How much of an advantage is having a publication in a lower impact journal?

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Albanian Mafia

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The student would end up being third or fourth author on something like this.

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I can't speak to the value of the pub itself, but the educational value of being significantly involved in a study is certainly worthwhile for med school apps - even if it's just for talking points during secondaries/interviews.
 
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The only type of interview where a lower tier publication is disadvantageous is for a basic science faculty interview. You'll be fine.
 
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It's a big step up from just having a poster, which is all that a lot of people have. Adds a kind of stamp of approval that you were productive/useful to your lab. Having a glowing letter from the PI you worked with is probs more important than officially being a 4th author on something though.
 
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I had a publication in an IF ~3 journal when I was applying and I think it helped. I was asked about it in a couple of interviews, so it's important to have an elevator talk prepared for what the research was and what the outcomes were. You should also be able to talk at length about your role in the project. Overall it's neither necessary nor sufficient but it will probably give you a slight advantage.
 
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