Response to Peer Reviewers

Produces a respectful, point-by-point response to peer-reviewer comments on a manuscript or grant proposal: structure, tone, line-numbered references, framing conventions ("we have now done this", "we respectfully disagree"), handling of conflicting reviewers, formatting of the response document, partial-response strategy, and grounds for appeal. Adapted by Pradyumna Jayaram from journal and funder guidance (ICMJE, COPE, Nature, eLife, PLOS, EMBO, NIH).

When to use

You have received peer-reviewer comments on a journal manuscript and need to write a point-by-point response for a revised submission.
You have received summary statements on a grant proposal and need to write a formal response (introduction page, response to critiques, or both).
You are running an internal mock-rebuttal for a colleague or trainee.
You are considering a partial response, an appeal of a desk reject, or a withdrawal, and need a structured framework for the decision.
You are co-authoring the response and need a shared template for coordinating across co-authors.

When NOT to use

For conducting the initial review of someone else's work (use ors-peer-review-manuscript-review or ors-peer-review-grant-review).
For evaluating a researcher's overall record (use ors-peer-review-scholar-evaluation).
For writing the original manuscript or proposal (use a scientific-writing or grant-writing skill).
For informal, off-record replies to a colleague or a single comment by email.

Prerequisites

A complete set of the reviewers' comments, the editor's decision letter, and any specific instructions (deadline, length, format).
A complete, marked-up copy of the original manuscript or proposal, with the planned changes tracked.
Co-author input on which changes to make, which to push back on, and which to defer.
Access to the funder's or journal's specific format requirements (e.g., NIH "Introduction" page length and content; journal-specific response templates).
Familiarity with the relevant reporting checklist (CONSORT, STROBE, PRISMA, etc.) for the manuscript type, since revisions are an opportunity to bring the manuscript into compliance.

Core workflow

1. Pre-flight checks

Re-read the editor's decision letter carefully: is this a reject, a major revision, a minor revision, or an accept-with-revisions? The decision letter sets the scope of what is appropriate to address.
Note the deadline, the maximum response length, and any required format (e.g., a single PDF response, an introduction page plus a detailed response, an annotated manuscript).
Re-read the reviewers' comments without reacting: separate the substance of each comment from the tone. Identify the underlying concern behind each comment, which is often a request for a clearer claim, a stronger method, or a more honest discussion.
Identify which comments are convergent (multiple reviewers raise the same concern) and which are divergent (reviewers disagree). Convergent comments almost always require action; divergent comments often allow for a more measured response.
Schedule a co-author meeting early in the revision process to align on strategy, divide work, and pre-empt internal disagreement.

2. Triage the comments

For each reviewer comment, classify it into one of four buckets. This triage drives the response structure.

Bucket	What it means	How to respond
Will address	Substantive concern; we agree or we will do the work.	State the change, give the new manuscript location, and quote the new text.
Will partially address	Substantive concern; we will do part of the work, citing feasibility, scope, or a principled reason for the limit.	State what we will do, explain the limit, and offer a justification.
Will respectfully disagree	Concern is misguided, factually incorrect, or out of scope; we will provide reasoning, not changes.	Acknowledge the concern, provide a respectful counter-argument with evidence, and, where appropriate, add a clarifying sentence to the manuscript.
Acknowledged, no change needed	Comment is appreciated; the manuscript already addresses it; we are pointing the reviewer to the relevant section.	Point to the existing section and quote the relevant text.

Avoid a fifth bucket, "will ignore": silent non-response to a reviewer's comment reads as dismissal and is rarely appropriate. If a comment is genuinely not actionable, classify it under "respectfully disagree" with a brief explanation.

3. Tone and framing conventions

The response document is itself a piece of scientific writing. It is read by the editor first, by the reviewers second, and may be quoted in published reviewer reports (e.g., eLife's open process publishes reviewer comments and author responses).

