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- Associate Professor Paul Gardner, Associate Professor Alex Gavryushkin
We are seeking a highly motivated PhD candidate to join an interdisciplinary research team at the University of Otago, to work on a project in genomic data science. The project is fully funded by a MBIE Data Science grant, including a stipend.
About the project
One of the strongest signatures of a functional genomic region is evolutionary conservation. While conservation is relatively straightforward to measure in protein coding and essential ncRNAs, it is considerably more difficult to quantify in more ephemeral non-coding elements such as promoters, enhancers and long non-coding RNAs. The constraints on these regions can be protein or RNA interactions or structure, each of which may be maintained while displaying low sequence conservation.
While some groups consider genomic activity such as expression, modifications or interactions to be sufficient evidence for function, recent experiments with randomised genome sequences show that these activities can be noisy. Therefore identifying evidence that evolutionary selection is acting to maintain an activity provides stronger evidence of function than activity alone. However, sequence alignment based conservation tools (e.g. PhyloP, GERP, etc.) may not perform well at identifying signatures of purifying selection in non-coding portions of the genome. Other sources of information such as higher order models of sequence evolution, INDEL and transposons free regions, synteny, interactions or structure may provide more robust evidence of evolutionary conservation.
The successful applicant will explore possible approaches to measure evolutionary conservation in the non-coding genome that best distinguish between functional and non-functional. We will develop and use rigorous statistical models to assess the likely functionality of non-coding sequences.
The successful applicant will have a BSc(Hons) degree or an MSc degree, or equivalent, in fields relevant to Bioinformatics. The applicants must meet the criteria for enrolment in the PhD programme at the University of Otago.
The successful applicant will receive a stipend of NZ$35,000 per annum, in addition to tuition fees. The tenure of the PhD scholarship is 3 years.
How to apply
Applications should include a full CV, brief cover letter, an academic transcript, and the names and contact details of at least two referees. Applications should be sent by email to:
Associate Professor Paul Gardner
Associate Professor Alex Gavryushkin
Please include the code “MBIEDSNC” in the subject line of your application.
ContactAssociate Professor Paul Gardner
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