Peer Review and Publication
This section explains the editorial processes at Nature Methods, which can be outlined in the following steps:
- The author submits a manuscript and it receives a tracking number.
- An editor is assigned to the manuscript.
- The editorial team decides whether to send the manuscript out to review. If the decision is not to send the manuscript for review, the editor contacts the author with the decision.
- The editor assigns potential reviewers to the manuscript and the author is notified.
- Reviewers agree to review the manuscript.
- Reviewers submit their reports to the editor.
- The editorial team discusses the reports and the editor makes the final decision. This process may involve further consultation with the reviewers and editor-mediated communications between the reviewers.
- The editor contacts the author with the decision.
- If the decision is negative, the author can choose to transfer their manuscript to another journal. If the manuscript was peer reviewed the referee comments are also transferred. Please see our Manuscript Transfer FAQ for more information about this service.
First editorial decision
When a new submission is received, it is assigned to a primary editor, who reads the paper, consults with the other editors, and decides whether it should be sent for peer review based on the editorial criteria of the journal of novelty and significance. The novelty of a submitted paper is considered to be compromised if it has significant conceptual overlap with a published paper or one accepted for publication by Nature Methods. Preprint archives do not compromise novelty. Many papers describing solid studies of interest to those in the field are nonetheless judged to be unlikely to compete successfully with the best work submitted to the journal.
Like other journals in the Nature family, Nature Methods has no external editorial board, however on occasion editors might consult with external researchers when deciding whether to review a paper.
If a paper was previously reviewed at another Nature journal, the authors can use an automated manuscript transfer service to transfer the referees' reports to Nature Methods via a link sent by the editor who handled the manuscript. In that case, the journal editors will take the previous reviews into account when making their decision, although in some cases the editors may choose to take advice from additional or alternative referees. Alternatively, authors may choose to request a fresh review, in which case they should not use the automated transfer link, and the editors will evaluate the paper without reference to the previous review process. However, this decision must be made at the time of initial submission and cannot be changed later.
If the authors ask the editors to consider the previous reviews, they should include a note explaining the relationship between the submitted manuscript and the previous submission and (assuming it has been revised in light of the referees' criticisms) giving a point-by-point response to the referees. In cases where the work was felt to be of high quality, papers can sometimes be accepted without further review, but if there were serious criticisms, the editors will consider them in making the decision. In the event of publication, the received date is the date of submission to Nature Methods.
When the editors have reached a first decision on the paper, they notify the corresponding author by email.
If the editor decides to send the paper to external peer reviewers, they will contact researchers with relevant expertise. Referee selection is critical to the review process, and we base our choice on many factors, including expertise, reputation, specific recommendations and our own previous experience of a referee’s characteristics. For instance, we avoid using referees who are chronically slow, careless, too harsh or too lenient. Authors may suggest referees; these suggestions are often helpful, although they are not always followed. By policy, referees are not identified to the authors, except at the request of the referee.
Conceptually similar manuscripts are held to the same editorial standards as far as possible, and so they are often sent to the same referees. However, each of the co-submitted manuscripts must meet the criteria for publication without reference to the other paper. Thus if one paper is substantially less complete or convincing than the other, it may be rejected, even if the papers reach the same conclusion.
Decision after review and revision
When all the referee reports are received, the editors then make a decision based on the reviewers’ advice, from among several possibilities:
- Accept, with or without editorial revisions
- Invite the authors to revise their manuscript to address specific concerns before a final decision is reached
- Decline publication, typically on grounds of specialist interest, lack of novelty, insufficient conceptual advance or major technical and/or interpretational problems
Editors consider not only how good the paper is now, but also how good it might become after revision. In cases where the referees have requested well-defined changes to the manuscript that do not appear to require extensive further experiments, editors may request a revised manuscript that addresses the referees' concerns. The revised version is normally sent back to some or all of the original referees for re-review. The decision letter will specify a deadline, and revisions that are returned within this period will retain their original submission date.
In cases where the referees' concerns are more wide-ranging, editors will normally decline publication of the manuscript.
