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Is it nature? I know that a lot of work is published in nature as letters. If so, definitely go with that over the other journal.
 
I submitted a manuscript for publication, and the journal responded to me by recommending I submit as a letter to the editor instead.

I was wondering how this will look on my future med school application? Does it look as good to have a letter in a well-ranked journal in comparison to a publication in a lesser-ranked? Is it still considered a "publication" even if it isn't peer-reviewed?

I know this is a big positive, but I want to gauge how much of a benefit I can anticipate. Thanks!
If it's presented as the way Nature does it will be a publication.
 
I'm having a little trouble finding what that entails. For reference, I will be converting a manuscript I wrote (including primary research data) into a letter to the editor, which the journal said will be subject to peer review and indexed in Medline. To your knowledge, is that a publication? Thank you!
Yes!
 
I'm having a little trouble finding what that entails. For reference, I will be converting a manuscript I wrote (including primary research data) into a letter to the editor, which the journal said will be subject to peer review and indexed in Medline. To your knowledge, is that a publication? Thank you!
This is definitely a publication. However - it very well may NOT be peer reviewed (I.e. sent to external reviewers, as most letters to the editors are not considered peer reviewed). This nuance doesn’t matter so much for med school apps (it is a pub regardless) as it does for your CV later on - technically it would go in a different section (it’s good form to separate peer reviewed and non-peer reviewed publications). That said, complicating matters is the fact that in addition to letters to the editor there are “research letters” (many journals have them, including big ones like jama) that are peer reviewed - so worth clarifying.

For the record, journals are doing this more an more (asking manuscripts to be submitted as research letters or even letters to the editors). Both letter types don’t necessarily count in the denominator of the impact factor calculation but can be cited (so they can increase the number of citations a journal gets -I.e. increase the numerator - but don’t add to the count of how many articles those citations are spread against - I.e. don’t increase the denominator -“artificially” raising the impact factor). Additionally, given the dearth of reviewers, letters to the editors let the info get published without the editor having to find reviewers (very possibly more of an issue at the type of journal you submitted to in a subspecialty space). Of course occasionally it makes less sense for something to be an original article and shortening it is a good editorial decision, but I think that’s honestly not as common a reason for these recommendations (my opinion only). Not important for med school apps, but in case you’re curious why it’s happening and why journals don’t just take things in the form they’re submitted.
 
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