Characterisation of cell-fraction specific DNA methylation of tumours using Nanopore sequencing, [Epigenetics/Data Science] – PhD (Funded)


   Department of Biosciences

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  Dr Amy Webster, Dr E Hannon  No more applications being accepted  Funded PhD Project (Students Worldwide)

About the Project

Project Description:

Epigenetics is the study of modifications of the DNA which alter how it is used. Epigenetic patterns are known to be disrupted in cancer development, however cellular heterogeneity of tumours has limited the resolution at which we can understand these patterns and their impact on disease development. Understanding the molecular patterns in tumours can give insight into the most appropriate treatment strategies for a particular patient (in a precision medicine approach), and can uncover novel therapeutic targets.

Long-read sequencing (LRS) technologies, for example Oxford Nanopore Technologies, allow us to investigate the genetic and epigenetic patterns at single-read resolution simultaneously for the first time. In this project, we aim to use the cell-specific epigenetic patterns to separate cell fractions from large whole genome sequence-based datasets. This project will involve working with large datasets at the forefront of genomic sequencing technologies by developing novel methods to analyse LRS data and provide a unique insight into tumour biology. The project offers an opportunity for a computational or mathematical graduate to develop skills in bioinformatics and knowledge of molecular gene regulatory processes by working within a multidisciplinary team at the University of Exeter and collaborations with internationally recognised leaders in the field at the University of Oxford.

The studentship will address a significant gap in cancer (epi)genomics and will improve our understanding of the fundamental processes that affect tumour development. There will be opportunities to develop novel analytical approaches within the infrastructure of the research team, and the student will receive extensive training including, genomic data processing, handling of large dataset, statistical analysis, and ethics. Importantly, the student will be part of an active research environment where support and supervision from experienced academics and peers will be abundantly available. In addition, the student will benefit from the extensive training and development opportunities available from the Exeter Doctoral College. 

This award provides annual funding to cover Home tuition fees and a tax-free stipend.  For students who pay Home tuition fees the award will cover the tuition fees in full, plus at least £18,622 per year tax-free stipend. Students who pay international tuition fees are eligible to apply, but should note that the award will only provide payment for part of the international tuition fee (~£23k) and no stipend.  

International applicants need to be aware that you will have to cover the cost of your student visa, healthcare surcharge and other costs of moving to the UK to do a PhD. 

The conditions for eligibility of home fees status are complex and you will need to seek advice if you have moved to or from the UK (or Republic of Ireland) within the past 3 years or have applied for settled status under the EU Settlement Scheme.

 Entry requirements:

Applicants for this studentship must have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. We are seeking applicants who are comfortable working with large datasets and who have some experience of coding, ideally with Python or equivalent language.

If English is not your first language you will need to meet the required level as per our guidance at https://www.exeter.ac.uk/pg-research/apply/english/

How to apply:

In the application process you will be asked to upload several documents. 

  • CV
  • Letter of application (outlining your academic interests, prior research experience and reasons for wishing to undertake the project).
  • Two references from referees familiar with your academic work. If your referees prefer, they can email the reference direct to [Email Address Removed] quoting the studentship reference number.
  • If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English.

The closing date for applications is midnight on 7th December 2023.  Interviews will be held virtually / on the University of Exeter St Luke’s Campus in the week commencing 11th December. 

If you have any general enquiries about the application process please email [Email Address Removed] or phone 0300 555 60 60 (UK callers) +44 (0) 1392 723044 (EU/International callers)  Project-specific queries should be directed to the main supervisor [Email Address Removed].

This same scholarship can be found on the Exeter University website, please follow this link - Award details | Funding and scholarships for students | University of Exeter


Biological Sciences (4) Computer Science (8) Mathematics (25)

Funding Notes

Department of Clinical and Biomedical Sciences, St Lukes Campus, Exeter.
The University of Exeter’s Department of Clinical and Biomedical Sciences is inviting applications for a PhD studentship fully-funded by the Faculty of Health and Life Sciences to commence on 8 January 2024 or as soon as possible thereafter. For eligible students the studentship will cover Home tuition fees plus an annual tax-free stipend of at least £18,622 for 3 years full-time, or pro rata for part-time study.

Where will I study?

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