For many young scientists, publishing a research paper marks the first step outside the walls of higher education and into the realm of professional, scientific discourse. Months or even years of experimentation, analysis, and writing culminate in a paper—an embodiment of insights and perseverance—poised to advance the field. Yet, the journey ahead can be fraught. On the road to publication, you may encounter rejection, a common though unwelcome obstacle.
Understanding how to navigate this situation is a vital skill for early-career researchers. This article explores the different types of rejections you might receive, when you should consider appealing, and explains why, when, and how to approach the rebuttal process. It also shares first-hand insights from CST Development Scientist Homa Rahnamoun, PhD on how she has successfully appealed a journal rejection.
The Difference Between Desk and Reviewer Rejections
Manuscript rejections fall into two main categories—editor rejections (also referred to as desk rejections) and rejections after peer review. The first type occurs at the editorial level by the journal’s editorial board and means that your manuscript was not sent out for peer review.1 Around 20 to 30% of papers are rejected without peer review.2
There are a multitude of reasons for a desk rejection, including:
- Insufficient Conceptual Novelty: Insights from the manuscript do not contribute meaningfully to the field.
- Preliminary or Underdeveloped Content: The data may not adequately support the conclusion.
- Editorial Consistency: The journal may have recently rejected similar manuscripts, though this information is not typically disclosed to authors.
- Misalignment with Journal Objectives and Focus: The content of the manuscript may not fit the scope, mission, or priorities of the journal.
Given the weight of these reasons, appeals to editors after a desk rejection are uncommon and rarely result in the reversal of their decision.3 However, try not to be discouraged, as desk rejections can represent a blessing in disguise. When received before entering the lengthy reviewer process, they can allow for efforts to be swiftly redirected toward a more appropriate journal.
Rejections Following Manuscript Peer Review
If a manuscript receives a green light from the editorial board, it will be passed on to reviewers. At this stage, independent experts in the field will evaluate your paper and provide constructive feedback and recommendations to the editorial board.4
Blog: The Peer Review Process: What Is It, and How to Suggest Reviewers
It is estimated that around 40% of papers are rejected following peer review for a variety of reasons, including:2
- Methodological Flaws: Reviewers might identify flaws in the experimental design, data collection, or statistical analysis, which undermine the validity or reliability of the study’s findings.
- Reviewer Disagreement: In cases where reviewers provide conflicting assessments or recommendations, the editor may decide to reject the manuscript based on the overall evaluation or lack of consensus.
- Presentation of Results: If the presentation of results is unclear, incomplete, or inadequately supported by evidence, reviewers may question the validity or robustness of the findings.
These types of rejections are more likely to warrant a rebuttal, as they can result from reviewers misunderstanding the data and conclusions or differing reviewer perspectives.
“As a graduate student, I certainly experienced my share of rejections,” says Homa. “If the editor isn’t on your side and the paper gets rejected by the desk, there’s often not much you can do about it. However, appeals after a reviewer rejection—especially when the editor is excited about the study—can result in the eventual acceptance of the manuscript if approached in the right way.”
Why and When to Appeal a Manuscript Rejection?
Appealing a reviewer rejection can be a daunting prospect, but the process can be worthwhile. Not only can it lead to a second chance for publication, it can also provide valuable insights about your manuscript. Regardless of the outcome, gathering more information about reviewer concerns can help you strengthen your arguments, consider outside perspectives on your research, and build a relationship with the journal’s editors.
However, before appealing, consider all your options. Sometimes, submitting a manuscript to a different journal can be a more efficient use of time and energy. It is worth noting that appeals are usually considered to be low priority by editors, and this is especially true for journals with high submission volumes. The chances of a paper being accepted after an initial rejection are significantly lower than at first submission. You’ll also want to consider your bandwidth, as well as that of your co-authors. If the research was a collaborative effort, be sure to discuss the viability of pursuing a rebuttal with the entire team. You’ll want to balance the feasibility of addressing reviewers’ concerns, and the potential impact revisions could have on overall manuscript quality against the team’s bandwidth and ultimate goals.
As you think through your next steps, take a few days to consider the decision carefully. Specifically, reflect on questions such as: Were there any technical issues in the original paper? If so, can they be resolved using existing methods within a reasonable timeframe? Could there have been a misunderstanding of the data or conclusions? Is the paper technically sound but falls short in conceptual advance or novelty? In the former scenarios, pursuing a rebuttal might be more likely to be accepted. However, in the latter case, where the issue is a lack of conceptual advance, a rebuttal is generally less likely to succeed.
“Overall, I’d say that as long as you have one favorable reviewer, reaching out to the editor to discuss how concerns can be addressed is fairly standard,” adds Homa.