Respectful throughout. No sarcasm, no sniping, no "the reviewer is mistaken." Frame as "we agree that this point is important" or "we respectfully disagree for the following reason." When a reviewer is right, say so explicitly: "We thank the reviewer for identifying this gap; we have now done X."
Constructive, not defensive. The goal is to bring the manuscript to publication, not to win a debate. A reviewer who is wrong is best handled with evidence and a brief, respectful counter-argument; do not over-defend.
First-person plural ("we") for the author team. "We have now done this" is the standard phrasing for changes; "the authors have now done this" reads as a third-party report.
Self-deprecating where appropriate. "We acknowledge that this was not clearly stated; we have now revised the text to make X explicit."
Specific, not general. "We have added a power analysis" is a beginning; "we have added a power analysis using G*Power 3.1 with effect size d=0.5, alpha=0.05, power=0.8, yielding n=64 per group (Methods, p. 9, lines 220-235)" is the response.
No ad hominem. Do not question the reviewer's expertise, motives, or language. If the reviewer's comment is in poor English, that is the editor's problem, not yours.
No reference to the review process in the manuscript. The revised manuscript should read as if the issues were never in doubt; meta-commentary about "the reviewer asked us to" does not belong in the manuscript text.

4. Structure of the response document

Use a consistent structure that the editor and reviewers can navigate quickly.

Cover letter (if required by the journal): a one-page summary of the major changes and a brief response to any specific editor concerns.
Point-by-point response: each reviewer addressed in a separate section. Within each reviewer, each numbered or bullet comment addressed in order.
For each comment:
- Quote the reviewer's comment verbatim (or summarize it accurately if the journal has already anonymized it).
- State the response and the action taken.
- Quote the new or revised text in the manuscript.
- Give the line numbers or section in the revised manuscript.
A consolidated "summary of changes" at the end: a one-page list of the major revisions with cross-references to the response sections.
A "highlighted" or "tracked-changes" copy of the revised manuscript to make the changes easy to verify.

If the journal or funder has a specific response template, follow it.

5. Handling specific comment types

"Add a control" or "rerun the analysis"

State whether you can do the work, in what time frame, and at what cost.
If the request is infeasible (e.g., the original samples are exhausted), say so explicitly and explain why; offer a proxy or a power-analysis justification.
If the request is feasible, do it and report the new result.

"The writing is unclear"

Rewrite the relevant passage and quote both the old and the new text.
Avoid saying "we have clarified" without showing the new text; reviewers and editors will be skeptical.

"Cite X" or "cite a more recent paper"

Add the citation where appropriate, or, if the citation is not appropriate, explain why (off-topic, low-quality, retracted).

"Contradictory finding in the literature"

Cite the contradicting paper in the Discussion, characterize it accurately, and discuss why the field is divided or what might explain the discrepancy.
Do not over-claim novelty; if a contradicting paper exists, the manuscript should acknowledge it.

"Speculation in the Discussion"

Re-label speculation as speculation ("we hypothesize that...", "we speculate..."), and add a one-sentence caveat ("this hypothesis remains to be tested directly").
Move the most speculative claims out of the abstract and into a clearly labeled paragraph in the Discussion.

"Statistics"

Address each statistical concern explicitly: name the test, the alpha, the multiple-comparison correction, the handling of missing data, the software and version.
Add a statistician as a co-author or acknowledge a statistical reviewer in the Acknowledgements if appropriate; this signals that the work has been independently validated.

"Figure issue"

Replace the figure, add a panel, add a scale bar, or relabel an axis. Quote the figure legend or panel label that has been changed.

"Data or code availability"

Deposit the data and code with a persistent identifier (Zenodo, Figshare, domain-specific repositories). Add the accession number or DOI to the manuscript. A "data available upon request" is no longer acceptable at most journals and funders.

"Out-of-scope request"

"The reviewer suggests we test our findings in population Y. While this would be a valuable follow-up, the scope of the present manuscript is population X. We have added a sentence to the Discussion noting this as a future direction."

"Anonymous or harsh comment"

Do not respond to tone. Respond only to substance. If a comment is unprofessional, address it in a separate confidential-to-editor note, not in the public response.

