@oristarA,
I think this author is not using the "identified with" construction. He happens to use both near each other, but I read this sentence as saying:
"Among the most keenly discussed issues were: i) the remarkably high number of autoimmune expressions; the homeostasis of immune function, ..."
"Molecularly identified" goes to primary immunodeficiences. Likewise with "with autoimmune expressions." I don't read this as using the "indentified ... with" construction.