Referee Guidelines

About The EMBO Journal

The EMBO Journal is an international print and online publication dedicated to providing full-length, rapidly published papers in all areas of molecular biology. The Journal is owned and run by the European Molecular Biology Organization and is editorially independent of its publisher.


Criteria for publication

Manuscripts are critically evaluated for compliance with the following criteria:

  • novelty
  • broad biological significance
  • importance to the specific field
  • strong evidence for the conclusions that are drawn

The review process

All submitted manuscripts are carefully assessed by the editorial staff for their potential suitability. The abstract or a PDF file of manuscripts may also be sent to Advisory Editorial Board members for further input toward this decision. To save authors and referees time, only those manuscripts judged most likely to meet our editorial criteria are sent out for formal review.

Manuscripts that are sent for formal review typically go to three referees. Based on their advice, the editor decides to: accept the manuscript, with or without minor revision; invite the authors to revise the manuscript to address specific concerns before a final decision is reached; or reject the manuscript, typically on grounds of insufficient conceptual advance or major technical limitations.

Referees may recommend a particular course of action in their confidential comments to the editor, but should bear in mind that the editors may have to make a decision based on conflicting advice. Furthermore, editorial decisions are not a matter of counting votes or numerical rank assessments, but rather are based on an evaluation of the strengths of the arguments raised by each referee and by the authors. The most useful referee reports, therefore, are those that set out clear, substantiated arguments and concrete recommendations for the improvements and experiments necessary to achieve suitability for publication.


The EMBO Journal makes the editorial process transparent for all accepted manuscript, by publishing as an online supplementary document all correspondence between authors and the editorial office relevant to the decision process, as well as the overall timeline of the editorial and publishing process. Internal communications and informal consultations between editors, editorial advisors or referees will remain excluded from these policies. Likewise, referee anonymity will be strictly maintained. Reviewers should however note that their reports as well as the authors' point-by-point responses will be included in this document. Care should thus be taken to avoid factually incorrect statements, and to thoroughly justify arguments in favour or disfavour of any given study. We also encourage referees to be as clear as possible about what revision will be required for a manuscript to become acceptable (subject to the results obtained). Ideally, it should be apparent to the author and the editor how to proceed without need for additional consultation.

To further ensure a transparent editorial process, The EMBO Journal does not ask for 'confidential comments to the editor'; instead, referees are asked to include all comments pertinent to the scientific evaluation of the manuscript in the referee report itself. Please note that urgent further issues that cannot be included in the referee report, in particular concerns about ethical standards, data integrity, biosecurity or conflicts of an academic or commercial nature, can and should be communicated directly to the editor via email.

To enhance the fairness and consistency of the peer-review process, and to ensure that the referees supply constructive, critical analysis to the authors, The EMBO Journal routinely asks referees to comments on each other's reports. As soon as all reports have been received, the editor sends them, anonymously, to all the referees, who then have one day to consider the others' views. This allows extreme opinions to be scrutinized at an early point, mistakes and errors to be detected, and helps the editor to get back to the author with balanced decisions.

Selecting referees

Referee selection is critical to the review process, and our choice is based on many factors, including expertise, reputation, specific recommendations, and our previous experience with the referee. We do not use referees who have been excluded by the authors, and avoid using referees who have repeatedly provided reports of low quality or delayed reports. We send manuscripts to referees only after having contacted them about the possibility first, and expect referees to treat even this initial request as confidential.

