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Revising Your First Scientific Manuscript

“Dear Author”.

That email salutation, and minor variations, still gives me a jolt of adrenaline and trepidation. I’ve been publishing scientific papers for almost three decades, but I frantically read through manuscript decision emails, trying to figure out whether the paper has been accepted, or at least has a shot at being published by the journal I’ve submitted it to.

That feeling of anxiety, followed by relief/celebration/angst, will always be with you throughout an academic career, but what I hope to help you with are strategies to getting a manuscript from the “Minor Revisions”, “Major Revisions”, or even “Reject” buckets to the “Accept” category.

Did I grab your attention with the reference to converting rejected manuscripts to the accepted state? Good, more on that later.

The first thing you should do upon receipt of a manuscript decision email is to read it thoroughly. Most of these emails are structured in the following order: statement of the decision type (“Minor Revisions”, “Major Revisions”, “Accept”, “Reject”), followed by reviewers’ comments (anywhere from one to four or more, with two or three being most common), and ending with editorial comments. The majority of editorial comments are related to requests for formatting manuscripts in order to align them with a journal’s standards for citations, manuscript organization, and other relatively mundane considerations. Occasionally a helpful editor will insert commentary that may facilitate eventual acceptance of a manuscript.

Unless your manuscript has been outright accepted, it will need to be revised. You should share the email with your principal investigator and all of your other co-authors, but only append a brief note and state that you will circle back soon to discuss next steps. If the reviewers’ and/or editor’s comments make you angry or upset, which is a common reaction, I advise walking away from the email for a few days. It may be tempting to dash off an email to the editor in the heat of the moment, and I have heard some entertaining stories of such, but a hostile message is almost certainly going to hurt your cause. Go for a run, drink some wine, destroy some effigies of your reviewers (without involving flamethrowers), whatever you need to blow off steam.

Once you’re feeling more rational, re-read the reviewers’ and editor’s comments. I recommend copy and pasting the comments into a word processing document. Even if the manuscript has been rejected, jot down rough responses to the comments (incomplete sentences and phrases are fine at this stage). Note that I am *not* necessarily advocating for responding to every reviewer comment. Sometimes reviewer comments are rhetorical, or unimportant. You’ll have to make judgement calls about which reviewer points need to be addressed, and which do not. If you think particular reviewer comments don’t warrant a response, consider not including them in this document. Set up a meeting with your principal investigator to discuss the manuscript decision, reviewers’ and editor’s comments, and your proposed responses.

In my mind this meeting is key to getting a grasp on the feasibility of successfully revising the manuscript and/or appealing a rejection decision. This discussion is also important for understanding the likely amount of effort required to get the manuscript accepted. Personally, I consider revisions “easy”, regardless of whether the editor has classified the manuscript decision as “Major Revisions” versus “Minor Revisions”, if no additional experiments need to be performed. The distinction between major and minor revisions being required is completely a judgement call made by the editor, largely based on the reviewers’ comments.

If you and your principal investigator deem that additional experiments need to be completed to satisfy the reviewers and editor, consider how long it will take to perform the work, as well as how expensive it will be. It’s also pertinent to consider whether these experiments are possible (perhaps a key reagent is no longer available), and if the required work is truly germane to your manuscript.

This is a good time to re-contact your co-authors and arrange a group discussion of the manuscript and next steps.

TIP: manuscript rejections can be appealed. Such appeals are not always successful, but if you put forward a compelling argument to the editor why your manuscript decision should be modified to major or minor revisions (this is where your point-by-point responses to the reviewers’ comments are critical), the editor may reverse the decision. The worst thing that could happen is that the editor can say “no, the decision remains to reject this manuscript”.

Alternatively, you, your principal investigator, and co-authors may decide that the reviewers’ and editor’s comments either are too onerous, or not possible to respond to. This may be a point at which you opt to send your manuscript to another journal. In fact, sometimes manuscripts are revised after additional experimentation is completed based on reviewer feedback, and then the co-authors decide to send the manuscript to a higher impactjournal because the paper has been improved!

If you choose to revise your manuscript with your co-authors, be organized and thorough. Assign specific tasks(with timelines) to your co-authors according to their original contributions to the manuscript. For instance, if co-author “A” provided technical expertise for a given technique, and co-author “B” primarily assisted with manuscript writing, you may want to delegate revision-related, technique-specific tasks to “A” and re-writing of certain manuscript sections to “B”. Discuss possible delegation of tasks with your principal investigator before approaching your co-authors.

Once collective decisions have been made by you and your co-authors regarding revision-related tasks, determine if you need a manuscript revision deadline extension. If you judge that an extension may be necessary, request it early. Most editors are happy to provide deadline extensions, as long as it appears that the co-authors are genuinely progressing on revisions.

After you receive revision-related feedback from your co-authors, collate it in a pair of “tracked changes” and “clean” (no tracked changes) versions of the manuscript. This will facilitate finalization of the manuscript by you and your co-authors, and is also required by most journals.

I suggest reassessing each co-author’s contributions to the manuscript, and discussing any authorship order changes with your principal investigator. During the revision process, the contributions of individual co-authors may be significantly different than those made during the writing of the original manuscript.

The majority of journals also mandate a cover letter and response to reviewers’ comments document. You can modify your original manuscript’s cover letter (see my prior blog entry on writing your first scientific manuscript for more information on this), and you should already have a response to reviewers’ comments document.

Before uploading and submitting the final revised manuscript, re-read the manuscript decision email and ensure that you have addressed everything that you think is important. Once you’ve verified this, re-submit your manuscript.

If you’re thorough and convincing in your revised manuscript and associated documents, hopefully you’ll only go through one round of revisions. In the event that more than one round of revisions is needed, cycle through the process I’ve outlined above as needed, and reassess the manuscript and reviewers’ comments at each revision stage. Good luck!