A Data-Driven Approach to Healthcare: Bioinformatics and Beyond
“Bioinformatics — to me — uses computers to understand life” -Vivian Chu
From Margaret Dayhoff to Paulien Hogeweg, women have made important contributions to the field of bioinformatics or computational biology. This interdisciplinary field of study merges tools and techniques from biology, computer sciences, and statistics to allow for applications in ecology, genomics, health and disease, and other fields. In spite of the foundational role women have held in the growth of bioinformatics, they are continually underrepresented and unappreciated: in 2023, a study found that only 35.2% of all bioinformaticians are women. Moreover, women are significantly less likely to hold a first authorship position in published primary research articles on bioinformatics, and those authored by women are much less likely to be cited than those authored by men. Thus, in an effort to showcase these intelligent and talented women, as well as draw attention to this growing field, I sat down with Vivian Chu, a PhD student in the department of Medical Biophysics here at the University of Toronto.
As both a doctoral student and Co-Director of Strategy & Operations at Nucleate, how would you describe a typical day for you?
I’m responsible for leading my thesis project, as well as participating in other research projects. As a PhD student, my day-to-day routine is very variable. Reading the literature takes a significant chunk of my day, although given the rapid pace that the field of AI has been developing, now I don’t even go to Nature, I just go to Substacks or X (formerly known as Twitter) where researchers release their developments on aRxiv or BioRxiv. I’m also continually refining my hypothesis, designing experiments, researching other individuals’ models and datasets, and troubleshooting. Most of my time is spent debugging and identifying problems, which can be very frustrating but also deeply rewarding. My days are also interspersed with various meetings, like project meetings, technical meetings, co-coding sessions, etc.
Beyond research, I’m really interested in bioinnovation and entreprenurship. At Nucleate, alongside my Co-Directors, we lead the Global Virtual Activator — a six-month, equity-free program tailored for academic founders to aid the formation of early-stage life science ventures. This year, I led the Tech Sourcing & Cohort Engagement teams — we identify and onboard emerging biotech startups and build community among our Activator teams. At the GVA, I engage with my Co-Directors to ensure goals are aligned among teams, manage stakeholder relationships and oversee program logistics.
I know that you are currently a graduate researcher at the Wang and He lab, where you are working on understanding the etiology of cancer, improving individualized cancer treatments, and developing deep learning models of multi-omic integration. Can you further elaborate on your current project and its potential impact?
My primary project, which is my thesis project, explores neoantigens, which are unique tumor-specific protein fragments. Using a large set of patient-derived organoid models (3D models grown from patient tissues) and their DNA/RNA sequencing, I am mining that data and harnessing deep learning to see if we can find these neoantigens. The goal of this project is to explore neoantigens as a potentially innovative, less harmful immunotherapy for cancer treatment, ultimately allowing for more individualized therapies to improve the quality of life for patients and their families.
What inspired you to pursue a career in bioinformatics, and what steps did you take to get to where you are today?
I think my journey into bioinformatics wasn’t necessarily a straight path, but it ended up being a convergence of my various interests and experiences that initially seemed very unrelated. I started coding when I was 12 years old, and my playground was Tumblr. I designed blog pages in HTML and CSS, and at the time, I didn’t even realize that what I was doing was coding, it was just a creative outlet. Whatever logic I learned — the colour, the hex codes — just made sense. Later, in high school, I really enjoyed biology, so it seemed like the natural course of action for me [to pursue it further]. Like many naive 17 year olds, I didn’t know what exactly I wanted to do afterwards, but the University of Waterloo had this amazing co-op program through which I discovered all the different doors that I could walk through […] In my second year of undergrad, I interned at the Canadian Space Agency in the department of Astronauts, Life Sciences, and Space Medicine, and during my time there, I noticed that there was a big focus on new tech innovations in Canada and implementing them in deep space or on the ISS. It was there that I became really interested in coding and merging my interests in computer sciences and the life sciences, and I learned how to program in Python and SQL in my own time. My supervisor at the time really encouraged me to continue approaching science through this interdisciplinary lens, and she was probably my biggest champion. I didn’t really know what I wanted to do during that time but she saw that I had passion, and she encouraged me to pursue that.
After that, I switched into bioinformatics and began searching for courses and workshops because I was starting from ground zero…I relied on CodeAcademy, participated in my hackathons, and more. Given my interest in health and disease, I later joined the RI-MUHC in Montreal, where I learned most of my bioinformatics skills, like Bash scripting, Pearl, Ruby, automating my analyses, exploring open-source bioinformatics tools, etc. In my senior year, I learned how to direct my own research project using the same skills, and now I’m pursuing graduate school!
What advancement in the field of computational biology do you think we can expect — or need to work towards — in the next five years? What does the future look like?
