September 3, 2020

Analyzing SARS-CoV-2: A cancer researcher trainee’s perspective

OICR-based PhD Candidate awarded University of Toronto COVID-19 Student Engagement Award

This scanning electron microscope image shows SARS-CoV-2 (round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2, also known as 2019-nCoV, is the virus that causes COVID-19. The virus shown was isolated from a patient in the U.S. Credit: NIAID-RML
This scanning electron microscope image shows SARS-CoV-2 (round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2, also known as 2019-nCoV, is the virus that causes COVID-19. The virus shown was isolated from a patient in the U.S. Credit: NIAID-RML

When the COVID-19 pandemic shut down labs across Canada, cancer research trainees looked for ways to help respond to the pandemic. PhD candidates Tom Ouellette and Jim Shaw saw an opportunity to combine their skills and contribute to the cause.

Ouellette and Shaw were recently awarded a University of Toronto COVID-19 Student Engagement Award for their project titled Network and evolutionary analysis of SARS-CoV-2: A vaccine perspective. Together, they will develop new machine learning tools to analyze the SARS-CoV-2 genome and how it evolves. 

Tom Ouellette, PhD Candidate in Dr. Philip Awadalla’s lab at OICR.

“We’re two like-minded individuals with complementary skillsets who enjoy coding, math and solving problems, which – fortunately – can be done remotely,” says Ouellette, who is a PhD Candidate in Dr. Philip Awadalla’s lab at OICR. “We saw the opportunity to help with COVID-19 research and we’re happy to apply our skills to help advance research towards new solutions for this pressing problem.”

Ouellette specializes in evolution and population genetics and Shaw specializes in network analysis and algorithm development. Through this award, they will investigate how SARS-CoV-2 is evolving by looking into specific regions of the virus’ genetic code from samples around the world, using mathematical modelling, machine learning, and evolutionary simulations. They are specifically interested in how these changes in the genetic code may alter the virulence, or severity, of the virus.

Jim Shaw, PhD Candidate in mathematics at the University of Toronto.

“Just like cancer, different pressures or stresses can make viruses evolve,” says Shaw, who is a PhD Candidate in mathematics at the University of Toronto. “Understanding these changes can have an impact on how we build vaccines. Furthermore, better understanding of the virus’ evolution may shed light on viral reinfection, which is an important issue as we move into the later stages of the pandemic.”

Ouellette and Shaw plan to publicly release the code that they develop through this initiative for other researchers to build upon.

“SARS-CoV-2 has a much simpler genome than a cancer genome, so it can serve as a simplified model to test out new analytical techniques,” says Ouellette. “Ultimately, I hope to bring the tools and technology we create back into my research on cancer so we can better understand how cancer evolves and becomes resistant to treatment.”

Read more on how OICR researchers are helping understand and overcome COVID-19

April 16, 2020

University students step up to flatten the COVID curve

Former OICR intern leads the development of a COVID-tracking site used by more than 400,000 people in Canada to date

Flatten is quickly becoming a go-to source of information about how COVID-19 is spreading across Canada.

In less than a month, more than 400,000 people have submitted data on their symptoms, travel history, age and medical conditions, making Flatten the country’s leading crowdsourced COVID data repository.

Behind the project is a team of first- and second-year university students who are determined to help.

Yifei Zhang, Vice President of Flatten.

“We just wanted to put our technical skills to good use during this time,” says Vice President of Flatten, Yifei Zhang, in a University of Waterloo story. “It’s been great working together with everybody trying to build a platform that will be useful for Canadians across the country.”

As a web-based, data-gathering platform, Flatten provides a real-time heat map of self-reported confirmed and potential COVID-19 cases across the country. The platform helps increase awareness and flatten the curve of COVID-19 cases.

Over the last four weeks, Flatten has rapidly evolved from an idea into an incorporated non-profit organization, with support from advisors such as Dr. Geoffrey Hinton and sponsors such as Google Cloud, the Vector Institute and CIFAR.

The team behind Flatten has established collaborations with health authorities across Canada, such as in Montreal, and plans to work with other municipal governments and provinces..

“We work with leading advisors and collaborators to make sure we’re surveying the right questions and providing the right information for Canadians today to help flatten the curve,” says Zhang.

Zhang, who is completing his second year as a software engineering student at the University of Waterloo and leads Flatten’s website development, attributes his website development knowledge to his internship with OICR’s WebDev team.

“My time at OICR reinforced my interest in working in health and biology, giving me the motivation and drive to pursue this initiative,” says Zhang. “At OICR, I gained experience working with a high volume of data using robust techniques and I was able to bring that knowledge into developing Flatten.ca. A lot of the fundamentals we used to build this site came from best practices that I learned from my term at OICR.”

Learn more at flatten.ca.