6. Handling conflicting reviewers

When two reviewers disagree, the editor's summary statement usually identifies the conflict and may take a side. Strategy:

Identify the editor's signal. If the editor's letter affirms one reviewer's position, treat that as the more binding guidance; address the other reviewer respectfully and briefly.
Address both, not just the editor's signal. Ignoring a reviewer because the editor sided against them is risky; the editor may change their mind, or the reviewer may be re-invited.
Where the conflict is methodological (e.g., Reviewer 1 wants frequentist, Reviewer 2 wants Bayesian), acknowledge both, choose one with reasoning, and note the alternative in the Discussion.
Where the conflict is interpretive (e.g., Reviewer 1 thinks the data support a strong claim, Reviewer 2 thinks the claim is overstated), moderate the claim in the manuscript to a level both could accept, and explain the moderation in the response.
Where the conflict is unreconcilable (e.g., Reviewer 1 wants major new experiments, Reviewer 2 wants the manuscript rejected), follow the editor's decision letter; if the decision is "major revision," the experiments are expected.

7. When to send a partial response

A partial response is appropriate when:

The editor's letter has given you the latitude to address only certain comments (e.g., minor revision, where the editor is satisfied with the substantive content and only wants presentational fixes).
A comment is genuinely infeasible (e.g., the original samples are exhausted, the original IRB approval did not cover the requested analysis), and the editor will accept a justification.

A partial response is not appropriate when:

The editor's letter says "major revision" and you have skipped a major concern. The editor will treat this as a non-response and may reject without re-review.
The comment is convergent (multiple reviewers raised it). A non-response on a convergent comment will be noticed.

When sending a partial response, make the limits explicit in the response document. Do not pretend the change was made; state the reason and the alternative you have chosen.

8. When to appeal a desk reject

A desk reject is a decision by the editor not to send the manuscript out for review. It is generally based on scope, novelty, methodological concerns, or fit with the journal's bar.

Appealable grounds: clear evidence that the editor misunderstood the manuscript's scope, novelty, or fit; factual errors in the editor's letter; a process error (e.g., the manuscript was sent to a reviewer who has a clear conflict of interest).
Not appealable: disagreement with the editor's judgment on scope, novelty, or fit. The editor has discretion; respectful disagreement is a reason to submit elsewhere, not to appeal.
Tone of an appeal: brief, factual, respectful. State the specific ground for appeal, quote the relevant editor language, and provide evidence. One or two pages, not a re-statement of the manuscript.
Consequences of an appeal: the editor may reconsider, may forward to a senior editor, or may decline. If the appeal is declined, the manuscript can still be submitted elsewhere; do not burn the relationship.

9. Formatting the response document

File format: a single PDF with the response, a tracked-changes copy of the manuscript, and a clean copy of the revised manuscript, in the format the journal specifies.
Page length: many journals allow 2–4 pages of response. Be concise; a verbose response is harder to read and signals defensiveness.
Quoting the reviewer: italicize or indent the quoted comment. Many response templates use bold "Comment" and "Response" labels.
Line numbers in the revised manuscript: many journals require a line-numbered copy of the revised manuscript; use the journal's preferred line-numbering scheme.
Color in tracked changes: red for additions, blue for deletions, is a common convention; some journals prefer strikethrough. Follow the journal's preference.
Highlight on a "high-resolution" change list: a one-page summary of the most important changes at the end of the response is useful for the editor and the reviewers.

10. Tone and ethics checks (final pass)

The response document is itself a piece of writing. Have a co-author who is not the corresponding author read it for tone.
No snark, no sarcasm, no pejorative adjectives about the reviewers.
No accusation of the reviewers' motives, competence, or language.
No confidential-to-editor comments that contradict what is said to the reviewers.
No over-claiming in the revised manuscript. If a reviewer said the manuscript over-claimed and the revision still over-claims, the reviewers will notice on re-review.
No reference to the revision process in the manuscript body (except where it would be useful, e.g., a "Reporting checklist" section).

11. Finalize the response

Run a final pass to confirm: (a) every reviewer comment is addressed, (b) every change is quoted with location, (c) the response document is internally consistent, (d) the cover letter summarizes the major changes briefly, (e) the deadline is respected or an extension requested proactively.
Submit the package in the journal's or funder's required format. Some systems require separate uploads for the response, the tracked-changes manuscript, and the clean manuscript.

