We are happy to invite you to the next Talks at the Square event at BioInnovation Institute.
On September 17th, 2025, we will welcome John Quackenbush to the Square, where he will present his keynote on “Embracing Biological Complexity to Understand Disease Drivers”.
Quackenbush will speak on his research and vision for the expansion of his work. His talk will also be an opportunity to hear firsthand during the Q&A about the management of research initiatives generally in this era of academic research cutbacks and specifically as regards the Harvard University grant reversals under the current administration.
More about the keynote talk
To truly understand diseases like cancer, we must go beyond identifying mutated genes and instead study how genetic and environmental factors influence when and how genes are turned on or off—gene regulation. This regulation, shaped by complex cellular interactions, forms “gene regulatory networks” that change during development and disease. For over a decade, my team has developed computational tools—like PANDA, LIONESS, and PHOENIX—that use machine learning and biological knowledge to map these networks from large gene expression datasets, even at the level of individual patients.
These networks act as “wiring diagrams,” showing how genes control each other in specific contexts. We’ve used them to explore diseases, especially differences in how men and women experience conditions like colorectal cancer. Surprisingly, the most telling differences aren’t in mutations or gene expression levels, but in how the networks are wired in different disease states and sexes.
To track how networks evolve over time, we built PHOENIX, which uses neural networks to follow regulatory changes during disease progression. This helps us identify critical moments when the network shifts from health to disease.
Now, we’re working to pinpoint these transitions and predict interventions that might steer the network back to health. Our goal is to harness these dynamic maps to discover drug targets and develop more precise, personalized treatments.
We’ll explore these methods, their applications, and their promise for the future of drug discovery.
Click here to read more and sign up.
Date: Wednesday, 17th September 2025
Time: 15:00 – 16:30
Venue: BioInnovation Institute, Ole Maaløes vej 3, 2200 Copenhagen N