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The journey of my Master’s project

By Mandhri Abeysooriya

I was initially introduced to field of bioinformatics during my Bachelor’s degree.

Main reason why I selected Deakin University to do my masters is because Deakin offers Master’s in biotechnology and Bioinformatics. When it was time to choose a topic of interest for the final year project, I hesitated a bit to choose bioinformatics based projects since I had more experience in wet labs rather than dry labs. Athough I was not confident to choose a dry lab-based project, I also wanted to gain more experience in computational biology.

Dr. Mark Ziemann was the unit chair for the “Research impact and management” unit during my first semester and I learned he was an active researcher in bioinformatics. His teaching skills were so remarkable that even after 2 years of time, I still remember most of the details of that unit he taught us (and moreover I do remember that he marked our assignments so accurately that he even reduced marks for the missing punctuation!). This made me realise that he is a perfectionist in the work he does. The fact that he is an expert in Bioinformatics as well as he is being a perfectionist in the work he does, I arrived at the conclusion that I am in good hands if I want to improve my bioinformatics skills.

I am an individual who is keen in learning new things and not shy to take on new challenges. I have never in my life coded in any computer language before. I remember during the initial weeks of my Master’s project, I used to sit by my desk from the morning till night and work on improving my coding skills in R language. It was because of my dedication and my supervisor’s systematic and methodical guidance that I was able to excel coding in R and my bioinformatics skills more broadly.

My final year project was supposed to be “A meta-analysis on the effect of homocysteine in DNA methylation and gene expression”. I was not able to conduct the proposed meta-analysis due to unavailability of most of the published datasets. We were only able to find one data set via GEO through a paper published by Kok et al (2015), and of the remaining 8 publications, were unable to obtain the corresponding microarray datasets which was very disappointing.

Therefore, I had to adopt to the situation where my final year project composed of two mini projects titled as “An assessment of the association of homocysteine of DNA methylation” and “Gene name errors: Lessons not learned”.

Via the first mini project, I was so fascinated with all the data I was able to produce, and this mini project related to homocysteine and DNA methylation made me realise that there are much more towards the genetics than what I have known through all my life.

My second mini project was based on erroneous gene symbol conversion to dates in supplementary data files. I used to be a fan of Microsoft Excel, but I never knew the fact that Excel could alter data like this. I was quite shocked to see how many world-renowned journals contained so many errors in their supplementary files. I came to know that gene symbol alteration could impact the data and research reproducibility.

Growing up, I was not certain as to what I want to do with my life or what type of a career I want to pursue. For most of my life, I was given a syllabus and was instructed to follow so. I have learnt so much during my Master’s course at Deakin, and I am so happy that the hard work I have put in is starting to open up new opportunities for me to begin a PhD project. This Master’s research project with Dr Ziemann opened my eyes to a whole new horizon of knowledge.

For the first time, I now know what I want to do with my life and what type of career I want to pursue.


Kok, D. E. G. et al. (2015) “The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects,” Clinical epigenetics, 7(1), p. 121.

Abeysooriya, M. et al. (2021) “Gene name errors: lessons not learned,” bioRxiv. doi: 10.1101/2021.03.30.437702.