In general, use periods in academic degrees:
   Ph.D.
   M.D.
   B.A.

The exception is MBA. Most reference books leave the periods out of that one, so we will, too.

In professional certifications, on the other hand, don’t use periods:
   CDE
   CKD 

Sometimes this will result in mixed formats in a single byline:
   Jane Johnson, Ph.D., CDE