Code patterns

Standard response-document skeleton (manuscript revision)

================================================================================
RESPONSE TO REVIEWERS
Manuscript ID: [ID]
Title: [Title]
Corresponding author: [Name]
Date: [Date]
================================================================================

We thank the editor and the reviewers for their thoughtful and
constructive comments. We have addressed each comment in turn below.
All line numbers refer to the revised manuscript (tracked-changes copy
attached). Major changes are summarized at the end of this document.

================================================================================
REVIEWER 1
================================================================================

Comment 1.1: "[verbatim reviewer comment]"

Response: We thank the reviewer for [acknowledging the issue / raising
 this important point / identifying the gap]. We have now [action
 taken]. Specifically:

Revised text (lines X-Y): "[quote of the new text]"

Comment 1.2: ...

================================================================================
REVIEWER 2
================================================================================

Comment 2.1: ...

================================================================================
SUMMARY OF MAJOR CHANGES
================================================================================

1. [Major change 1] — see Response to Reviewer [n], Comment [m],
   lines X-Y of the revised manuscript.
2. [Major change 2] — see Response to Reviewer [n], Comment [m],
   lines X-Y of the revised manuscript.
3. ...

Standard response-document skeleton (grant resubmission, NIH)

================================================================================
INTRODUCTION TO RESUBMISSION
Application ID: [ID]
PI: [Name]
Title: [Title]
Date: [Date]
================================================================================

The Introduction is structured to address each of the major and minor
concerns raised by the reviewers in the prior summary statement. We
begin with a one-page overview of the major changes, then provide a
detailed, point-by-point response to the prior critiques.

1. Overview of major changes
-----------------------------
[One-page summary of the changes, organized by aim.]

2. Point-by-point response to prior critiques
-----------------------------------------------
Critique 1: [Verbatim or accurate paraphrase of the prior summary
 statement's critique.]
Response: [Action taken, with location in the revised application.]

Critique 2: ...

3. Updated reporting and compliance items
-------------------------------------------
[IRB / IACUC, data sharing, trial registration, etc.]

Reusable framing conventions

Situation	Phrasing	Note
Issue identified; we agree	"We thank the reviewer for identifying this gap. We have now [action]."	Direct, specific.
Issue identified; we disagree	"We respectfully disagree. [Reasoning with evidence]. To address any ambiguity, we have added a sentence to clarify: [quote]."	Reason, then small concession.
Issue out of scope	"While this would be a valuable follow-up, the scope of the present manuscript is X. We have added a sentence to the Discussion noting this as a future direction."	Defers without dismissing.
Comment already addressed	"We agree this point is important. The manuscript already addresses it on lines X-Y: [quote]."	Quote, don't summarize.
Comment partially addressed	"We have [action], but note that [limit]. We have added [smaller fix] to the manuscript as a partial response."	Be explicit about the limit.
Editor's specific concern	"Per the editor's letter, we have [action]."	Cite the editor's letter.

Reusable decision framework

Decision	When appropriate	When not appropriate
Address the comment in full	Convergent comment; comment is feasible and the change improves the manuscript	Comment is out of scope or impossible; the change would not improve the manuscript
Address partially	Comment is feasible in part, but the full request is out of scope or impossible	Comment is feasible in full and the change clearly improves the manuscript
Respectfully disagree	Comment is factually incorrect, out of scope, or conflicts with a stronger reviewer	Comment is a legitimate methodological concern; the change is feasible and improves the manuscript
Point to existing text	Comment is already addressed; the reviewer missed it	Comment is not addressed and the change is feasible
Appeal a desk reject	Clear evidence of misreading, factual error, or process error by the editor	Disagreement with the editor's judgment on scope, novelty, or fit
Submit elsewhere	Rejection after review; convergence among reviewers that the work is out of scope	Major-revision decision with the editor's support for further work

