SciLifeLab Fellow Series: Simon Koplev
We continue our new SciLifeLab Fellow Series, where we meet some of the researchers working at SciLifeLab, with this interview with Simon Koplev!
Can you tell us a bit about your academic background?
I completed my PhD in Medical Science at the University of Cambridge in 2023, where I co-developed a microscopy-based method with applications in pancreatic cancer, which simultaneously detects clonal expansion and transdifferentiation while also characterising adjacent tumour microenvironments inducing cellular transdifferentiation. Prior to that, I completed a BSc in Biochemistry at the University of Copenhagen and a MScEng in Systems Biology at the Technical University of Denmark. I’ve also worked as a research scholar at Harvard Medical School, where I focused on influenza epidemiology; a research assistant at the University of Copenhagen, investigating time-dependent combinations of cancer drugs; and a bioinformatician at the Icahn School of Medicine, where I specialised in the genetics of cardiovascular diseases.
More recently, I have been working as a postdoctoral senior bioinformatician in Sarah Teichmann’s lab at the Sanger Institute and Cambridge Stem Cell Institute, with an interest in cross-organ analysis for the Human Cell Atlas spanning the heart, thymus, and gut, while also specialising in the diverse roles of fibroblasts and tissue-resident immune cells in maintaining healthy tissue structure.
How do you see your expertise contributing to the SciLifeLab research environment?
In the biological sciences, effective discovery often relies on progressively advanced instrumentation and analysis. As a computational biologist, my ambition is that my computational skills and interdisciplinary way of developing research ideas will complement the work of other researchers and colleagues, leading to new collaborations within and beyond SciLifeLab. So I’m excited about being part of SciLifeLab and the cutting-edge research already happening here in single-cell and spatial genomics. My aim is to pursue opportunities for myself, my lab, and other research fellows to develop an excellent research program that drives discovery and better understanding of human tissue architecture in health and disease, using advances in machine learning and AI techniques.
Something specific that I’m enthusiastic about is the chance to collaborate with SciLifeLab researchers on the link between inflammatory bowel diseases and risk of colorectal cancer with applications for early clinical detection. During my postdoc, I worked on single-cell characterisation of healthy and diseased gastrointestinal tracts, leading to discoveries into how inflammation-associated changes in stem cells advance inflammatory bowel disease. Other research interests include how fibroblast cell identity is governed by transcription factors and potentially rewired by alternative splicing. I’m delighted that other researchers at SciLifeLab are working on related questions, creating opportunities for synergistic collaboration and joint grant applications.
Could you describe your research in a way that’s easy to understand?
Overall, I am keenly interested in the ongoing synthesis of two types of information defining our modern age: biological and computational information, asking how this amalgamation can accelerate scientific discovery.
Incorporating advances in single-cell genomics, my work focuses on developing innovative statistical and machine learning methods that address fundamental research questions regarding cellular and tissue architecture. From there, the aim is for these insights to be used to spark breakthroughs in translational science across human diseases.
Moving forward, my goal is to build a computational biology research program that investigates human cells across healthy and diseased adult tissue samples, and which tests hypotheses surrounding how genetic disease risk may be explained by fine-mapping genetic variation to tissue structures.
What do you hope to gain from the SciLifeLab Fellows program and the network it offers?
I’m looking forward to being part of an active, engaged, expert research community. SciLifeLab has an excellent reputation, and is known for its strong publications and positive work culture. I hope to meet new collaborators and to establish fruitful, new research partnerships, within Sweden as well as internationally.
What’s one thing about you that people might be surprised to learn?
Although much of my time is spent focusing on science, I also like to read widely. Some favourites include Catch-22 by Joseph Heller and Moby-Dick by Herman Melville, and a recent standout is Mary Shelley’s Frankenstein (though without any endorsement of the scientific practices it portrays!).
Where do you see yourself in five years, professionally?
I hope to have successfully established a productive and well-functioning research lab, and to have made meaningful contributions towards better understanding the functioning of human cells in disease contexts. More specifically, I aim to illuminate how cancer stem cell architecture relates to immune evasion and genomic instability; explore the diverse functions of fibroblasts in the human heart; and identify cell-cell interactions related to trans-differentiated tumour cells, whose interplay I hypothesise may contribute in as yet unknown ways to processes of tumour angiogenesis and intravasation.
In one word, how would you describe your feelings about becoming a SciLifeLab Fellow?
‘Motivated’ probably captures my feelings best. It’s an honour as well as hugely encouraging to have been offered this opportunity, and I feel newly invigorated to develop the best research I can, as well as to support others in my lab and beyond in doing so as well.
