Donnelly Centre PhD candidate Jacob Fine named 2025 Vanier Scholar
The Vanier Canada Graduate Scholarships program aims to strengthen Canada's ability to foster world-class doctoral students to become global leaders in research across a wide range of disciplines, including natural sciences, social sciences, humanities, engineering and health. Jacob Fine, a PhD student conducting research at the Donnelly Centre for Cellular and Biomolecular Research, has been awarded the 2025 Vanier Canada Graduate Scholarship from the Natural Sciences and Engineering Research Council of Canada. The scholarship will support Fine’s research in developing computational and statistical approaches to analyze and model RNA codes that govern gene regulatory networks.
“On behalf of the Donnelly Centre community, I congratulate Jacob on this distinguished honour,” said Dr. Stéphane Angers, professor and director of the Donnelly Centre and Charles H. Best Chair of Medical Research at U of T. “The Vanier Scholarship is only awarded to early-career scientists of the highest calibre. Jacob has demonstrated he is deserving of this recognition through his dedication to research excellence and collaboration across disciplines to answer some of the biggest questions in science. I look forward to seeing the contributions he will continue to make to the research community through this scholarship.”
Fine has been drawn to the natural and formal sciences since his childhood. Through the self-motivated study of textbooks, school courses, science books, and numerous trips to the Ontario Science Centre, Fine developed an interest in the origins of the universe and the evolution of life during his early youth.
Fine cultivated his passion for science and leadership in high school, graduating as valedictorian and earning a full scholarship to study biology at York University. During his time there, Fine took the opportunity to conduct research every summer with his mentor Dr. Ronald Pearlman; his projects covered topics in theoretical biology, molecular evolution, genetics, bioinformatics and molecular biology. For his undergraduate thesis project, Fine performed a species-wide bioinformatic analysis of ribosomal RNA, which shed light on a major theory on life’s origins, where the ribosome evolved from a simple RNA catalyst. Based on his undergraduate research interests, Fine published an “RNA-focused synthesis and narrative” on the origins of life in the journal RNA in 2023.
After earning his Bachelor of Science and ranking 1st in York’s Faculty of Science for academics and leadership, Fine joined the Donnelly Centre as a graduate student in 2022. Now a member of the Computational Biology in Molecular Genetics (CBMG) program, Fine’s PhD work focuses on analyzing and modelling RNA codes that govern gene regulation using computational approaches in the group of his supervisor, Dr. Ben Blencowe, professor of molecular genetics, Canada Research Chair in RNA Biology and Genomics and Banbury Chair in Medical Research at U of T.
“Ben’s lab is internationally recognized for the kind of research I wanted to do, and the Donnelly Centre is a leading hub for interdisciplinary research in computational biology and genomics in Canada,” said Fine. “In the summer before graduate school, Ben reached out to tell me that my application stood out to him, which was very encouraging. I was sold on his lab after one rotation with him, and Ben has been exceptionally supportive of my personal and professional development ever since.”
As a third-year graduate student, Fine has already pioneered the development and application of information theory, statistical algorithms and other computational methods to study RNA sequence codes that impact gene regulation. The integration of these methods has resulted in Fine discovering an RNA regulatory network that harbours rare codon patches linked to critical biological processes.
Fine also collaborates closely with his academic mentor Dr. Alan Moses, professor of Cell & Systems Biology and Computer Science, for his main thesis project as well as his continued work in theoretical approaches to model the origin of life. In particular, Fine and Moses integrated principles from information theory and thermodynamics to develop a model for the origin of life based on self-replicating RNA condensates published in the Journal of Molecular Biology.
In collaboration with Dr. Philipp Maass, assistant professor of molecular genetics and scientist at SickKids Research Institute, Fine also developed and implemented statistical methods to reveal how changes in tRNA abundance elicit codon-specific and genome-wide changes in gene expression. Presently, Fine is pursuing a large-scale project with Blencowe, Moses, as well as with Jernej Ule, who together with Blencowe founded the Brain RNA Regulatory Networks Satellite Laboratory at The Francis Crick Institute. This ambitious project will further develop our understanding of RNA codes, leveraging large repositories of high-throughput data combined with machine learning and statistical modelling.
Passionate about bioinformatics and interdisciplinary collaborations, Fine founded the Toronto Bioinformatics Hackathon, the city’s first hackathon focused on bioinformatics and computational biology. At the event, over 70 trainees and researchers from diverse STEM fields were hosted at the Donnelly Centre in September 2024 for the hackathon. The aim of the organizing team, led by Fine, was to create an opportunity for trainees to collaborate on interdisciplinary projects using cutting-edge computational methods. Following a successful first event, their long-term aim is to create a nationwide intellectual hub of youth-led computational biology. The second annual hackathon is scheduled for September 19-21st 2025.
Fine’s interdisciplinary research at the Donnelly Centre was previously recognized by the Donnelly Centre’s Cecil Yip Award for “innovative and highly collaborative work that crosses formal disciplinary boundaries.” Fine was also awarded the NSERC Canada Graduate Scholarship – Master’s (CGS-M) and the Roman Pakula Award for the “best acclaimed all-around M.Sc. student registered in the Department of Molecular Genetics.” During his PhD, Fine has benefitted from close interactions and collaborations with members of the Blencowe and Moses labs, as well as with additional Donnelly Centre and UofT faculty, including Drs. Artem Babaian and Haissi Cui.
Fine’s long-term goals include leading interdisciplinary scientific efforts that leverage computational approaches to better understand biology. The award of the Vanier Scholarship affirms Fine as one of Canada’s top PhD students and will help position him to achieve his aims in research and leadership in science.
“It is a great pleasure to have Jacob pursue his PhD research in my laboratory and I am thrilled that he has been selected for the prestigious Vanier Scholarship”, said Ben Blencowe. “This highly deserved honour attests to Jacob’s ambition, drive and scholarship. I look forward to continuing to work with Jacob and seeing him develop breakthrough science in the years to come.”