I think the next five years are extremely exciting. We can expect to see the slow migration of bioinformatic analyses into the clinic, in the form of tools or support for clinicians in screening, diagnoses and treatment. I think we can also see the integration of A.I. with biology, specifically, developing synthetic representations of biological systems (i.e., cells, organs, entire systems). Maybe not in the next five, but next fifty years — we can expect to see digital twins, which are essentially computer versions of you, complete with the knowledge of your DNA, organs, neuronal processing, etc., to also aid with treatment, diagnoses and screening.
I recently read that as of 2023, only 35.2% of all bioinformaticians are women. Have you ever personally experienced this gender disparity in your workplace or throughout your education, or ever felt invisible due to your sex?
In my freshman year of high school — 2013 I think — I took an Intro to Computer Science course, and I was only one of three females in a class of thirty. That experience made me uncomfortable and turned me off other coding classes, especially because my peers continually expressed how creative and artistic I was, which I interpreted as “I’m not logical or rational.” The environment that you’re in, what you hear really impacts the choices that you make. As a 13/14 year old, my brain was super impressionable, so I saw that class and thought “this doesn’t look like a place that I would fit into,” and for the rest of my highschool career, I didn’t take any other coding courses. That same year, I chose to go to the robotics club, and once again, I was the only female in a group of fifteen male students. It was so discouraging, and I immediately felt like turning around and walking out the door. But I chose to stay and listen to the information session, and afterwards, I approached the club supervisor, Bruce. Surprisingly, Bruce had this mile-wide smile on his face — he was excited that I was interested, and he was so welcoming, and this had such an impact on me that I chose to stay and join the robotics club until I graduated.
As I’ve gotten older, there have been moments where the gender disparity in the field was more pronounced — I was always one of the few women in the room, and I felt like my contributions were overlooked or that I had to assert herself more to be heard, and I think this is a feeling that many women in STEM can relate to. However, if it weren’t for those experiences, I would not have been as motivated to be a fearless advocate for girls, youth and underrepresented groups interested in STEM, nor would I have realized the importance of mentorship and community. What I’ve taken away from those experiences is that…it doesn’t matter that I’m a girl, if anything, it reflects more on the community if they don’t accept people as they are, for who they are. I think that you belong anywhere that you feel like you fit.
What steps do you think need to be taken — either at the individual or global level — in order to increase female representation in the field?
So I worked as a camp counsellor during high school, and I just loved interacting with children and doing science experiments, and I think that’s the key. I think you need to start from a young age — you need to maintain that curiosity and wonder, and not dull anyone’s shine when they’re that young and impressionable. Along those lines, teachers shouldn’t underestimate the impact that they have on changing somebody’s life. That’s why I think outreach, representation, and mentorship, especially geared towards young women, is so important. It’s also important that we build active communities and safe spaces where women can feel heard, and explore their interests without fear of judgement. Furthermore, it’s extremely important that we see women represented in STEM as professors, leaders and mentors. In the bioinformatics sphere, there is opportunity to leverage grant funding to create more opportunities for women and underrepresented groups to explore research and cultivate their skills, whether it is through internships, skill-developing coding camps or conferences.
What advice do you have for young women interested in entering the field of bioinformatics?
My advice to young women interested in entering the field of bioinformatics is two-fold: become your own greatest champion and extend that advocacy to support your peers. Being a champion means offering unwavering support for one’s ambitions and dreams. Take a seat at the table, find someone who has your dream career and take similar steps with them.
In the realm of bioinformatics, build a robust foundation in biology and computer science, actively seek opportunities for hands-on experience through internships or research projects, and network at conferences, workshops, online communities and more. Send those cold emails to professors, ask questions in your class and don’t be afraid to let others see you trying. There are many resources to help you get started in bioinformatics — Rosalind, Coursera, sandbox.bio, the HBC Training Program and more. If you’re unsure if bioinformatics is right for you, the best way for you to find out is to try — and that advice extends to every field you might be interested in
Given the significant gender disparity in the field, how do you cope with Queen Bee Syndrome (i.e. being pitted against other women in competition within male-dominated fields for promotions, respect, and opportunities)?
At the end of the day, Queen Bee Syndrome represents more systemic biases in the workplace and requires a blend of self-awareness, solidarity and strategic action. It’s about what you want to take away from each experience. From all my work experiences, I’ve held the mindset that, when I enter this space, I am building a community, and these people are not my competition. My coworkers are not my rivals — they are my collaborators. When I see opportunities or resources, I extend them to my peers. Success is not a zero-sum game. Coping with gender dynamics can be stressful, so it’s also important to set healthy work-life boundaries. Queen Bee Syndrome is a systemic issue, and it is not representative of anyone’s skills or abilities. By celebrating each other, we can challenge the competitive narratives that fuel this.
I sincerely hope that Vivian’s journey has inspired you to consider pursuing a career in bioinformatics, merge your interests and adopt a more interdisciplinary approach, or made you more aware of bioinformatics and some of the extraordinary women within the field.