Upon receiving a manuscript to referee

To avoid unnecessary delays in processing manuscripts, please do the following immediately upon receipt of a manuscript for review:

  • check the quality of the PDF-file/hardcopy figures sent to you
  • double-check the deadline to ensure that there have been no misunderstandings regarding timing, and contact the editorial office immediately if you anticipate any difficulties in meeting it
  • skim the manuscript and consider whether there might be a conflict of interest for you (with the authors, their institution, their funding sources) and whether you can judge the article impartially
  • read the editor's letter carefully and be sure to note any points specific to the manuscript that the editor may have requested your opinion on


Referees should treat the review process as being strictly confidential, and should keep the following guidelines in mind:

  • manuscripts refereed for The EMBO Journal should not be discussed with anyone not directly involved in the review process.
  • if colleagues are consulted, they should be identified to the editors in the approproate field in the referee submission system.
  • if experts from outside the referee's own laboratory are consulted, referees should check with the editors beforehand to avoid involving anyone who may have been excluded by the editor or the authors.
  • referees should, as a rule, not disclose their identities to the authors or to other colleagues since they may be asked to comment on the criticisms of other referees and may then find it difficult to be objective. Should they feel strongly about making their identities known to the authors, they should do so via the editor. We strongly disapprove of any attempt by authors to determine the identities of referees or to confront them, and encourage referees to neither confirm nor deny any speculation in this regard.

Writing a report

As a general guideline, referee evaluations should mainly focus on the significance and conclusiveness of the study at hand, i.e. whether the findings and conclusions at the current stage might be considered sufficiently important in principle, and whether the presented data actually support these conclusions. Referees are prompted to assess these two points directly via a ratings table, in which they can also indicate whether or not they would need to see an eventual revised version before acceptance, and whether a manuscript would be of such particular interest as to warrant highlighting.

Referees are asked to maintain a positive and impartial, but critical, attitude in evaluating manuscripts. Criticisms should remain dispassionate; offensive language is not acceptable. As far as possible, a negative report should explain to the authors the weaknesses of their manuscript, so that they can understand the basis for a decision to ask for revision or to reject the manuscript. Similarly, positive reports should explain the reasons for why a study would be seen as an important advance of wider biological significance. Please keep in mind that comments to the authors will be included and published in the 'editorial proceedings' supplementary file in case of publication, even if they may have been pertinent only to an initial version of the eventually published manuscript.

The ideal report should include:

  • an initial paragraph that summarises the major findings and the referee's overall impressions, as well as highlighting major shortcomings of the manuscript.
  • specific numbered comments, which may be broken down into major and minor criticisms if appropriate (numbering facilitates both the editor's evaluation of the manuscript and the authors' rebuttal to the report).

The report should answer the following questions:

  • what are the major claims and how significant are they?
  • are the claims novel and convincing?
  • are the claims appropriately discussed in the context of earlier literature?
  • is the study of interest to more than a specialised audience?
  • does the paper stand out in some way from the others in its field?
  • are there other experiments that would strengthen the paper?

For manuscripts that may merit further consideration, it is also helpful if referees can provide advice on the following points where appropriate:

  1. how the clarity of the writing might be improved (without necessarily going into specific details of spelling and grammar)
  2. how the manuscript might be shortened
  3. how to do the study justice without overselling the claims
  4. how to represent earlier literature more fairly
  5. how to improve the presentation of methodological detail so that the experiments can be reproduced
  6. the submission of supplementary data on the The EMBO Journal web site to enhance the presentation (depositing, for example, crystallographic information, source code for modelling studies, microarray data, detailed methods, mathematical derivations, long tables and movies).

This author report should not include a direct recommendation regarding publication, as the final decision regarding acceptance, revision or rejection rests with the editor.

On the Referee's Evaluation Form in our online submission system, referees will find a text box for entering information about any co-referees involved in the evaluation, and a text box for writing/pasting the actual referee report. Placeholder text in that box is only meant to remind reviewers of the encouraged report structure, and should be overwritten.

Editing referee reports

As a matter of policy, we do not suppress referee reports. On rare occasions, however, we may edit a report with permission where the referee has made a mistake, or to remove offensive language or comments that reveal confidential information. We further ask referees to avoid saying anything that may cause offence or may be libellous, but also expect authors to recognise that criticisms are not necessarily unfair or able to cloud the editor's judgement simply because they are expressed in robust language.


