Though I don’t do research as much as before, I still think, hear, and read about it quite a bit. But as we all know: before your research can be finally published, it has to make it past the editor(s) and reviewers—especially Reviewer #2.

Part of this recipe for success requires writing compelling cover letters to the editor, and polite-yet-firm rebuttals to the reviewers. A recent string of collaborations has been particularly fruitful, and led by different folks, so I got to see a couple different cover letters. And the recent push for greater transparency means that many journals now publish the peer review files, so one can easily look up those; in fact, some are pretty spicy. 🌶️

… Wow. Let me just say, there is so much variation in the quality of this writing. I mean, sure, this is not something they typically teach you in school, but I’ve seen some cover letters—and especially rebuttals—recently that are so cringe, I had to feel bad for the editors and reviewers. Perhaps I was lucky and got amazing mentors who taught me how to write (thank you Qian, Evan, Mark, and Tim!) or maybe I was raised to show respect and humbleness (thanks fam!), but I feel like there are some very sensible standards that should be incorporated into these documents. But, now that I think about it, I only learned how to write them through trial and error myself, so I thought this could be a good opportunity to share my thoughts with some concrete examples. This topic is also top of mind for me because I have now had the opportunity to review several papers, and I really wish the authors’ rebuttals could be more consistently formatted.

Cover letters

When you submit your manuscript to a journal for review, you have the option of including a cover letter, and this package of documents gets first seen by an Associate/Senior Editor. If it’s not clear, the cover letter is definitely not optional, so you should take it seriously. It is only seen by the editors and gives you a chance to convince them why your work is important.

A quick search online reveals a couple of good guides from Springer and Elsevier. Though I personally have never referred to these guides, in hindsight they’re pretty decent, short and sweet. There’s a much longer guide from San Francisco Edit, though honestly it sounds like it could be written by AI, so you might get just as much out of that.

Since general guides exist, I thought what would be most helpful is to give some concrete examples, so I’ll share a few from my recent GRIP paper where I was a corresponding author (so I feel comfortable in sharing it). First impressions are key, so the most important cover letter is the first one. This is usually the longest (but don’t make it too long!) and is where you say very clearly what you’ve done. Additional details are in the previous link, given in profuse comments (please don’t make suggestions 🙃). Another cover letter I wrote (years earlier) for our Jupyter Book paper can be found here, so you can see how my own style has changed as I gained more experience.

Subsequent submissions of your manuscript (after each revision) should also be accompanied by a cover letter, unless it’s the final submission where you’re just collecting all files without any changes. These subsequent cover letters can be much shorter, as seen here.

Rebuttals

If you made it to the first round of reviews, congratulations! 🎉 Hopefully your work was well received and you can see the light at the end of the tunnel. If the reviewers did their job right, they will have left many constructive comments to help you improve your work before final publication. Regardless of how well they wrote their reviews, you obviously have high standards for yourself and will craft a sterling rebuttal.

To contextualize what follows, you can see the rebuttal we wrote for the GRIP paper published online. For starters, you should always copy the reviewer comments verbatim, even if they contain typos and odd formatting (believe me, it bugs the hell out of me). Each reviewer’s set of comments should be clearly delineated, I prefer with a prominent header and a page break.

Next you need to identify each comment (or a small chunk of connected 2–3 comments) for all reviewers and put a reply after each one. All my replies have three sections:

  1. Author reply: Here is where you speak directly to the reviewer and their comment, addressing their point, answering any questions, and explaining why they're wrong you agree or disagree. You know best what information to include, and you may find yourself referencing existing parts of your manuscript or supplementary materials. 🙄
  2. Changes to manuscript: Here is where you specify verbatim what aspects of your manuscript you have changed, if any. These changes in the actual manuscript should be reflected in a different color.
  3. Pages changed: Not everyone does this, but I think it’s a nice touch. You just write which pages your changes are found on. Note that as you revise the manuscript these numbers might have to be adjusted as paragraphs get bumped around!

Additional style pointers:

  • You absolutely need to use different colors to differentiate the reviewer comments from your replies. Since your replies are what’s new and important, I like to use black for that and change the reviewer comments to a lighter shade of something else. I’ve found soft blue (CornflowerBlue) to be quite nice, though a lighter gray (LightSlateGray) and maybe even orange (SandyBrown) or purple (Plum/MediumOrchid) is OK. Any shade of red feels too angry for my liking. Note at the top of my rebuttal I specify what color choices I made.
    • I have seen other methods like different fonts, italics vs. non-italics, adding a horizontal line, etc., but these have either been clunky, confusing, or insufficiently nondescript.
  • I like to start each reviewer comment on a new page as well, for readability and to keep ideas chunked.
    • Sometimes a reviewer will write a giant paragraph with many comments. In these cases, I’ve found it helpful to break the paragraph into thematically similar sets and respond to each one separately (on a new page).
    • Analogously, sometimes they’ll write many single-sentence paragraphs on the same point. You can write a single reply addressing all of them, but copy over the reviewer comments as is, i.e., don’t combine them into a single paragraph.
  • Strategy: All good battles need a clear strategy for victory. I’ve been taught that there’s three types of replies:
    • Direct comments: These are easiest to just acknowledge and directly change (typos, clarity, references, and where you’re legitimately wrong).
    • Philosophy: Thanks, but no changes are probably needed. They’re not saying what you’re doing is wrong or misleading, they just have a different perspective (that you acknowledge as valid, but you believe your views better aid the messaging/presentation).
    • Disagreements: Stand firm, but acknowledge that you were perhaps unclear and suggest a few changes to appease the reviewer.
  • Expressing thanks: You definitely should, but you don’t need to overdo it. I do it once in the cover letter to the editor, so they’re aware I’m grateful for the reviewers, and I do it at the end of each reviewer’s comments, instead of at the start or after a few/each comment. To me this feels like the most professional approach.
  • Additional changes: If you make any substantial changes to the manuscript that weren’t brought up by the reviewers (such as correcting some notation, analysis, or figures), you should make a note of this at the end of the rebuttal in a dedicated section. It is important to emphasize how these changes affect the conclusions of your work.
  • Mindset/tone: This is your work, and you should be proud of it! I strongly recommend going in with a positive mentality, that the reviewers are there to elevate your work. This makes the process a lot less painful and could lead to some surprising revelations. If a reviewer is being difficult for no good reason, it’s on you to remain professional and steadfast in your beliefs, though that can be difficult at times—here is where you might say something in your cover letter to the editor!
  • I’ve recently started a habit of keeping track of the current page and total page numbers on all documents I write, including rebuttals, but this is uncommon. If you’ve written a long rebuttal though, it might be a nice reminder to the editors and reviewers of the ordeal they put you through.
  • This is not a style point, but know that reviewers, upon receiving your reply, will also see your replies to the other reviewers (i.e., the full rebuttal) and hence their peers’ comments since you’ve copied them over (they won’t see this in the initial round). So it pays to be generally reasonable to all!

I know this is a lot to just read through and keep track, which is why you should cross reference with my actual rebuttal here. Of course, all of these suggestions come second compared to the quality of your work and writing, but I hope having a better structure will lead to a more enjoyable peer review process for all.