An invited revision should be submitted via the revision link to the online submission system provided in the decision letter, not as a new manuscript. The revised manuscript should be accompanied by a cover letter that includes a point-by-point response to referees' comments and an explanation of how the manuscript has been changed.
Acceptance and publication
If the authors have successfully addressed all the comments of the reviewers and the editors, the editors will deem the paper acceptable for publication in Nature Methods. They will send a request for final submission possibly requiring some text changes but usually no revisions to the data or conclusions. These letters are accompanied by detailed comments on the paper's format. At this stage, authors may receive an extensively edited manuscript from the editor indicating editorial concerns that must be addressed in the revision. A high priority of Nature Methods is that all papers be accessible to non-specialists. Manuscripts are subject to substantial editing to achieve this goal. After acceptance, a copy editor may make further changes so that the text and figures are readable and clear to those outside the field, and so that papers conform to our style. Nature Methods uses American English spelling.
For the final revision, authors should use the revision link to the online submission system provided in the decision letter to upload a final version of the text with all the requested format changes. Electronic files of the final figures, at high resolution, should be sent separately via ftp.
When all remaining editorial issues are resolved, the paper is formally accepted. The received date is the date on which the editors received the original (or if previously rejected, the resubmitted) manuscript. The accepted date is when the editor sends the acceptance letter.
Contributors are sent proofs and are welcome to discuss proposed changes with the editors, but Nature Methods reserves the right to make the final decision about matters of style and the size of figures.
Advance online publication
Nature Methods provides Advance Online Publication (AOP) of research articles, which benefits authors with an earlier publication date and allows our readers access to accepted papers before they appear in print. Note that papers published online are definitive and may be altered only through the publication of a print corrigendum or erratum, so authors should make every effort to ensure that the page proofs are correct. All AOP articles are given a unique digital object identifier (DOI) number, which can be used to cite the paper before print publication. Follow this link for details about advance online publication.
Cover and other artwork
Authors of accepted papers are encouraged to submit images for consideration as a cover. Cover images are normally linked to a specific paper in that issue, but we may also be able to use other images elsewhere in the journal, such as on the table of contents. Illustrations are selected for their scientific interest and aesthetic appeal. Please send prints or electronic files (rather than slides) in the first instance. Please also include a clear and concise legend explaining the image.
Even in cases where editors did not invite resubmission, some authors ask the editors to reconsider a rejection decision. These are considered appeals, which, by policy, must take second place to the normal workload.
Decisions are reversed on appeal only if the editors are convinced that the original decision was a factual mistake. Further consideration may be merited if a referee made substantial errors of fact or showed evidence of bias, but only if a reversal of that referee's opinion would have changed the original decision. Similarly, disputes on factual issues need not be resolved unless they were critical to the outcome.
If an appeal merits further consideration, the editors may send the authors' response or the revised paper to one or more referees, or they may ask one referee to comment on the concerns raised by another referee. On occasion, particularly if the editors feel that additional technical expertise is needed to make a decision, they may obtain advice from additional referees.
If the editors of Nature Methods decline publication of a manuscript, before or after peer review, the authors can easily resubmit it to a different journal within the Nature Research family, in most cases without the need to reformat or upload the files, by following the link provided in the editor’s decision email.
If the paper was peer-reviewed at Nature Methods and it is transferred to another Nature-branded title (Nature, Nature Research Journals and Nature Communications), the existing referee reports and identities will be shared with the receiving journal. The editors of the receiving journal will take the previous reviews into account when making their decision, although in some cases they may choose to take advice from additional referees. If authors prefer not to make the history of the paper at Nature Methods known to other Nature research titles, they should not use the transfer service and they should submit a new submission instead. If the authors decide to transfer the manuscript, they should include a note explaining any changes done to the manuscript compared to the Nature Methods submission and giving a point-by-point response to the referees. In cases where the work was felt by the receiving journal to be of high quality, papers can sometimes be accepted without further review, but if there were serious criticisms, the editors will consider them in making the decision. In the event of publication, the received date is the date of submission to the receiving journal. If the manuscript is transferred to the Nature Partner Journals or Scientific Reports, referee reports or identities from Nature Methods will not be shared.
More information about the manuscript transfer service can be found here.
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