Portrait of Jonathan M. Carlson

Jonathan M. Carlson

Managing Director, Health Futures


I am the Managing Director of Microsoft Research Health Futures , Microsoft’s multidisciplinary research organization with the mission to empower every person on the planet to get the right treatment at the right time. We are focused on catalyzing the emergence of multimodal biomedical generative AI that can reason from bedside to bench, accelerating the discovery, development and delivery of medicine. To this end, Health Futures’ portfolio includes deep technical investments in generative AI applied to the languages of both humans and biology, spanning medical text to images, and DNA to proteins, cells, and immune systems. We collaborate closely with external partners to ground our research and incubation in high-impact scenarios, and work across the Microsoft ecosystem to bring innovations to the world. As a computational biologist, I have collaborated with dozens of labs across the globe, publishing over a hundred papers at the intersection of machine learning, immunology and virology.  I hold a Ph.D. in computer science from the University of Washington and an undergraduate degree in biology from Dartmouth College.

Previously, I led the Antigen Map Project, a partnership with Adaptive Biotechnologies that has led to multiple clinical diagnostics and scientific discoveries using ML-based decoding of immune system genetics. The basis of this approach is Adaptive’s immunosequencing technology, which provides high-throughput sequencing of T-cell receptors, effectively turning a blood sample into an encoded representation of a person’s immunological history. By decoding this information, we could in principle develop diagnostics for autoimmune diseases, infections and cancer, along with identifying targets for therapeutic and prophylactic vaccines and engineered T cells.

Before that, I was deeply involved in Project Premonition, where I 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.

Much of my early published research 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. Some of those papers are featured below.