three will be allocated to each institution after the deadline has passed, based on a collaborative decision made between the UoE and NTU.  The final decision on the successful applicant for each project will be made by the institution hosting the project.  Project allocation will be based on the applicant’s best fit to a project, following a review of applications submitted to each institution.  Applications to undertake the projects at the UoE and NTU are open to all nationalities.
The programme start dates are August 2019 for NTU and September 2019 for UoE
The home institution will determine the regulations that will apply to the successful applicant.  The student’s main supervisor will be based at the home institution.

Project Description:

Understanding how individual people respond to medical therapy is a key facet of improving the odds ratio that interventions will have a positive impact. Reducing the non-responder rate for an intervention or reducing complications associated with a particular treatment is the next stage for any medical advance. The Precision Medicine Initiative, launched in January 2015, set the stage for enhanced collaboration between researchers and medical professionals to develop next-generation techniques to aid patient treatment and recovery, and increased the opportunity for impactful pre-emptive care. The microbiome plays a crucial role in health and disease, as it influences endocrinology, physiology, and even neurology, altering the outcome of many disease states, including its ability to augment drug response and tolerance.

Therefore, in precision medicine, the focus is on the identification of effective approaches for particular patients based on their genetic, lifestyle and environmental factors. Asian and European phenotypes of respiratory disease and infection are unique and therefore require such precision. While such approaches have been successfully employed to investigate contrasting clinical phenotypes; and by disease trajectories, little is known about ‘precision through microbes’. Precision medicine can be applied to the lung microbiome that includes both bacteria and fungi and their associated metabolic states. These ‘microbial fingerprints’ permit patient stratification and we can identify particular disease phenotypes associated to clinical outcomes potentially amenable to precision and individualised intervention. It is clear that our microbes tell us something about disease, something representing a potential target for clinical intervention.

Using a well phenotyped and prospectively curated Asian and European dataset across a variety of chronic inflammatory respiratory disease states including severe asthma, chronic obstructive pulmonary disease (COPD) and bronchiectasis, this PhD project aims to perform the following:

1. Prospectively curate novel datasets focused on the Asian microbiome/mycobiome (and their associated metabolomic profiles) in patients with severe asthma, COPD and their associated overlap syndrome states (e.g. asthma-COPD overlap syndrome and bronchiectasis-COPD overlap syndrome). The candidate will gain experience in sequencing, bioinformatics and mass spectrometry. This work will be performed in Singapore.

2. Model mathematically microbiome and mycobiome populations and their interactions across a range of pulmonary disease states: this will utilize computational approaches to identify mathematically significant co-operative and competitive relationships within and between species. There is a scope for spatio-temporal modelling approaches, which would allow us to account for potential differences in anatomical distribution of the microbiome and mycobiome populations within the lung. This work will be performed in Exeter.

3. Apply the developed model systems to clinical settings in diagnosis, prognosis and predicting disease progression across a range of respiratory disease states This work will be performed in Singapore.

4. Finally, the use of microbial metabolomic datasets will further extend the developed models in order to take into account the affected pathways and signalling networks. This will further power our microbial airway interaction models and provide therapeutic and pharmaceutical relevance to their in vivo relationships. This work will be performed in Exeter.

Please contact the supervisors for project-specific queries.

Entry requirements

Successful applicants will need a good first degree (preferably 1st Class Honours or at least an upper Second class honours, or international equivalent) in a relevant field.  Applicants with a Lower Second Class honours degree may be considered if they also have a Master's degree in a relevant field. 

Candidates applying to the University of Exeter, for whom English is not their first language will also need to satisfy our English language entry requirements, prior to commencing the programme.

How to apply

Please read all of the information below on how to apply to the UoE prior to submitting an application for this project. 

Note enquiries about NTU's application process should be emailed to

In order to apply for funding for this studentship, you must click the 'How to Apply' button on this page.

In the application process you will be required to upload several documents as detailed below;
• CV
• Cover Letter
• 2 References*
• Transcripts
• IELTS or equivalent (if from a non-english speaking country)

Please note our preferred format is PDF, each file named with your surname and the name of the document, eg. “Smith – CV.pdf”, “Smith – Cover Letter.pdf”, “Smith – Transcript.pdf”

The closing date for applications is 31 January 2019.  Interviews are anticipated to be held March 2019, date to be confirmed.

If you have any general enquiries about the application process please email

Please quote reference 3053 on your application and in any correspondence about this studentship.

Reference information
References should be submitted to us directly in the form of a letter. Referees must email their references to us from their institutional email accounts. We cannot accept references from personal/private email accounts, unless it is a scanned document on institutional headed paper and signed by the referee.

It is your responsibility to ensure that your two referees email their references to, as we will not make requests for references directly; you must arrange for them to be submitted by 31 January 2019.

All application documents must be submitted in English. Certified translated copies of academic qualifications must also be provided.

Data sharing
During the application process, the University of Exeter may need to make certain disclosures of your personal data to Nanyang Technological University to be able to administer your application, carry out interviews and select candidates.  These are not limited to, but may include disclosures to:

  • The selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from NTU.
  • Administrative staff at NTU related to the relevant programme.

Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.


Application deadline:31st January 2019
Value:4 year studentship providing tuition fees and an annual stipend allowance at Research Council rates, currently £14,777 per year for 2018-19
Duration of award:per year
Contact: PGR Enquiries