Profile: Up close with Assistant Professor Bernett Lee

Since joining LKCMedicine in October, Assistant Professor of Biomedical Informatics Bernett Lee has been steering the Data Science theme towards building a strong core team of bioinformaticians to support the School’s research. Also the Director of the Centre for Biomedical Informatics, Asst Prof Lee shares his love for molecular biology and how data analytics could be used to improve healthcare.

Q: Have you always been interested in science and research?

As a child, the world was a simpler one with less distractions so books offered a window to new and exciting things. I realised that I liked to understand the world around me so I was very interested in books on facts and how things work.

When I entered formal education, naturally the subject that really spoke to me was science as it helped to explain the world around me. Understanding how things work was really fascinating to me. I was very fortunate to have parents who gave me the freedom to pick the subjects and courses which I liked and this is how I started my journey in Science when I undertook a Diploma in Biotechnology in Singapore Polytechnic. Since then, I have been very fortunate to continue on this exciting journey of discovery.

Q: What is it about bioinformatics that you find fascinating?

My love for molecular biology started while pursuing my Diploma in Biotechnology. I was very intrigued by the fact that a simple DNA blueprint could result in a complex human being. This was also a period of time where computers become more commonplace and I was amazed at how much more productive one could be on it.

In my free time, I started learning programming and other computer-related skills like digital design and productivity software. This was mostly to be more productive in school but I soon developed a fondness for it. During my undergraduate years, I came into contact with bioinformatics and realised I had a passion for it as it allowed me to work with computers to better understand the complexity of life.

Since then, technological advances have enabled ever larger amounts of biological data to be collected. In the early years of genomics, all the DNA sequences known to man were printed in books but today, the explosion of genomics data has made this impractical. This explosion of data also meant that trying to understand all these data without the use of computers is next to impossible.

Bioinformatics enable us to apply computational techniques on vast biological data to make insights possible. From being able to understand the implication of a single gene, bioinformatics makes it possible for us to understand the entire complement of genes in the cell. We term this a systems biology approach and it is critical to understanding the complexity of life. The internal workings of a single cell is complex enough with multiple biological entities interacting in complex temporal and spatial patterns. But this is nothing in comparison to the complexity of a human being with 37.2 trillion cells working together.

We will need to collect ever larger bodies of biological data to understand this complexity and this will drive bioinformatics to develop newer and better methods so that we can make sense of the data. So bioinformatics is going to be an extremely important element going forward as we learn more about the inner workings of life.

Bioinformatics is a cross-disciplinary science where we attempt to answer biological questions using computational methods. And because of its cross-disciplinary nature, we work closely with biologists and computer science experts where we learn and understand new biology to identify biological questions and then to translate the biological questions into computational problems so that they can be solved to gain insights. We then interact with biologists to communicate the analytical findings to further refine the biological understanding and to devise new questions to answer.

The nature of our work means that we encounter a wide variety of biology so we are constantly learning something new and exciting. Furthermore, there is a real sense of fulfilment when we see how the analytical results improve our understanding of biology bit by bit.

Q: What is your vision for LKCMedicine’s Data Science research theme and Centre for Biomedical Informatics?

The vision for the research theme and centre is really a simple one and that is to support the research that is being done in the school. To do so, we are putting together a team of bioinformaticians with diverse backgrounds to have a multi-faceted perspective on research problems.

We will also invest in infrastructure especially in the area of compute and storage resources so that we can handle the computation workload. We cannot do everything on our own so we will leverage on the diverse and strong research capabilities in the larger NTU ecosystem to work together collaboratively to advance the research activities in the school. This will also be the case for our clinical partners where we will leverage on their clinical expertise and strengths.

In short, we hope to build a strong core team to directly support research activities while leveraging on collaborative partners to broaden our capabilities and reach.

Q: How will the research make a positive impact on the lives of patients and Singaporeans in general?

The School has made a strong commitment to impactful research and this will certainly require close collaboration with our clinical partners who are on the ground and understand the medical needs. The data science theme, being a cross-cutting theme, will support this by working directly or via the other research themes with our clinical partners to impact medical practices. Hospitals have lots of data and we have an opportunity to work with our clinical partners to apply analytics to better understand the data and draw new insights.

Going forward, digital health, which includes wearables, will allow for more data as well as new types of data that represents more opportunities for data analytics to discover findings that would have an impact on medical cost and disease management. Digital health would also move beyond patients into the broader population where the impact could be even bigger.

Q: Having worked in various research institutes and organisations over the years, what are some of the insights that you bring to your role at LKCMedicine?

Given the collaborative nature of our work where we serve as a bridge between life science and computer science, communication, an open mind and a broad understanding of both fields are essential skills bioinformaticians would need. Regular open communication is really key to a successful collaboration. I find that it is important to try to understand the problem from the collaborator's perspective so we can best tailor the analysis or design.

A simple example would be the number of samples for an experiment. Any analyst would desire large sample sizes as it gives them the best chance to discover meaningful insights. However, most experiments are limited by the number of samples that can be collected or the cost. A better understanding of the difficulties in sample collection and cost would allow an analyst to be more realistic in their recommendations and drive them to plan experiment designs that gets the most from limited sample sizes.

As we often juggle multiple projects at the same time, time management and being objective-focused are other soft skills that we need. These two things are somewhat related, given that we can only spend a fixed amount of time on any project. We need to be very clear on the analytical objectives and focus on getting the analysis to the desired end point. Often, I see colleagues get sidetracked from the main objectives or generate results which do not answer the original question. This is largely due to the very detailed and technical work that we do where we can easily lose focus of the larger picture.

For our collaborators, I strongly encourage them to talk to us about their analytical needs and questions. It is often far easier to modify an experimental design to get better outcomes rather than trying to perform complex analyses to overcome some experimental design flaws. I have often found these discussions to be very stimulating and they often resulted in new approaches to problems.

Q: Outside of work, what are some of the activities or hobbies that you enjoy?

I am an introvert by nature so I like to stay indoors and do stuff like watching shows and having food with the family. I do photography as a hobby given its digital nature these days so you can often catch me at home editing and organising my photos. I like macro photography as it provides a very different visual perspective to what we usually see. It is amazing to see how ordinary objects can look so different up close.