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Referee Guidelines


About Molecular Systems Biology

Molecular Systems Biology is an open access publication dedicated to rapidly publish research in all areas of molecular systems biology, synthetic biology and systems medicine. The journal is published by EMBO Press in partnership with Wiley and HighWire Press. Editorial independence and scientific quality are guaranteed by an international group of distinguished Senior Editors and a broad and highly qualified Advisory Editorial Board, supported by EMBO in-house Editors.

Molecular Systems Biology aims to publish only the best manuscripts focusing on the analysis, integration and modeling of molecular and cellular biological systems. It is therefore important that manuscripts are critically evaluated for compliance with the following criteria:

  • strong evidence for the conclusions that are drawn
  • conceptual novelty
  • broad biological significance
  • importance to the fields of systems biology and synthetic biology
  • for methods and resources, utility to a large community of researchers


All submitted manuscripts are assessed by the Editors for suitability for the review process. The manuscripts may be sent to Senior editors and / or 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 peer 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 specialist interest, lack of novelty, insufficient conceptual advance or major technical and/or interpretational problems.

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.


Molecular Systems Biology makes the editorial process transparent for all accepted manuscript, by publishing the referee reports alongside published papers, as well as all correspondence between authors and the Editors relevant to the decision process.

Referee anonymity will be strictly maintained.

Reviewers should note that their reports as well as the authors' point-by-point responses will be included in this document. Factually incorrect statements should be avoided, and arguments in favour or disfavour of a given study should be justified. We also encourage referees to be very clear about what revision will be required for a manuscript to become acceptable. 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, Molecular Systems Biology does not ask for 'confidential comments to the editor'. 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, should be communicated directly to the editor via email.

To enhance the consistency of the peer-review process, the Editors provide the opportunity to referees to comment on each other's reports before making their decision. This allows extreme opinions to be scrutinized at an early point and mistakes to be detected.

Authors have the option to request that the journal posts reviews obtained via peer review at the journal alongside a preprint version of the manuscript on bio/medRxiv, including an author response to the reviews. As above, referee anonymity is preserved.


Referee selection is based on a balance of factors, including expertise, scientific reputation, and our previous experience with the referee. We send manuscripts to referees only after having contacted them about the possibility first, and expect referees to treat this initial request as confidential.


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

  • double-check the deadline and contact the editorial office immediately if you anticipate any difficulties in meeting it
  • consider whether there might be a conflict of interest for you (see guidelines below) and whether you can judge the article impartially


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

  • manuscripts refereed for Molecular Systems Biology should not be discussed with anyone not directly involved in the review process
  • if colleagues are consulted, they should be identified to the editors
  • 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
  • referees should 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.


The primary purpose of referee reports is to provide the editors with the information that they need to reach a decision, but they should also instruct the authors on how to strengthen their manuscript if revision is a possibility.

Referees are asked to maintain a critical but constructive and impartial attitude in evaluating manuscripts. Criticisms should remain dispassionate; offensive language is not acceptable. 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.

Referee reports tend to follow the following general structure:


  • Describe your understanding of the story
  • What are the key conclusions: specific findings and concepts
  • What were the methodology and model system used in this study

General remarks

  • Are you convinced of the key conclusions?
  • Place the work in its context.
  • What is the nature of the advance (conceptual, technical, clinical)?
  • How significant is the advance compared to previous knowledge?
  • What audience will be interested in this study?

Major points

  • Specific criticisms related to key conclusions
  • Specify experiments or analyses required to demonstrate the conclusions
  • Motivate your critique with relevant citations and argumentation

Minor points

  • Easily addressable points
  • Presentation and style
  • Trivial mistakes


We do not suppress referee reports. On rare occasions, however, we may edit a report to remove offensive language or comments that reveal confidential information. We ask referees to avoid saying anything that may cause needless offence, but also expect authors to recognize that criticisms are not necessarily unfair simply because they are expressed in robust language.


Molecular Systems Biology 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.


Competing reviewer/advisor interests exist if the referee/advisor is currently engaged in, is planning to engage in or would consider engaging in, related experiments that could benefit from unpublished information acquired from the manuscript under consideration, has financial or commercial interests or previous personal or professional connection to the authors. This information must be shared with the editor regardless of the referees’ level of support for the work.

Reviewers are expected to decide whether they have competing interests based on the abstract and author list (for non-blinded papers) before they accept to review the manuscript. Because it is not possible for the editors to know all potential conflicts or biases, we request potential referees to alert the editors to anything that might affect the neutrality of their report, and to decline in cases where they feel unable to be objective. Should a referee accept the invitation and discover during manuscript assessment that he/she has competing interests, we expect the referee to notify the editor immediately and to permanently delete any of the accessed manuscript files.

Examples where reviewers should consult with the editor:

  • Author and referee previously worked closely together (e.g. in the same department, or had a professional cooperation).
  • Employed by the same institute: The referee and author work on the same campus and directly interacted. Note that some institutions are very large, and the referee and author may not have any interaction on campus – in such cases no further discussion is necessary. At smaller institutes, the referee and author may know or have had some level of engagement with each other even if they do not work in the same department.
  • The referee sits on a scientific advisory board that was involved with approving the authors’ research proposal or position.
    Editorial: The referee is an editor at a competing journal and has interests in the paper being published at his/her journal.
  • Former advisors/mentors: It is recommended to avoid having a former advisor/advisee from the past 10 years review an authors’ work. Please discuss with the editor as each case will be decided individually.
  • The reviewer disagrees a priori with the conclusions or the research presented, or with the work from a given laboratory, which interferes with his/her neutrality on the study.

We encourage referees to ask for a senior member of his/her lab to co-review a paper. Co-review implies that the co-referee is supervised to provide an authoritative, professional referee report and the primary referee explicitly agrees with all the points raised by the co-referee. Co-review with other senior colleagues, for example to complement expertise, maybe be possible, but requires pre-consultation with the editor as the co-referee might have been excluded by the authors. Co-referees must be named in the dedicated text box in the referee form. 


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 recognize such problems and should alert the editors to any potential problems in this regard.


When we ask referees to re-review a manuscript that has been revised in response to their criticisms, we normally send them copies of the other referees' comments. Upon request, we inform referees of our decisions and send 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.


We are collaborating with ORCID and Publons to give you the recognition you deserve for your peer review contributions. Once you submit your review you will have the option to immediately add your review to ORCID, and/or you can forward the "thank you for reviewing" email to [email protected] to register your review with Publons.