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I received my bachelors in 2014 and started a Ph.D. program in 2017 after taking some time off to work in an unrelated field. I am currently applying to a graduate fellowship (similar in vein to NSF/NDSEG, etc.), and am not sure how to appropriately choose my references given that most of them are 3-4 years old at this point.

I have one from my research supervisor in undergrad whom I published a paper with, so this one is a no-brainer. The professor I'm working with to write my proposal is also writing me a letter. As for the third one, I have a couple of options:

  1. A professor at my current institution who I worked on my NSF GRFP proposal with last semester. I did well in his class, and his research is related to my interests, but I have no research experience with him (or anyone at my current institution since first years do not typically do research)
  2. Research advisors from short-term (5 months) projects I did in 2014 and 2015, respectively. They can obviously speak to my research ability, but are quite dated. I used these letters in my grad school apps and presumably, they helped get me into a top 5 program in my field

If my other research references were more recent, I wouldn't hesitate to use them. But the professor I'm working with on my proposal suggested that I should try to get a second letter from my current institution if possible. Does it look bad for me as a first-year graduate student applicant to only have one reference from my current institution? And would it be a poor decision to use letters from people whom I last worked with 4 years ago?

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It is perfectly normal to have one letter from your current research, since you presumably only have direct, extended experience with only one faculty member.

In picking your letters of recommendation for fellowships, the most important criterion is who can comment meaningfully on your potential to become a researcher. Whoever can provide the strongest letters should be your top priority.

However, I would tend to lean against asking someone who has never written for you before to do so after a gap of some years without providing more recent information on what you've been working on since.

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