Innovation systems (IS) and science policy scholarship predominantly focus on linkages between universities and industry, and the commercial translation of academic discoveries. Overlooked in such analyses are important connections between universities and academic hospitals, and the non-commercial aspects of translational science. The two types of institutions tend to be collapsed into a single entity-'the university'-and relational flows are lost. Yet the distinctions and flows between the two are crucial elements of translational science and the biomedical innovation system. This paper explores what has been called the 'hidden research system' that connects hospitals, universities, and their resources, with the clinical and scientific actors who make the linkages possible. Then, using a novel conceptual model of translational science, we examine the individual interactions and dynamics involved in a particular example of the biomedical innovation system at work: the diagnosis of IRAK-4 deficiency, a rare immunological disorder, and the translational flows that result. Contra to conventional IS analyses, we are able to point to the strong role of public-sector institutions, and the weak role of the private-sector, in the translational processes described here. Our research was conducted within a Canadian network of scientists and clinician-scientists studying the pathogenomics of immunological disorders and innate immunity.