Blog: Mastering the Many Forms of Scientific Writing in Academia
Writing an Effective Rebuttal and Appeal Letter
If you decide to move forward, an appeal typically takes the form of a rebuttal or appeal letter, which is a formal response written by the authors to address the concerns and criticisms raised by the editor and reviewers during the initial evaluation process. It serves as an opportunity for you as the author to defend the scientific validity, significance, and originality of your work, as well as to propose solutions or revisions to resolve any perceived shortcomings.3
Before crafting your rebuttal letter, the first step is often to reach out to the editor to discuss the potential for an appeal. “In my experience, the principal investigator is almost always the one to reach out to the editor to set up a discussion, either via email or phone, depending on the existing relationship,” says Homa. “This process has the greatest chance of success if a minority of the reviewers had a negative review of the manuscript.”
As you work with your PI and other authors to plan for the meeting and craft your appeal letter, begin by composing a comprehensive point-by-point response and action plan to address the feedback provided as you would normally during paper revision. Highlight any new data or experiments you have conducted since the initial publication that could strengthen the paper or address the concerns. You’ll want to provide a concise overview of the key issues and explain why you believe the rejection is unwarranted. A well-crafted rebuttal should persuade the editor to reconsider their decision through reasoned arguments presented with professionalism, clarity, and rigor.
To give the editor time to review arguments and prepare for a dialogue, it’s best to share the point-by-point response either in the initial email correspondence or at least several days before the scheduled discussion.
Note that the tone of the rebuttal and the communication with the editor is incredibly important. It’s important that everyone be open to feedback, receptive to suggestions for improvement, and proactive in proposing solutions to address reviewers’ concerns.
“In one experience where I’ve had a manuscript accepted after a rebuttal, two of the three reviewers had a positive review of the study, and the editor was excited about it, which I think is important,” continues Homa. “My PI met with the editor to discuss the third reviewer’s concerns and our plan for addressing them. The editor was very much on board, and we completed the revisions and resubmitted. The paper was sent to the reviewers again and very quickly after that, it was accepted!”
Engaging in a constructive dialogue with the editor can significantly influence the outcome of the appeal, and the editor can be a valuable resource. They can place the decision letter in context and help prioritize your experiments and thinking. Keep in mind that attempting to persuade the editor without presenting new data or a detailed experimental plan is seldom effective. Instead, authors should collaborate to develop a logical and feasible plan, specifying which experiments will be conducted, what perceived shortcomings they will address, and how the overall manuscript will be strengthened.
Alternatively, the editor may also help you consider and prioritize other journals that may be appropriate homes for your manuscript.
After the discussion, the editor may consult with colleagues or reviewers for specific feedback on the proposed experiments before formally inviting a revision. Sometimes, predicting whether certain experiments will address the reviewers' concerns is challenging. If these concerns are central to the rejection, the editor may request to see the results before inviting a revision.
After finalizing the revision plan with the editor, it is essential to execute it effectively. Despite meticulous planning, unexpected delays or changes can occur in scientific research. In such cases, authors should openly discuss concerns about feasibility and potential outcomes with the editor, ensuring transparency and realistic expectations. Building contingencies into the action plan and maintaining regular communication with the editor can help manage timelines and keep the manuscript on track for resubmission.
Potential Outcomes of Rebuttals
The outcomes of an appeal are highly dependent on the circumstances and reason for the rejection. They can range from reconsideration upon reviewing new data to providing a rationale for sustaining the rejection. Ultimately, the outcome is influenced by the effort that you have put in and the persuasiveness of your argument.
Overall, stay positive and don’t let rejections get you down. They’re part of the learning experience, and the decisions aren’t always final. If you go into the process with an open attitude and a willingness to listen to feedback, the worst that can happen is that you’ll come out of it with some useful insights—and if you’re successful, you’ll hopefully get to see your name in print!
While we’re keeping our fingers crossed that your manuscript will be accepted following review, we hope this article serves as a source of guidance and support for those instances when acceptance may not be immediate.
References and Further Reading
- Scholz, F. Writing and publishing a scientific paper. ChemTexts. 2022;8(8). doi:10.1007/s40828-022-00160-7
- Ali J. Manuscript rejection: causes and remedies. J Young Pharm. 2010;2(1):3-6. doi:10.4103/0975-1483.62205
- Taylor & Francis. [Online] Peer review appeals and complaints from authors.
- Kelly J, Sadeghieh T, Adeli K. Peer Review in Scientific Publications: Benefits, Critiques, & A Survival Guide. EJIFCC. 2014;25(3):227-243. Published 2014 Oct 24.
- Lin, Y. "We agree completely with the reviewer, but…: Stance in author rebuttal letters for journal manuscript reviews. Engl Specif Purp. 2024;73:159-171. doi:10.1016/j.esp.2023.10.004
- Sullivan GM, Simpson D, Yarris LM, Artino AR Jr. Writing Author Response Letters That Get Editors to "Yes". J Grad Med Educ. 2019;11(2):119-123. doi:10.4300/JGME-D-19-00161.1
- Tress, G., Tress, B. and Saunders, D. (2014). How to write a paper for successful publication in an international peer-reviewed journal. Pacific Conservation Biology, 20, 17–24. https://doi.org/10.1071/PC140017
