I'm in the same situation but my interests are more in hardware for medical applications. I'd pick UCSD personally because the bioE program is really good and you could be co-advised. Dr. Coleman is in the BioE department and is someone worth checking out. I don't know enough about CMU to say anything there. As far as JHU, they are good at BIoE and have a good med school but I've never heard much about their EE department. UCSD is more highly ranked in that regard.
meh7623 got a reaction from Ramji in CMU vs USCD vs John Hopkins - EE Phd.