Portrait of Jonathan M. Carlson

Jonathan M. Carlson

General Manager, Life Sciences


I lead Life Sciences research and incubation within Microsoft Health Futures , where our goal is to empower ever person on the planet to live a healthier future. This includes research and incubation programs in Genomics, Immunomics, and Biomedical Machine Learning.

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 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.