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Improving the power of genetic studies for complex diseases with deep learning

  • Full or part time
  • Application Deadline
    Friday, April 17, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

This project is one of 16 four year PhD Studentships funded by Medical Research Scotland (https://www.medicalresearchscotland.org.uk) to be delivered jointly by the named University and External Partner Organisation (EPO). The Studentship will provide the first-class academic and additional training provided by the EPO needed to equip the successful candidate for a science career in an increasingly competitive market.

The project, "Improving the power of genetic studies for complex diseases with deep learning" is to be delivered by the University of St Andrews [Supervisors: Dr Silvia Paracchini http://neurogenetics.st-andrews.ac.uk/ (School of Medicine), Dr John Thomson (School of Computing)] and Canon Medical Research Europe Ltd (https://research.eu.medical.canon/) [Company supervisor: Dr Ian Poole].

It will build on a three-way interdisciplinary partnership between Dr Paracchini and Dr Thomson, who are investigating the application of machine learning (ML) methods on genomics data, and Dr Poole, principal scientist at Canon Medical Research Europe Lt) based in Edinburgh,who brings expertise in the development and application of ML approaches in an industrial setting.

The project
The field of genomics has made huge advances for a number of diseases for which large sample sets (e.g hundreds of thousands) can be achieved. This is not the case for all conditions including language disorders (e.g. dyslexia, developmental language disorders and stuttering) where only modest size cohorts can be assembled because of the complexity around diagnosis and assessment. In parallel, huge resources of pooled biological information relating to gene interactions and expression are becoming available. Through advanced computational approaches, we will develop novel methods to integrate these valuable functional genomic datasets into gene mapping studies. By making an intelligent use of pooled information, we will reduce the number of tests so that meaningful genetic studies can be carried out on relatively small samples, such as those currently available to study language disorders. However, the tools that we will develop will be applicable to a wide range of diseases.

Training
This project provides a unique training opportunity for the student who, at the end of the PhD, will have the skills to work with large genomic datasets at the interface between medicine, bioinformatics and artificial intelligence (AI). The student will receive training for all scientific areas required by the project and in addition, through internship at Canon Medical Research Europe Ltd, will get exposed to different aspects of research commercialization.

ENQUIRIES:
Enquiries should be sent by email to Dr Silvia Paracchini:


APPLICATIONS:
Applicants must have obtained, or expect to obtain, a first or 2.1 UK honours degree, or equivalent for degrees obtained outside the UK, in an appropriate area. Applications are encouraged from graduates with backgrounds in bioinformatics, biology, statistics, mathematics, computer science and related disciplines.The ideal candidate will have an interest in the genomics of human diseases and an aptitude for computational approaches. Experience of working with genetic data would be highly desirable. A Masters degree in relevant disciplines would be an advantage.

Applicants should send a CV, the contact details of 2 references (including email addresses) and a covering letter, explaining why the applicant wishes to carry out this project, by email to Dr Silvia Paracchini:
.

Please note, your application may be shared with the funders of this PhD Studentship, Medical Research Scotland and Canon Medical Research Europe Ltd.

Interviews are expected to take place 3-4 weeks after the closing date for applications.

It is anticipated that the PhD Studentship will start in September 2020.

Funding Notes

PhD Studentship provides: an annual tax-free stipend of £17,500, increasing to £18,000 over the four years; tuition fees at UK/EU rates only; consumables; and generous travel allowance. International fees are not covered.

References

http://neurogenetics.st-andrews.ac.uk/
https://scholar.google.co.uk/citations?user=sOIVTC4AAAAJ&hl=en

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