Supervisors

Lead Supervisor: Dr Eilis Hannon, University of Exeter, Department of Medicine

Co-Supervisors: 

Professor Jonathan Mill, University of Exeter, Department of Medicine

Dr Amy Webster, University of Exeter, Department of Medicine

Dr Josine Min, University of Bristol, Department of Medicine

The GW4 BioMed2 MRC DTP is offering up to 21 funded studentships across a range of biomedical disciplines, with a start date of October 2025.

These four-year studentships provide funding for fees and stipend at the rate set by the UK Research Councils, as well as other research training and support costs, and are available to UK and International students.

About the GW4 BioMed2 Doctoral Training Partnership

The partnership brings together the Universities of Bath, Bristol, Cardiff (lead) and Exeter to develop the next generation of biomedical researchers. Students will have access to the combined research strengths, training expertise and resources of the four research-intensive universities, with opportunities to participate in interdisciplinary and 'team science'. The DTP already has over 90 studentships over 6 cohorts in its first phase, along with 58 students over 3 cohorts in its second phase.

The 120 projects available for application, are aligned to the following themes;

• Infection, Immunity, Antimicrobial Resistance and Repair

• Neuroscience and Mental Health

• Population Health Sciences

 

Applications open on 10th September 2024 and close at 5.00pm on 4th November 2024.

Studentships will be 4 years full time.  Part time study is also available.

Project Information

Research Theme: Population Health Sciences

Summary: The epigenome’s dynamic nature and it’s responsiveness to environmental changes make it particularly attractive in the study of health and disease. This interest has resulted in various technologies for mapping it in individual samples, such as microarrays and Nanopore sequencing. This data science project aims to optimize and combine the benefits of these technologies to generate detailed maps of the epigenome across multiple individuals. By doing so, we can better understand how to make best use of the tools available to advance our understanding of how the epigenome influences the development of disease.

Project Description:

Description Background:

Genetic studies have concluded that gene regulation, which controls when and in which cells a gene is active, is a key mechanism for understanding the development of diseases such as Alzheimer’s disease, diabetes, and heart disease. The epigenome is a key component of gene regulation. It consists of a diverse range of modifications that attach to DNA and manipulates when and where genes are active. Unlike your DNA which stays the same throughout life, the epigenome is dynamic. It changes in response to both genetics and the environment. Therefore, it is of significant interest to researchers aiming to identify which genes play a role in the development of disease. This interest has been noticed by biotechnology companies, and there are multiple tools available to profile the epigenome. This includes Illumina microarrays which are affordable for large numbers of samples but only profile a small fraction (3%) of the epigenome and Oxford Nanopore sequencing which is very expensive but data rich giving an almost complete map of the epigenome in a single sample. The overarching objective of this data science PhD project is to determine the optimal approach for generating the most comprehensive map of the epigenome across multiple individuals while minimising experimental cost. This will look to combine the technologies available, harnessing their individual strengths and propose a strategy that could be applied to identify novel differences in the epigenome associated with disease and the genes affected by these.

Specific objectives:

1. Develop a framework for using Nanopore sequencing to identify positions in the epigenome associated with disease. This will involve using simulations to model the effect of sample size and magnitude of effect on experimental parameters such as statistical power, true positive rate, false positive rate and financial and computational cost.

2. Evaluate the use of imputation to bridge between microarray and sequencing technologies to provide comprehensive maps of the epigenome in multiple individuals. Characterise how the amount of data from each technology influences accuracy and statistical robustness to determine the optimum study design.

3. Assess the performance of commonly used epigenetic biomarkers (e.g. epigenetic clocks and algorithms to predict smoking status, protein abundance, cellular composition) in Nanopore sequencing data. Propose strategies for translating these tools typically developed using data from microarrays to sequencing based technologies.

4. Apply these findings to an epigenetic epidemiology question of the students choosing. This could be to identify positions in the epigenome associated with a specific disease such as diabetes or Alzheimer’s disease or that change in response to an environmental exposure such as cigarette smoking or air pollution.

While objective 4 is completely open for the student to customise to suit their own specific interests, it should be noted that objectives 1-3 are not sequential. Therefore, the student will have opportunity to prioritise these, depending upon not only their interest but the skills and techniques they want to develop. The project will involve a combination of data simulations and analysis of existing data. These data are available not only through the supervisory team and their networks, but there is additionally a lot of appropriate data in the public domain. This resource again provides the student with an opportunity to tailor the direction of the project depending upon the data they find.

