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Mathematical analysis and data integration for clinical trials


   Nuffield Department of Medicine

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  Prof H Byrne, Prof Heather Harrington , Prof X Lu  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

Laboratories

 

The student will be supervised by Professors Heather Harrington, Helen Byrne and Xin Lu. Harrington and Byrne are mathematicians, interested in mechanistic understanding of complex biomedical systems like cancer, and develop mathematical and data analysis approaches to study them. The Lu lab identifies molecular mechanisms that control cellular plasticity and suppress tumour growth

 

Project

The Emerson Collective joint with the Ludwig Institute is supporting the mathematical study of data from a checkpoint-inhibitor immunotherapy cancer clinical trial. Deep phenotyping data from two cohorts are available from this clinical trial. When sample sizes are small and the data inherently complex (i.e. nonlinear relationships), standard machine learning approaches are not suitable. Thus, a new approach is needed to analyse and integrate data from deep phenotyping of small numbers of patients. The student will develop mechanistic models to study patient cohort dynamics and outcomes and also study the genomic data using data analysis techniques involving networks and/or higher-order network structures, and potentially topological data analysis approaches.

Training

In this project, clinical trial data will be analysed. The student will be trained in mathematical modelling, data analysis, computing, genomics, as well as related immune and oncology topics.

References

Otter, N., Porter, M.A., Tillmann, U. et al. A roadmap for the computation of persistent homology. EPJ Data Sci. 6, 17

(2017). https://doi.org/10.1140/epjds/s13688-017-0109-5

Peña-Chilet, M., Esteban-Medina, M., Falco, M.M. et al. Using mechanistic models for the clinical interpretation of complex genomic variation. Sci Rep 9, 18937 (2019). https://doi.org/10.1038/s41598-019-55454-7


Funding Notes

Funding will be provided for course fees at the home rate. There will be an annual tax free bursary of £20,000 pa for 4 years. Further guidance on fees rates https://www.ox.ac.uk/admissions/graduate/fees-and-funding/fees-and-other-charges/fees
APPLICATIONS SHOULD BE MADE ONLINE TO THE MATHEMATICAL INSTITUTE at https://evision.ox.ac.uk/urd/sits.urd/run/siw_ipp_lgn.login?process=siw_ipp_app_crs and should include a CV, cover letter (1 page), 2-3 reference letters, and transcript(s) of all previous degrees. In the section of the application form “Departmental Studentship Applications” applicants will be asked whether they are applying for an advertised studentship. In this section please state “Yes” followed by “22MATH02WEB”.
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