T cells and B cells have the unique ability to change their own genome to get better at what they do. T cells are often different from one another in their ability to “see”. Their combined perspective makes up the Immunological Repertoire. This ability, this repertoire, is imperative to the function of the immune system in such a manner, and in turn, to health.
Recent progress in the ability to sequence genomes (recently dubbed Flatley’s Law) computational tools, and, in general, high-throughput biology, now allows us to observe the T-cell repertoire by looking at the CDR3 makeup of thousands to millions of T cells.
At the Systems Biomedicine Lab, we are producing such repertoires, develop computational tools and improve on these technologies.
We develop tools to use pathway and network knowledge to discover hidden properties of cell regulation out of high-throughput data.
We have been using pathway knowledge on top of gene and protein information to perform diagnosis and prognosis of samples from cancer patients. We have shown the advantage of using such approach in multiple papers (all of them appear in the “Publications” section in this website)
We are able to uncover the pathways most critical to make diagnosis (or prognosis). We follow up on these findings in wet-lab experimentation to learn more about the mechanisms of these critical pathways.
Single cell transcriptomics. With help from Dr. Assaf Rotem and Dave Weitz’s lab, we recently set-up a droplet microfluidics system that gives ability to look at the whole-transcriptome of single cells. We are using this technology to look at epithelial cells and T cells at the tumor microenvironment.