What we are looking for:

This project would suit someone interested in developing advanced bioinformatics and data science skills. The student will be immersed in the dynamic and rapidly evolving fields of epigenetics and epidemiology while having the opportunity to work with cutting-edge technologies like Nanopore sequencing. At the end of the project the student will have acquired a host of highly desirable transferable skills. We can offer you the opportunity to work with large datasets on high-performance computing clusters, to sharpen up your coding skills in UNIX, R and/or Python and to master statistical analysis. There will be a strong emphasis on open and reproducible practices throughout, providing insight into collaborative software development using version control.

Funding

This studentship is funded through GW4BioMed2 MRC Doctoral Training Partnership. It consists of UK tuition fees, as well as a Doctoral Stipend matching UK Research Council National Minimum (£19,237 p.a. for 2024/25, updated each year).

Additional research training and support funding of up to £5,000 per annum is also available.

Eligibility

Residency:

The GW4 BioMed2 MRC DTP studentships are available to UK and International applicants. Following Brexit, the UKRI now classifies EU students as international unless they have rights under the EU Settlement Scheme. The GW4 partners have agreed to cover the difference in costs between home and international tuition fees. This means that international candidates will not be expected to cover this cost and will be fully funded but need to be aware that they will be required to cover the cost of their student visa, healthcare surcharge and other costs of moving to the UK to do a PhD.  All studentships will be competitively awarded and there is a limit to the number of International students that we can accept into our programme (up to 30% cap across our partners per annum).

Academic criteria:

Applicants for a studentship must have obtained, or be about to obtain, a first or upper second-class UK honours degree, or the equivalent qualification gained outside the UK, in an appropriate area of medical sciences, computing, mathematics or the physical sciences.  Applicants with a lower second class will only be considered if they also have a Master’s degree. Please check the entry requirements of the home institution for each project of interest before completing an application. Academic qualifications are considered alongside significant relevant non-academic experience.

English requirements:

If English is not your first language you will need to meet the English language requirements of the university that will host your PhD by the start of the programme. Please refer to the details in the following web page for further information https://www.exeter.ac.uk/study/englishlanguagerequirements/

Data Protection

If you are applying for a place on a collaborative programme of doctoral training provided by Cardiff University and other universities, research organisations and/or partners please be aware that your personal data will be used and disclosed for the purposes set out below.

Your personal data will always be processed in accordance with the General Data Protection Regulations of 2018. Cardiff University (“University”) will remain a data controller for the personal data it holds, and other universities, research organisations and/or partners (“HEIs”) may also become data controllers for the relevant personal data they receive as a result of their participation in the collaborative programme of doctoral training (“Programme”).

Further Information

For an overview of the MRC GW4 BioMed programme please see the website www.gw4biomed.ac.uk

Entry requirements

Academic Requirements

Applicants for a studentship must have obtained, or be about to obtain, a first or upper second-class UK honours degree, or the equivalent qualification gained outside the UK, in an appropriate area of medical sciences, computing, mathematics or the physical sciences. Applicants with a lower second class will only be considered if they also have a Master’s degree. Please check the entry requirements of the home institution for each project of interest before completing an application. Academic qualifications are considered alongside significant relevant non-academic experience.

English Language Requirements

If English is not your first language you will need to meet the English language requirements of the university that will host your PhD by the start of the programme. Please refer to the relevant university website for further information.  This will be at least 6.5 in IELTS or an acceptable equivalent.  Please refer to the English Language requirements web page for further information.

How to apply

A list of all the projects and how to apply is available on the DTP’s website at gw4biomed.ac.uk.  You may apply for up to 2 projects and submit one application per candidate only.

Please complete an application to the GW4 BioMed2 MRC DTP for an ‘offer of funding’.  If successful, you will also need to make an application for an 'offer to study' to your chosen institution.

Please complete the online application form linked from our website by 5.00pm on Monday, 4th November 2024.  If you are shortlisted for interview, you will be notified from Friday, 20th December 2024.  Interviews will be held virtually on 23rd and 24th January 2025.

Further Information

For informal enquiries, please contact GW4BioMed@cardiff.ac.uk

For project related queries, please contact the respective supervisors listed on the project descriptions on our website.

Summary