Responding to reviewers is a critical step in the publication process. A well-structured, respectful response can significantly improve your chances of acceptance.

You’ll need 3 files. The first is for your point-by-point response to the reviewers, and the second is your revised manuscript. The third (to be generated by a tool) is to mark the changes in your revised manuscript compared to the original. The revised manuscript is something you have to prepare on your own. Here, we will just talk about how to prepare the response to the reviewers and how to generate the LaTeX file that shows the difference between the manuscripts.

Preparing the Response to Reviewers File

This is an example response to the reviewer file:

Responding to reviewer feedback is a crucial, and often challenging, part of the academic publishing process. A thoughtful, organized, and respectful response not only addresses the reviewers’ concerns but also demonstrates your professionalism to the journal editor. The goal is to show that you have engaged seriously with the feedback and have improved your manuscript accordingly.

I. The Golden Rules: Overall Philosophy

Before you type a single word, adopt the right mindset.

1. Be Grateful, Not Defensive: The reviewers are volunteering their time to help improve your work. Even if a comment seems harsh or off-base, treat it as a genuine attempt to help. Start by thanking them.
2. The Editor is Your Primary Audience: While you are responding to the reviewers, your ultimate goal is to convince the editor that your revised manuscript is now suitable for publication. Your response letter is a key piece of evidence.
3. Answer Everything: Do not ignore a single comment, no matter how small or seemingly irrelevant. Every point must be acknowledged and addressed.
4. Make it Easy for Them: The editor and reviewers are busy. Your response document should be clear, well-organized, and easy to navigate. The easier you make their job, the more favorable they will be.

II. Structuring Your Response Letter

A standard response letter has three main parts.

1. The Opening

Start with a polite and professional opening.

• Address the editor by name.
• Thank the editor and all reviewers for their time and insightful comments.
• Clearly state the manuscript title and ID number.
• Briefly provide a high-level summary of the major changes you have made. For example: “We have substantially revised the manuscript based on the reviewers’ feedback, including conducting a new analysis for Figure 3 and rewriting the introduction to better frame our research question.”

2. The Point-by-Point Response

This is the core of your document.

• Address each reviewer individually (e.g., “Response to Reviewer #1,” “Response to Reviewer #2”).
• List each of the reviewer’s comments verbatim. It’s a common practice to format the reviewer’s comment in italics or a different color to distinguish it from your response.
• Number each comment for clarity.
• Below each comment, write a clear and concise response.
• Start your response by thanking the reviewer for their suggestion (e.g., “We thank the reviewer for this excellent point.”).
• Clearly state what changes you made and, crucially, where to find them in the revised manuscript (e.g., “We have now clarified this point in the Methods section, page 5, lines 110-115.”).

3. The Closing

End with a brief, polite closing.

• Reiterate your thanks to the editor and reviewers.
• Express your hope that the revised manuscript is now suitable for publication in their journal.
• Sign off with your name and affiliation.

Best Practices for Answering Comments

When You Agree with the Comment

This is the most straightforward scenario.

• Do: State your agreement, make the change, and direct the reviewer to the exact location of the change.
• Example:
  Reviewer Comment: “The authors should clarify what statistical test was used for the data in Figure 2.”
  Response: “We thank the reviewer for pointing out this omission. We have now specified that a two-tailed t-test was used and have added the exact p-values to the figure legend (Page 8, lines 150-152).”

When You Disagree with the Comment

This requires more tact. The goal is to respectfully decline the suggestion while providing a compelling, evidence-based reason.

• Do: Start by acknowledging the reviewer’s point and showing that you have considered it carefully. Then, provide a polite and logical rebuttal. Back up your reasoning with evidence from your data or citations from the literature if possible.
• Don’t: Never be dismissive, arrogant, or emotional. Phrases like “The reviewer clearly misunderstood…” are a red flag. Instead, say, “We apologize if our initial phrasing was unclear…”
• Example:
  Reviewer Comment: “The study should have included a cohort from a different country to test for generalizability.”
  Response: “We thank the reviewer for this valuable suggestion. We agree that a multi-national cohort would indeed strengthen the study’s conclusions. However, collecting such data is a significant undertaking that is beyond the scope of the current project. We have acknowledged this limitation and suggested it as an important direction for future research in the Discussion section (Page 12, lines 230-235).”

When a Comment is Unclear

If you genuinely don’t understand a comment, do your best to interpret it.

• Do: State your interpretation of their concern and address that. This shows you are making a good-faith effort.
• Example:
  Reviewer Comment: “The discussion is weak.”
  Response: “We thank the reviewer for this feedback. We interpreted this to mean that our discussion did not sufficiently connect our findings to the existing literature. We have therefore rewritten the first three paragraphs of the Discussion to provide a more thorough synthesis and contextualize our results (Pages 10-11).”

Handling Math Equations in Your Response

Pasting raw LaTeX code for reviewers to read is not ideal. Here are the best approaches:

• Recommended: If you don’t use Latex but use Word, Word has equation mode. If you use Google Docs, to type an equation, go to Insert > Symbol > Equation to insert the equation.
• Alternative (if not using LaTeX for the letter): If you prefer writing your response letter in a tool like Word or Google Docs, then using an external equation editor is a great idea.
  • Go to a site like CodeCogs Equation Editor (https://editor.codecogs.com/).
  • Create your equation.
  • Download it as an image (PNG/SVG) or copy the image and simply paste that image into your response document. This is clear, professional, and very easy for the reviewer to read.

How to prepare the file that highlight the difference between the revision and the original manuscript

The best way to show changes is not by manually coloring text, but by using a dedicated tool. The industry standard is latexdiff.

• What is latexdiff? It’s a command-line utility that compares two .tex files (original.tex and revised.tex) and automatically generates a new file (diff.tex) where all additions are highlighted (usually in blue and underlined) and deletions are marked (usually in red and struck through).
• How to Use It:
  1. Save your original submission as original.tex.
  2. Make all your revisions in your main manuscript file, let’s call it revised.tex.
  3. Open a terminal or command prompt.
  4. Run the command: latexdiff original.tex revised.tex > diff.tex
  5. Compile the new diff.tex file. The resulting PDF will be a beautiful, easy-to-read document showing every single change you made.
     Example output: