This forum made possible through the generous support of SDN members, donors, and sponsors. Thank you.
So what exactly do you want to get your PhD in?
 
That should help shape your choices a bit. Pick programs that have a strong Mol. Bio or Med. program as well as a funded MD/PhD (MSTP or not) - maybe around 30 schools or so. Once you have your initial list - try to find 3-5 PI's doing work that interests you. Then you could further shorten the list by taking into account geographic location, COL, size of the city, etc. Usually 15-20 schools is sufficient (a breakdown that @Fencer likes to use is 5 reach, 5 target, 5 safety). With your GPA, MCAT, and ECs you should be successful baring no complications and a well thought out list of schools.
 
Top