Could use advice for post-bacc/application plans!

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You have a decent chance of getting in, and your MCAT will largely determine where you may be competitive. Your research experience will be around (slightly above) average for applicants, which is a good thing. It really behooves you to do the absolute best you can on the MCAT (36+), in which case you will almost certainly have many options. Shoot for your absolute best, and the 'bottom' where you should feel comfortable is perhaps at 32 or so.

I do not think the HES is very important. The MCAT is really what you should be focused on and will make or break you.

Note that if you want to matriculate right after this 2 year research gig, then you will need to apply during the next cycle (starting June 2013). This means you will take the MCAT between now and then, write your personal statement, MD/PhD essay, and research essay, and get all of your Rec letters completed for your application to be submitted by mid-July at the latest.

Best of luck.
 
If I manage to score reasonably well (36+) would I have a chance at upper-tier programs?

Even with a 36, expect not to receive much response from upper-tier programs, but you never know. I would encourage you to apply broadly (lower, middle and upper tier programs, at least 15-20, perhaps even to 25-30 programs). The application process is unpredictable, and your GPA will prevent you from getting interviews- but you can't predict at which programs! A 3.3 GPA is greater than 1 standard deviation below the average GPA for accepted students. You should be willing to go to pretty much anywhere you get accepted (if you get accepted), even if it was not high on your radar before the cycle. Perhaps other people who have experience with URM applicants could comment. Regardless, it behooves you to do the best you can on the MCAT.

Taking the MCAT in early Spring (March/April) is a good plan because you could re-take it in May/June if needed. The publications are good as they suggest you have meaningful research experience and may get your application more attention. However, I cannot overemphasize the importance of the MCAT.
 
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