Alex Pico with his arms crossed outside the Gladstone building

Gladstone Bioinformatics Core Director Alex Pico, PhD, is using data science tools to understand the novel coronavirus.

 

In response to the COVID-19 pandemic, the Bioinformatics Core staff are turning some of their effort toward understanding the novel virus. By leveraging the power of WikiPathways and joining an international team of collaborators, the core staff hope to contribute to fundamental discoveries about the virus and its pathological mechanisms. And now, you can lend your own expertise to further these projects.

One of the ongoing WikiPathways projects involves extracting pathway knowledge from published figures. The Bioinformatics team applied this tool to thousands of coronavirus-related articles that have been collected into a publicly available data set called CORD-19. In doing so, they identified 221 published pathway figures and extracted 4,818 gene mentions from these figures. You can help by further mining the CORD-19 data set or exploring the extracted figures using an early (unpublished) release of the team’s pathway figure viewer tool.

In addition, the Bioinformatics staff have joined an international collaboration coordinated by the Luxembourg Centre for Systems Biomedicine. This collaboration seeks to map COVID-19 host-pathogen interactions and construct COVID-19 disease maps. If you have relevant biological pathway knowledge, in particular expertise in viral infection, immune responses, and pathological responses, your participation would be welcomed.

Contact Alex Pico to find out how to get involved.

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