Response to Reviewers

When to use

Preparing the response letter for a revised manuscript.
Drafting a rebuttal for a reject-with-resubmission decision.
Reviewing a colleague's response letter before submission.
NOT for initial submission cover letters (use cover-letter-medical for that).

Core principles

Every comment gets a response. Even if the answer is "we agree and have changed X" — silence is read as ignoring.
Tone: respectful and assumes good faith, even when the reviewer is wrong. Editor reads the response too.
Format: the editor and reviewers should be able to track changes without re-reading the manuscript.
Disagreement is allowed, but must be supported with evidence (citation, clarification, additional analysis).

Process

Phase 1 — Triage all comments

Categorize each reviewer comment into one of:

| Category | What to do | |---|---| | Valid + easy | Make the change, acknowledge gratefully | | Valid + costly (new analysis, new figure) | Make the change if feasible; if not, explain trade-off | | Misunderstanding | Clarify in manuscript AND in response | | Disagreement | Push back politely with evidence | | Out of scope | Acknowledge the point, defer to future work, justify deferral | | Contradictory between reviewers | Pick one path, explain the choice to both |

Phase 2 — Structure of the response document

Standard format:

Dear [Editor name],

We thank the editor and reviewers for their constructive feedback on our 
manuscript [REF #]. We have carefully addressed each comment below. Changes 
in the revised manuscript are highlighted in [color/track-changes]. We believe 
these revisions have substantially strengthened the manuscript.

Sincerely,
[Authors]

----

Reviewer 1

Comment 1.1: [Verbatim quote of reviewer's comment]
Response: [Your response]
Changes: [Page X, lines Y-Z, or "no changes needed because..."]

Comment 1.2: [...]
Response: [...]
Changes: [...]

----

Reviewer 2
[Same structure]

Phase 3 — Drafting individual responses

Template for "we agree"

Comment: [verbatim]

Response: We thank the reviewer for this important observation. We have 
[specific action: re-analyzed X, added Y to the discussion, clarified Z 
in Methods]. The revised text now reads:

"[New text from manuscript]"

Changes: Page X, lines Y-Z.

Template for "we disagree but politely"

Comment: [verbatim]

Response: We respectfully disagree with this interpretation, although we 
appreciate the reviewer's careful reading. Our reasoning is as follows:
[Evidence-based argument: citation, methodological justification, additional 
sensitivity analysis result]

To address the underlying concern, we have [softening action: added a 
limitation, clarified the rationale, conducted a sensitivity analysis 
showing the conclusion is robust].

Changes: [If any made; or "We did not modify the original analysis 
because..."]

Template for "out of scope"

Comment: [verbatim]

Response: This is an excellent suggestion that we agree warrants future 
investigation. However, [specific reason it's out of scope: data not 
available, sample size insufficient, requires prospective design]. We have 
acknowledged this point in the Discussion as a direction for future work:

"[Quote from revised manuscript]"

Changes: Page X, lines Y-Z.

Template for "misunderstanding / clarification"

Comment: [verbatim]

Response: We thank the reviewer for highlighting this point of confusion, 
which suggests our original wording was insufficiently clear. To clarify: 
[plain-language explanation of what was actually done]. We have revised 
the [Methods/Results/Discussion] section to make this explicit:

"[Quote from revised manuscript]"

Changes: Page X, lines Y-Z.

Phase 4 — Tone calibration

Phrases that work well

"We thank the reviewer for this insightful comment."
"We appreciate the reviewer's careful reading."
"We respectfully disagree, and our reasoning is..."
"This is a valuable suggestion. We have..."
"We acknowledge this limitation and have..."

Phrases to AVOID

| Don't write | Why | Alternative | |---|---|---| | "The reviewer is mistaken" | Confrontational | "We respectfully disagree" | | "As we clearly stated..." | Implies reviewer didn't read | "To clarify our original statement..." | | "This is beyond the scope" (without justification) | Dismissive | "This warrants future investigation; specifically because [reason]..." | | "We have addressed this concern" (without specifics) | Vague | Quote the change verbatim | | "Obviously..." | Condescending | Just explain |

Handling Reviewer 2 (the difficult one)

Stay even-toned. The editor sees both reviews.
If a request is unreasonable (e.g., "redo the entire analysis with a different cohort"), explain WHY it's unreasonable in factual terms (data unavailable, beyond stated scope, prior multi-center validation already shows generalizability).
If a reviewer demands a citation to their own work that isn't relevant, decline politely: "We considered this reference but found it addresses [different topic X], whereas our study focuses on [Y]."
If two reviewers contradict, pick the one more aligned with the editor's letter and explain the choice to both.

Phase 5 — Final checks

[ ] Every reviewer comment has an explicit response.
[ ] Every change has a page/line reference.
[ ] Tone is respectful throughout, even on disagreements.
[ ] Response letter is also numbered/structured (not a wall of text).
[ ] Quoted reviewer comments verbatim (avoids "you said something I'm interpreting" arguments).
[ ] Manuscript changes match what's described in the response.
[ ] Track changes / colored highlighting consistent in revised manuscript.
[ ] Reviewer-numbered response (Reviewer 1, Reviewer 2 — keep them anonymous in your text).
[ ] No defensive language, no excuses, no implicit blame on reviewers.
[ ] Editor's letter also addressed if it had specific points beyond reviewer comments.

Anti-patterns

| Pattern | Why it fails | Correction | |---|---|---| | Bulk responses ("We have addressed all comments below...") | Editor needs traceability | Numbered, point-by-point | | Defensive tone | Suggests author can't take feedback | Even when right, frame collaboratively | | Ignoring a comment | Treated as not addressing | Always respond, even if just to clarify | | Making changes without flagging where | Reviewers will ask | Always cite page/line | | Long philosophical justifications | Reviewers tire | Keep responses focused, evidence-first | | Apologizing for limitations of the field | Unprofessional | State limitation factually, propose mitigation |

Output format when invoked

When invoked, ask the user for:

The reviewer comments (paste verbatim).
The relevant section of the original manuscript (so changes can be drafted).
The author's preferred stance (agree/disagree/clarify) per comment, if known.

Then produce:

Drafted point-by-point response in the standard format.
Suggested manuscript edits as quoted text with track-change markers.
Flag any comments where the user should reconsider their stance based on review of the comment's validity.