Meet visiting PhD student Ian Tsang, who is doing a three-month work experience placement with the Ensembl Plants team. We talked all about his PhD, what projects he is working on during his time in Ensembl and what he does during his free time.
What’s your PhD research about and why is it important?
My PhD project focusses on Triticum aestivum (wheat) trait genetics. Specifically, I work on investigating root hair development in wheat. Root hairs are very small, fine hair projections on root surfaces, and they are critical for nutrient and water uptake in plants. To date, most fundamental knowledge on root hair development has been in the model plant Arabidopsis, and translating this knowledge to a much more complex species, like wheat, is challenging. My work aims to investigate how root hair development occurs and is regulated in wheat, as well as investigating the natural variation in root hair morphology across available wheat cultivars, with the ultimate goal of targeting root hairs as an exploitable trait for future wheat improvement.
Why did you choose to do a placement at Ensembl?
During my PhD, I discovered how much I enjoy bioinformatics and programming. Having come from a biology background, I wanted to experience what bioinformatics was like on an industrial scale, before I knew whether to fully commit to a career in this field. For my PhD work, I routinely used Ensembl Plants on a daily basis, and I always loved how many features were available and the wealth of information presented to users. When I had to decide where to spend my three-month placement, I knew that an opportunity to work at EMBL-EBI with the Ensembl Plants team would be extremely beneficial for my research and my future career. It would provide me with a new set of skills and help enhance my existing skills in Python and SQL, and also allow me to meet and learn from many vastly more experienced bioinformaticians than myself!
What are you working on and how long is your placement at Ensembl?
During my three-month stay, I will be working on a few different projects. On the production side, I have been working on using internal pipelines to upload the new barley pangenome to Ensembl, which consists of 76 primary accessions. On the side, I have been working on scripts/recipes to mine useful data from Ensembl Plants. As a user of Ensembl, there were certain ideas and features that I wanted to retrieve during my research that were unavailable or difficult to access through the website. The scripts I am writing will help other users access data in a high-throughput manner with next to no required knowledge of Python, SQL or API. I will also be working on rice pangene IDs, and also helping the Ensembl Outreach team with some teaching!
How did you get into bioinformatics?
As you can probably tell from my answer on my PhD research, my PhD is not bioinformatics-focussed! Before I started my PhD, I knew nothing about programming or bioinformatics – I only knew how to use ggplot2 in R. At the very beginning of my PhD, I inherited a large amount of wheat exome and RNAseq data, and I had to spend the best part of my first year learning bioinformatics, from learning to use the HPC and Python to process and analyse this data. I very quickly realised how much I enjoyed bioinformatics compared to wet lab work, and have since been steering my PhD more and more towards bioinformatics. This early realisation in my PhD has helped me decide that I want to pursue a career in bioinformatics.
What do you enjoy doing outside of work?
I love cars, and I spend most of my free time thinking about and looking at cars on Autotrader. If I’m not looking at cars, I’m probably buying car parts on eBay or tinkering with my car here and there. Aside from cars, I routinely go to the gym, run and play video games with my friends.
Do you have a hidden talent or skill that most people don’t know about?
This is a very random hidden talent, but I have perfect pitch. It’s an innate ability that allows me to immediately recognize any musical note, or determine the key of a song, without any reference. In essence, it’s like how most people can identify colours immediately, but I can do it with musical notes. It allows me to tell if anything is out of tune, whether it’s a song or an instrument that’s not been tuned/calibrated. It was very helpful growing up when I was learning musical instruments!