In CIID, we believe we can reveal bet­ter med­ical treat­ments and devel­op a com­pre­hen­sive under­stand­ing of phys­i­ol­o­gy of impor­tant human pathogens by inte­grat­ing holis­tic and reduc­tion­ist exper­i­men­tal approach­es. Clas­si­cal bio­chem­i­cal, genet­ic and genom­ic approach­es have been employed over the years to yield impor­tant insights in host-pathogen inter­ac­tions. Most of these exper­i­men­tal approach­es are pop­u­la­tion-based (“bulk”), end-point analy­ses where obtained infor­ma­tion rep­re­sents an aver­age across the pop­u­la­tion and where impor­tant para­me­ters can be missed as they become “aver­aged out” in the bulk mea­sure­ment. The dif­fer­ent states of bio­log­i­cal sys­tems, such as for exam­ple, the dif­fer­ences between the health and the dis­ease state, are ulti­mate­ly gov­erned by the indi­vid­ual, sto­chas­tic and often rare mol­e­c­u­lar events. We believe that to tru­ly under­stand dif­fer­ent phys­i­o­log­i­cal states, we need to employ a reduc­tion­ist exper­i­men­tal approach that is able to cap­ture and quan­ti­ta­tive­ly exam­ine these indi­vid­ual mol­e­c­u­lar events. Such infor­ma­tion can then be incor­po­rat­ed into math­e­mat­i­cal mod­els togeth­er with the obser­va­tions made using the pop­u­la­tion-based approach­es ulti­mate­ly lead­ing to a com­pre­hen­sive under­stand­ing of the under­ly­ing patho-phys­i­o­log­i­cal processes