Common pitfalls

Defensiveness: the response is the most-read piece of writing in the revision. A defensive response signals that the authors have not actually engaged with the critique. Write calmly, with evidence, and acknowledge the reviewer's point even when you disagree.
Vague change language: "We have clarified the text" is not a response. Quote the new text, give the line numbers, and explain why the new text is the right one.
Burying the changes: do not make a substantive change without highlighting it in the response document and the cover letter. The editor and reviewers should be able to verify the change in seconds.
Over-defending a weak point: if a comment is correct, accept it. Fighting a comment that is clearly right wastes reviewer goodwill and reads as tone-deaf.
Contradicting the editor: the editor's letter sets the scope. If the editor's letter is silent on a reviewer comment, you have more latitude; if the editor's letter is explicit, follow it.
Ignoring a comment because it is hard: the editor and reviewers will notice. A clear explanation of why the comment is infeasible is a valid response; silence is not.
Inconsistent response across co-authors: have one author draft the response, and a second author read it for tone and accuracy. Internal disagreement is fine; presenting it in the response is not.
Over-claiming in the revised manuscript: a revision that doubles down on an over-claim that a reviewer flagged is a fast path to a second rejection.
Pasting the response into the manuscript body: the response is a separate document. The revised manuscript should read as a clean, self-contained document.
Missing the deadline: most journals and funders have a strict revision window. If you cannot meet it, request an extension proactively, with a brief explanation.
Forgetting the cover letter: the cover letter is the editor's first read. A clear, one-page cover letter that summarizes the major changes is the single highest-leverage piece of writing in the package.

Validation

A good response document is itself a piece of scientific writing. Before submitting, check:

Open alternatives

Open peer-review platforms (eLife's reviewed preprints, F1000Research, Open Review) publish the reviewer comments and author response alongside the article, making the response document a public scholarly artifact. Closed review platforms (ScholarOne, Editorial Manager) keep the response private to the editor and reviewers.
Open-source manuscript and proposal templates (e.g., Quarto, LaTeX templates on Overleaf) make the response document and the tracked-changes manuscript easy to produce in a version-controlled, reviewable format.
Open citation and reference managers (Zotero with Better BibTeX, JabRef) help in updating references during a revision without manual error.
Open repositories (Zenodo, Figshare, OSF, domain-specific repositories) for data, code, and pre-registration linked to the revised work.
Open response templates published by journals (e.g., eLife's reviewed-preprint format, PLOS's revision guidelines) provide a public model for the structure of a response.
AI assistants for prose polish are useful for tightening the response document, but the authors' judgment remains the deciding factor; do not paste confidential reviewer comments or the unpublished manuscript into a third-party LLM without the journal's or funder's approval.

References

Internal cross-links

ors-peer-review-manuscript-review — for conducting the initial review of someone else's work.
ors-peer-review-grant-review — for reviewing a grant proposal.
ors-peer-review-scholar-evaluation — for evaluating a researcher's overall record.
ors-scientific-writing-response-to-reviewers — author's side of the same process (this skill).
ors-scientific-writing-manuscript-structure — IMRAD structure, useful for orienting the response.
ors-ethics-compliance-irb — ethics / IRB framing for methods that may be revised in response to reviewers.
ors-open-science-data-sharing — data and code deposition expectations linked to revisions.

External links (verifiable, public)

ICMJE Recommendations: https://www.icmje.org/icmje-recommendations.pdf
COPE Peer Review guidance: https://publicationethics.org/resources/guidelines/peer-review
COPE appeals guidance: https://publicationethics.org/resources/guidelines-0/appeals-complaints-process
Nature — Editorial processes / peer review: https://www.nature.com/nature-portfolio/editorial-processes/peer-review
eLife — Reviewed preprints: https://elifesciences.org/reviews
F1000Research — Open peer review: https://f1000research.com/
EMBO Journal — Author guidelines: https://www.embopress.org/
PLOS — Author guidelines: https://plos.org/
NIH — Grant resubmission policy and introduction-page format: https://grants.nih.gov/grants/rewarding.htm
EQUATOR Network: https://www.equator-network.org/
CRediT — Contributor Roles Taxonomy: https://credit.niso.org/

Changelog

1.0.0 (2026-06-10): Initial adaptation by Pradyumna Jayaram. Heavy rewrite of upstream response-to-reviewers skill: added triage framework (4 buckets), added tone and framing-conventions table, added section on handling conflicting reviewers, added partial-response decision rules, added desk-reject appeal framework with appealable vs. not-appealable grounds, added cover-letter and summary-of-changes structure, added "do not paste confidential reviewer comments into third-party LLMs" guardrail, added reusable decision-framework table, replaced detailed step lists with rubric tables for faster reuse.

skills/peer-review/reviewer-response