Dr. Quayle shares his dream of integrating bioinformatics with lab-based and clinical oncology research
It’s another Spotlight edition!
Our Spotlight articles aim to shine a light on the people that make up the Industry and Innovation Research Institute (I2Ri). Alongside the BreakThru Research podcasts on Spotify hosted by Márjory Da Costa-Abreu, we hope this will be a great way to celebrate our successes and get to know our researchers more.
This edition, we caught up with Dr Lewis Quayle to find out a bit more about him and his work in I2Ri.
“My primary ambition is to establish a multidisciplinary team that integrates bioinformatics with lab-based and clinical oncology research, complementing the latter fields with in-silico analytics.”
Please can you tell us a bit about yourself?
My name is Lewis, and I am a cancer bioinformatician (computational biologist) and a senior lecturer in data science and analytics in the Department of Computing.
I completed my PhD in the Department of Oncology & Metabolism at The University of Sheffield Medical School between 2014 and 2017. During my PhD and the first two years of my postdoctoral work, I was a wet lab-based cancer cell biologist. I developed and studied novel models of tumour cell dormancy in metastatic breast cancer, utilising next-generation sequencing, among other techniques.
My primary research interest remains in metastatic breast cancer, although I work across various cancer types and occasionally other fields such as reproductive medicine.
My projects range from understanding the drivers of chemoresistance in rare cancers, such as osteosarcoma and gestational trophoblastic neoplasia (GTN), to conducting large-scale whole genome profiling studies as part of Genomics England’s 100,000 genomes project.
I am also involved in clinical trials for both rarer cancers like GTN, and more common cancers, like bladder cancer.
What path led to your current work and position at SHU?
In 2019, while still working as a wet-lab researcher, I undertook a three-month placement at the Kinghorn Centre for Clinical Genomics at the Garvan Institute in Sydney, Australia. The primary aim was to learn high-performance computing and pipeline development for analysing next-generation sequencing data, which I was generating extensively at the time. This experience marked the start of my transition into bioinformatics.
During this placement, Dr Nenad Bartonicek, a senior bioinformatician that acted as my mentor during this time, recognised my natural aptitude for programming, an area in which I had no prior experience. His encouragement prompted me to consider pursuing this further.
Upon returning, I became fascinated by the problem-solving aspects of coding and embarked on a three-year journey to master R, Unix Shell, and SQL programming, while also expanding my capability into as many next generation sequencing technologies as possible and obtaining professional certifications as a data scientist alongside my research duties.
This led to a position in Prof. James Catto’s group at The University of Sheffield, where I was embedded in the Sheffield Bioinformatics Core facility. There, I worked on the 100,000 genomes cohort, and spent my spare time delving into machine learning and network graph-based analytics, as well as running workshops teaching all the skills I had acquired over the few years prior.
A job advert for my current position at SHU caught my eye, particularly as they sought someone proficient in and handling big data using distributed systems and R programming, which remains a favourite aspect of my work. Believing I was ready to transition from a collaborative researcher to an independent leader, I applied, and here I am, a year later.
What is the most exciting thing about your work? What are some of the challenges?
The most exciting aspect of my work is the diverse range of projects, technologies, and the incredible people I collaborate with. I use various analytical tools and techniques to uncover unique biological insights which would often not be accessible to those without computing ability.
As a bioinformatician, I often employ cutting-edge methods that are revolutionising biology. For instance, while many are just beginning to explore single-cell RNA-Seq experiments, I am already analysing data from spatially resolved single-cell RNA-Seq, a technique that won Nature’s Method of the Year in 2020. The constant learning and requirement to master a diverse yet specialised skill set keeps me engaged and motivated.
The main challenge is the high demand for my expertise. Balancing numerous collaborative projects, my own research, teaching responsibilities, and grant writing alongside homelife can be difficult.
Additionally, keeping my skills updated with the latest developments across the multiple fields that cancer bioinformatics spans is a constant challenge, requiring careful time management and selective collaboration.
Who or what inspired you to pursue your career?
Several individuals have significantly influenced my career. My MRes supervisor, Dr Timothy Bates, nurtured my early career development, providing fantastic opportunities and tuition. He ignited my passion for lab work and the intricate details of biochemistry, which was my favourite undergraduate subject and the focus of my master’s degree.
My PhD supervisors, Professor Ingunn Holen and Professor Penny Ottewell at The University of Sheffield Medical School, recognised my potential and awarded me a PhD scholarship. The transferable skills I acquired under their mentorship are crucial to my ongoing success. We remain good friends and continue to collaborate on various projects.