The EMBO Journal is committed to rapid editorial decisions and publication as efficiency in this process is a valuable service both to our authors and the scientific community as a whole. We therefore ask that referees respond promptly or inform us if they anticipate a significant delay, which allows us to keep the authors informed and, where necessary, find alternative referees.

Conflicts of interest

We honour the authors' request to exclude certain individuals as referees due to potential conflicts of interest. In rare cases where an unreasonably high number of experts is excluded, we may however request a more restricted exclusion list from the authors. We also try to avoid referees who have recent or ongoing collaborations with the authors, have commented on drafts of the manuscript, are in direct competition, have a history of dispute with the authors, or have a financial interest in the outcome. Because it is not possible for the editors to know of all possible biases, we ask referees to draw our attention to anything that might affect their report, including competing work or commercial interests, and to decline to referee in cases where they feel unable to be objective. We do not find it necessary to exclude referees who have reviewed a paper for another journal; the fact that two journals have independently identified a particular person as well qualified to referee a paper does not decrease the validity of her/his opinion in our view.

Publication policy and ethical considerations

In spite of our best efforts to identify breaches of publication policy or ethical conduct, such as plagiarism or author conflict of interest, the referees who are more familiar with the field are more likely to recognise such problems and should alert the editors to any potential problems in this regard, either by e-mail or using the confidential comments to the editor.

Feedback to referees

Once a final decision on a manuscript has been reached, it is our policy to inform all referees of that decision and to send final copies of the other referee reports. Referees who find that their recommendations have been overruled should realise that this does not imply any lack of confidence in their judgement. It is not uncommon for experts to disagree and, in the absence of a consensus, the editors must still reach a decision one way or the other. When we ask referees to re-review a manuscript that has been revised in response to their criticisms, we also send them copies of the all the original comments of all reviewers.

Navigating the System

When you first log into the system,,  you will be taken to your "Home" page. It will have different catagories of tasks. If you are required to perform a pending action item, there will be a red arrow next to a manuscript link. After clicking on this link, you will be presented with a "Manuscript" screen containing:

  • Detailed Information about a specific manuscript.
  • Links to the manuscript and associated figures/images.
  • A list of "Manuscript Tasks" or links allowing you to:
    • Accept/Decline Reviewer Position.
    • Check Status
    • Review Manuscript

(Not all links will be present all the time. Only the applicable links will be visible.)

If there are no red arrows visible on the "Home" page, then you are finished. There is no pending work you need to worry about.

Review Manuscript

After logging into the system, pressing on a manuscript link preceded by a red arrow, you will be presented with a "Manuscript" screen as described above. At the bottom of this screen under "Manuscript Tasks" will be displayed a "Review Manuscript" link. Clicking on this link will display the "Review Manuscript" Screen. This screen is broken into 4 parts as follows:

  • Manuscript background information.
  • A review pop-down selection.
  • Remarks to the author.

If you prefer to work offline, you may find it quickest to download and print the PDF file, draft your review remarks using your favorite word processor and cut/paste it back into the reviewer remarks text area on this screen.

Be careful if you intend to copy and paste your written remarks back into the online system. Please do not assume that all lines of your original text were successfully copied back into the text box on the online page, and ensure you manually check that all of the write-up has been included.

In your evaluation you may want to consider the following points:

  • Is the paper original?
  • Is it well written?
  • Are critical references given?
  • Is the length of the paper commensurate with the message?
  • Are all tables, figures, graphs and photographs necessary?
  • If applicable, is "Material and Methods" section adequately written and referenced?

If you have not done so recently, for our future files please remember to Modify Profile when you are logged in to this site, providing 3-4 keywords to briefly describe your field(s) of expertise.

Getting help

If you need additional help, you can click on the help signs spread throughout the system. A help dialog will pop up with context sensitive help. For additional help, please contact the journal office: