PhD Position (with Stipend)

Opportunity: PhD Position (with Stipend)

Research Topic: The Epigenomics of Multiple Sclerosis

Closing date: 22/02/2019

Brief Outline:This project will involve analysis of genome-wide methylation data sets in relation to Multiple Sclerosis (MS) outcomes. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis including the use of novel approaches.

Detailed Description:MS is a common autoimmune disorder that can lead to severe neurological symptoms like such as reduced cognitive function, psychiatric problems and physical disabilities. The disease is complex, arising from the complex interplay of genetic factors and environmental exposures. A major goal in MS research is to understand these gene-environment interactions and to use this information to personalise treatments to improve patient outcomes. Epigenetics is the study of DNA-based factors that can influence gene expression independently of underlying DNA sequence and can be modified by environmental exposures (eg, medicines). As such, epigenetics provides a natural interface for the environment to interact with the genome to influence disease onset, severity and progression. DNA methylation is an one epigenetic mechanism that can now be measured on a genome-wide scale (ie. epigenomics) and has given rise to the epigenome-wide association study (EWAS) design. The MS group at the Hunter Medical Research Institute have been performing MS EWASs for a number of years and have identified a number of exciting findings. Thanks to some newly awarded funding we are now continuing this line of investigation in an effort to identify epigenetic factors that influence MS onset, severity and progression This project will involve analysis of MS EWAS data sets currently being generated using the Illumina Epic Arrays. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis. Specifically, the project will involve using a number of different bioinformatics approaches to address the specific research questions. These include identifying differentially methylated regions with programs like MINFI, cellular deconvolution of methylation signal using custom algorithms, estimation of epigenetic aging using DNAage, and application of machine learning to build predictive models (eg. GLMNet).

Eligibility Criteria: The applicant will have an aptitude and interest in fields including data science, bioinformatics, computational genomics and statistical genetics. A basic knowledge and skills in using linux operating systems, biostatistical methods and R programming to analyse data sets is required. Good written and oral communication skills and the ability to work independently are desirable. The successful applicant will need to be accepted as a PhD student with either UoN or QUT and will receive a scholarship stipend of $27 082 per annum, tax free, indexed annually for 3.5 years. International students may be required to pay university (tuition) fees.

Contact:  For more information on the project and application process please contact Assoc. Professor Rodney Lea (rodney.a.lea@gmail.com) before Jan 29th, 2019.