John Whittaker

Contact

John Whittaker – john.whittaker@mrc-bsu.cam.ac.uk

Potential PhD Projects

I am interested in supervising projects developing and applying statistical methods to high dimensional data, to understand the causal mechanisms underlying human disease, and to inform on the development novel therapies. I’m particularly interested in the statistical problems arising in the integration of multiple data types, for instance population scale genetic/genomic data, phenotypic data from electronic health records and other types of ‘omics, together with lab scale data eg from gene editing perturbations of cellular models.

Examples of the sorts of questions we might try to address are:

1. Can we develop better statistical methods to understand clonality in tumour samples or cancer cell lines, and hence better predict response to treatment in people?
2. How best should we use human genetics in drug discovery? We think drug targets that are “genetically supported” by a particular definition are more likely to succeed, but there are many ways we could define “genetically supported”—which is best? How can we integrate other data, eg combining genetics with measurements of protein levels or gene expression, and how can we “borrow” information across genes with similar functions?
3. Can we build statistical models integrating the data types above to predict what will happen if we modulate a given human protein? In particular, will we get a therapeutic effect that would suggest a drug discovery programme is justified? Even poorly predictive models could be an important contribution to drug discovery, given the failure rate of such programmes is >95%.

Projects would typically be in collaboration with biologists, epidemiologists and clinicians at Cambridge or elsewhere, in particularly at CRUK Cambridge, the Wellcome Sanger Institute and Harvard Medical School.  A wide range of statistical methods might be applied, from simple regression based models to the biostatistical application of AI/ML approaches.   Ideas around causality are often key, and I prefer to work in the Bayesian framework where possible.

How to apply

For details of the MRC BSU application process please see How to apply

To be considered for funding applications need to be submitted to the University of Cambridge application system by 23:59 (GMT) on January 5th 2023