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My impression from talks from PDs at my school to our MSTP is that for many specialties, your demonstrated ability to be productive in science and speak intelligently about it is universally appreciated. You sounds reasonably well matched from your neuroscience to your clinical interests. Being productive in your thesis work and practicing being articulate when describing your research will go a long way. Being able to slant your current research or possible new directions for your research to whatever specialty you are interested in is a great way to make the basic science relevant to PDs. Older MSTPs who have done interviews may have good tips for you.
If you really want to gun it up or chase a specialty that is pickier about research backgrounds, you should just start chatting with people in the clinical dept. Odds are you could find something to help out with that you could cram in while doing thesis research. This is especially true if you find a project that can mostly be done from a computer on your own time line. You'll be in grad school for a while, so you could probably find something doable in that time frame that will pan out to a clinical publication in the next 5-6 years.
When I chose my PhD mentor...they told me not to worry about my future specialty (especially because I had no clue back then) and just to pick based on interest and the potential of learning good science.
I hear from a lot of classmates that in order to be competitive for certain specialties (e.g. ortho, opthal, radiology), you have to do specialty-specific research.
Will my PhD (neuroscience, with a pretty well-known PhD as PI) still help me in applying for residency, or will directors simply not care unless I'm applying to neurology/psychiatry?
I'm considering finding a MD mentor soon to help me prepare for the match process, but I don't think it's feasible for me to take on a clinical research opportunity while doing my PhD. Rather, I'm trying to integrate certain aspects of other medical specialties into my study design (e.g. fMRI).
Also, my M1-M2 grades are pretty bad. I had to take a year off (I was about 4 weeks away from finishing first year when I had to take a leave of absence - came back the next year to start at the point where I left) for personal reasons that were causing me problems in school. My dean already told me they will mention this in my letter, so I have to be able to field questions about it. I scored decently on Step 1 (254), so hopefully that helps a little bit. What else can I do now to boost my resume and prove that I am competent?
Neuronix - the official reason is depression (so I guess I fall under mentally ill), but even my psychiatrist says that's private and I should tell residency directors (if they ask) that I just had to rethink my career options.
However, my dean is insisting she has the right and duty to report this information...so I have no clue what I'm going to do.