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Understanding genome regulation via DNA methylation and enhancer interactions in cancer


Department of Mathematics and Statistics

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Dr Matt Parry , Dr A Chatterjee Applications accepted all year round Competition Funded PhD Project (Students Worldwide)

About the Project

Gene expression changes are likely in cancer patients, as well as methylation changes. However, there is a paucity of enhancer data for cancer patients. Can we make data-driven predictions for methylation altered enhancers (and as a result gene expression changes) in cancer patients?

Objective 1: Mapping enhancer and DNA methylation co-occurrence patterns in normal cell types

Objective 2: Understanding disrupted DNA Methylation-enhancer networks in cancer

This is primarily a bioinformatics project. However, our lab aims to seamlessly integrate computational analysis with laboratory experiments to establish causality or mechanistic basis of initial findings.

The candidate needs to have bioinformatics, statistics and programming skills. Further development of these skills will occur during the PhD. The candidate will work as part of a team and will interact and benefit from regular interactions with other scientists.





Funding Notes

The University of Otago awards generous scholarships and fees waivers to candidates on a competitive basis. The awards are open to all international students. As well as a strong background in bioinformatics, statistics and programming, proficiency in written and spoken English is essential.

References

https://academic.oup.com/bioinformatics/article/30/13/1814/2422202

https://www.sciencedirect.com/science/article/pii/S1044579X17300536

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351615/
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