Statistical Inference of the Immune System Repertoire

The adaptive immune system has several strategies to facilitate its basic functions of identifying foreign epitopes while not reacting to self epitopes. In this talk we describe, in a fully quantitative and probabilistic manner, the generative VDJ recombination process, somatic selection, and underlying hypermutation rates. Parameters for these models are are self-consistently inferred from large throughput DNA sequencing of both T cells and B cells. The implications for the informational dilemmas of the immune system are also discussed.