Dr Andrew Sims at the Institute of Genetics and Cancer in Edinburgh was a career mentor during my postdoctoral years and played a pivotal role. His inspiring talk during my first PhD year, detailing his journey from analysing soil samples to becoming a leading figure in breast cancer bioinformatics, convinced me of bioinformatics’ potential as a revolutionary field in medical research. His mentorship was instrumental when I decided to transition to bioinformatics. Sadly, Andy passed away in 2021 from stage IV melanoma, and I often wonder how my career might have evolved under his continued guidance.
I am fortunate to have had such excellent role models and mentors, and I aspire to be a similar source of inspiration and guidance for the next generation of students and researchers.
Can you share a turning point or defining moment in your work as a researcher?
Securing my PhD studentship, embarking on the Sydney placement, and obtaining my lectureship were significant turning points in my research career. However, if I were to highlight one pivotal moment, it would be the Sydney placement.
I regard this experience as the major nexus in my career. While obtaining the Master’s Scholarship enabled me to pursue a master’s degree, which subsequently facilitated my PhD and the corresponding scholarship, the Sydney placement was the critical factor in where I am today.
Without it, I might still be another wet lab researcher and have my career progression and security be way more constrained by the prevailing funding climate. That placement fundamentally shaped my professional trajectory and has ultimately enabled me to secure my current position.
What advice would you give to someone looking to embark on a career in research?
That is a tough question. For those aspiring to enter the field of research, my primary advice would be to ensure you are fully committed and passionate about it. If you are considering pursuing a PhD, take the time to thoroughly evaluate your career options and ensure you are prepared for the journey ahead.
Research can often feel like a marathon, filled with highs and lows. If you are passionate about a topic, pursue it wholeheartedly. However, if you have any doubts about your commitment, it might be wise to wait until you are certain of your motivations.
In terms of bioinformatics specifically, I have observed that it may be easier for biologists to transition into the field by acquiring computational skills than for computer scientists to develop the intuition and foundational knowledge of biology to be able to work with large-scale biological data, but there are no hard and fast rules and I do know bioinformaticians that came from backgrounds in computer science.
What do you most enjoy about teaching? What are the challenges?
I have always relished the technical aspects of my work and enjoy empowering students with new skills. It’s incredibly fulfilling to witness their moments of understanding or proficiency in skills I have taught them.
Engaging with students, explaining the context of what they’re learning, and how it applies to the cutting-edge research being undertaken by myself and colleagues is highly rewarding. Integrating practical skills and my research into my teaching motivates my students, which in turn, motivates me.
The main challenge is balancing teaching with my other responsibilities, such as research, collaboration, and administrative tasks. Staying motivated during periods of heavy marking and administrative duties can be tough.
Additionally, while I invest a lot into my teaching, dealing with disengaged students can be frustrating, especially when they affect their peers’ learning experience.
What are your ambitions and the next steps for your research?
My primary ambition is to establish a multidisciplinary team that integrates bioinformatics with lab-based and clinical oncology research, complementing the latter fields with in-silico analytics. The next steps involve securing more funding and hiring staff and PhD students.
I have already hired a PhD student starting an exciting project in October and submitted several significant funding proposals as a principal investigator, and I will continue to do so in the coming months.
I aim to advance the field of bioinformatics by developing new computational methods and applying them to cancer research, ultimately contributing to better diagnostic tools and treatments for patients.
Is there an opportunity for colleagues to collaborate with you on your research?
Absolutely. I am currently collaborating with colleagues in the BMRC on various projects including biomarker discovery, next-generation sequencing, proteomics, and machine learning.
Collaboration is a key component of my work, and I am always open to working with colleagues on projects that align with my research interests.
I believe that interdisciplinary collaboration can lead to ground-breaking discoveries and am keen to explore new collaborative opportunities that can benefit from my expertise or offer new perspectives on my own research.
What real-world impact do you hope your research will make?
All my work is translational, aiming to improve patient outcomes. I hope that my research will lead to a better understanding of poorly understood conditions and major breakthroughs for diseases with currently poor prognoses, such as metastatic breast cancer.
By leveraging cutting-edge bioinformatics techniques, we can gain deeper insights into cancer biology, which can ultimately improve diagnostic tools and treatments.
My ultimate goal is to contribute to advancements that could save lives and alleviate the unseen impact on patients’ families.
What do you like to do when you’re not working on your research?
I used to be an avid climber until a knee injury two years ago sidelined me for about six months. I plan to return to climbing with the same dedication once I’m ready.
Currently, my partner and I are renovating our first home and expecting our first baby, which keeps me quite busy.
I also enjoy gardening, growing our own fruits and vegetables, cycling, swimming, and spending time with friends whenever possible.
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