Jonathan Carlson

General Manager, Microsoft Health Futures

Role: Scientist

Site: CDL-Seattle

Stream: Computational Health

Jonathan is the General Manager of Immunomics in Microsoft’s Health Next group. In partnership with Adaptive Biotechnologies, our goal is transform the way we diagnose, monitor, treat, and prevent disease by creating a blood test to scan the body for past and present signs of infections, cancers and autoimmune diseases. The basis of our approach is the T-cell Antigen Map: nature’s mapping of your disease-fighting T cells to antigens, the signals of disease that they target. If we can learn to decode this information, a small blood sample would yield a readout of the antigens your immune system is monitoring, allowing your immune system to tell its own story. Checkout our blogs or project page for more info.

As a researcher in computational biology and machine learning, Jonathan’s interests have largely focused on immunology and virology. He has been deeply involved in Project Premonition, where he led the metagenomics efforts: given a sample of unknown DNA, what organisms contributed the genetic material? In the context of Premonition, we get DNA from mosquitos. Such DNA will come from the mosquito, the host(s) on which it fed, the mosquito’s microbiome, and both vector-borne viruses and blood-borne viruses from the mosquito host. Our long-term vision is to use blood-feeding insects as sensors for tracking viruses and vertebrates in the environment.

Much of Jonathan’s published research has focused on using virus evolution as a window into the host immune response, with HIV serving as a particularly useful substrate. Because HIV has a high rate of mutation, each HIV-positive individual carries a genetically distinct virus. Moreover, as the adaptive immune response learns to target the virus, evolution selects for genetic variants that reduce the effectiveness of the immune response, leaving genetic “footprints” on the virus that we can learn to track. So by developing models of virus evolution, we can generate and test hypotheses about how the immune system interacts with the virus. In addition to providing guiding principles for vaccine design, this approach can reveal fundamental new insights into basic immunology. Tools Jonathan has developed for this space are available at the PhyloD web service.