Identification of drivers of somatic evolution using machine learning

Application deadline: 31 January 2024

Start date: April 2024

This Barts Charity funded project will commence in April 2024 and has funding for 4 years. The successful candidate will be based at Barts Cancer Institute, Faculty of Medicine and Dentistry (FMD), Charterhouse Square in the City of London.

Primary Supervisor: Prof Francesca Ciccarelli

Centre for Cancer Genomics and Computational Biology

Recent high-throughput sequencing screens coupled with computational analysis have revealed that seemingly normal tissues progressively acquire genetic alterations in the genome of their cells much before showing any sign of cancer transformation. These mutant cells expand into mutant clones but may never become cancer. What drives this expansion and when do these healthy clones transform into cancer clones? This PhD project aims to address these questions, which are key to understand the early phases of cancer initiation. The approach that we will use relies on systems biology and machine learning. In particular, the student will analyse the mutant genomes of hundreds of healthy individuals and will develop a classifier to recognise mutational patterns associated with the clonal expansion of the mutant cells. Using systems biology and the principle of computational cancer genomics, they will then predict what mutations are causative of the transformation of healthy mutant cells into cancer cells.

The ideal candidate will have a background in computer science or statistics. Some knowledge in ML and/or data classification and/or cancer biology will be favourable.

Our lab is partially seconded at the Francis Crick Institute and the student will have access to seminars, courses and workshops held at the Barts Cancer Institute, QMUL and the Francis Crick Institute. They will have access to state of the art high performance computer cluster fully dedicated to the analysis of cancer data supported by Cancer Research UK City of London Centre.

Academic Entry Requirements

All applicants should have or be expecting:

  • A first or upper second class honours degree in a relevant biological subject from a UK university or the international equivalent from a recognised institution. For international equivalencies please see Queen Mary International Office. Or;
  • A medical degree from a recognised institution.

English Language Requirements

Applicants for whom English is not a first language will also require a minimum IELTS score of 6.5 (with 6.0 in the written component) or equivalent, unless your undergraduate degree was studied in, and awarded by, an English speaking country. For more information on acceptable English language qualifications please see here.

Fee Status

The funding for this studentship covers tuition fees both at the Home and Overseas rate.

The studentship includes the following funding for 4 years:

  • A tax-free annual stipend (Year 1: £24,278; Year 2: £26,093; Year 3: £28,057; Year 4: £28,057)
  • Tuition fees at the Home or Overseas rate
  • Project consumables

To apply you will need to complete an online application form. You should select the 'non-clinical' PhD option.

The following supporting documents will be required as part of your application:

  • Your CV
  • Statement of purpose
  • Details of 2 referees
  • Copy of your transcript(s), including a breakdown of marks
  • Copy of your passport
  • If applicable, proof of English proficiency

If you have a question about the project, or would like to arrange an informal discussion, please contact the supervisor directly (subject ‘PhD applicant’). For general enquiries about the PhD studentship or application process please contact the Teaching Office.

Successfully shortlisted candidates will be invited to an interview at Barts Cancer Institute.