Bob's nickname was “Elvis,” a 'reference to' the way he styled his hair. [=people called Bob “Elvis” because he styled his hair in the same way Elvis Presley did]
The course covers ancient history 'with' special 'reference to' the Roman Empire. [=the course is about ancient history and especially about the Roman Empire]
I have something further to add 'with reference to' [='with respect to', 'in regard to'] what was said earlier.
(..) Your report doesn't show I realize your ordeal affected you, but the holes in your account... ...leave us with no choice but to delete these references... ...until hard evidence becomes available that could cause us to pursue an investigation. I don't believe the FBI has an investigative (..)1998 The X Files