General Instructions (2024)

How we publish

Submitting

Peer review process

Publication and research ethics

Availability of data and materials

Submitting your bioRxiv preprint to the journal

Digital preservation

Self-archiving

Publishing agreements and charges

Changes to published papers

Promoting your work

Preparing your manuscript

Contact us

NARprovides rapid publication of papers on physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. All manuscripts must present some novel development and meet the general criteria of originality, timeliness, significance and scientific excellence.

NARis published online and in print. Methods, Database and Web Server papers only appear online.

Papers which are considered to be a better fit in another related journal within theNARportfolio are offered a direct transfer to the most relevant journal in the widerNARportfolio.

The Journal publishes the following types of papers:

Standard research articles
Methods articles
Critical Reviews and Perspectives
Database articles
Web Server articles

More information can be found via the following link:https://academic.oup.com/nar/pages/Criteria_Scope

How we publish

Nucleic Acids Research is a peer reviewed fully open access journal publishing 24 issues per year online and in print. All papers published in the Journal are made freely available online under open access publishing agreements, with applicable charges. Please refer to the open access section.

After copyediting and review of the final proof, papers are published in NAR in Advance Access before being assigned to an issue of the journal.

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Submitting

Publishing in Nucleic Acids Research means that you are publishing with Oxford University Press (OUP), a not-for-profit publisher and a department of the University of Oxford. Learn more about how publishing with OUP reinvests in the scholarly community on the OUP Authoring page.

After preparing your manuscript according to the guidance in the Manuscript preparation section, you can submit your work through the Journal’s online submission site. If you have not used our submission site before, you will need to create an account. Additional help and instructions are available on the submission site as you go through the submission process. Please contact us with any questions about submitting your manuscript.

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Peer review process

The Journal uses the ANSI/NISO Standard Terminology for Peer Review. If you would like further description of the peer review terms used here, please refer to the most recent standard definitions. If further clarification is needed, please contact the editorial office at nar.editorialmanager@oup.com.

Peer review summary:

• Identity transparency: single anonymized
• Reviewer interacts with: editor
• Review information published: none
• Post publication commenting: open

The Journal operates single-anonymized peer review, meaning that the identity of the authors is known to the editors and to the reviewers, but that the reviewers’ identities are known only to the editors and are hidden from the authors.

During peer review, reviewers communicate directly with the editors but not the authors or other reviewers.

Initial Submission

Once a submitted manuscript passes initial assessment by the Journal’s Senior Executive Editors, it will then be passed to an Executive Editor, who will oversee peer review and make the final decision. The corresponding author will receive all correspondence, including an initial acknowledgment and the decision, by email.

Editors and reviewers must not handle manuscripts if they have a conflict of interest with an author or the content. Editors make every effort to avoid potential conflicts of interest in the assignment of other editors and peer reviewers. For more information, please see the section on Disclosure of potential conflicts of interest. During the peer review phase, your manuscript is typically sent to a minimum of two reviewers.

Choosing Referees

You must suggest at least six potential reviewers at submission. However, there is no guarantee the suggested reviewers will be selected by the Journal. Recommended reviewers should be experts in their field and able to provide an objective assessment of your manuscript without financial or interpersonal conflicts of interest with any authors. We encourage you to consider reviewers from a diverse range of backgrounds, including those from under-represented communities.

At the time of submission, you may request that specific individuals not be used as reviewers of your manuscript. You may enter no more than three opposed reviewers. However, there is no guarantee these individuals will be excluded by the Journal. We suggest that authors add one additional qualified suggested reviewer (beyond the six minimum) to their list, for each requested excluded reviewer, to help ensure timely evaluation.

If your manuscript is accepted for publication, the reviewer comments will not be published alongside the paper.

If your manuscript is accepted for publication, no information about the review process or editorial decision process is published, unless one of the authors has a role on the journal. See the Disclosure of potential conflicts of interest section for more information in that case.

For full details about the peer review process, see Fair editing and peer review.

Revision

Revised manuscripts should preferably be uploaded within 60 days of the decision email. Authors will receive an automatic reminder if this does not occur. If the revised version of a manuscript is not uploaded within six months of the decision email, the manuscript will be withdrawn from the system, unless the Executive Editor agrees to extend the deadline.

Resubmission

The resubmission of manuscripts must satisfy the following conditions, regardless of whether the resubmission covers the entirety of the previous work or only a part, and regardless of any changes in authorship:

• The resubmission should have been previously invited by the journal editorial staff. NAR does not encourage resubmission of work that has previously been rejected after peer review, except in exceptional cases.
• All resubmissions must be accompanied by a cover letter containing full details of the previous version.
• The manuscript number of the earlier submission must be provided.
• Where appropriate, a file must be uploaded which contains the authors' responses to any previous Editorial or Referee reports and a summary of the changes that have been made.

You are encouraged to carry out resubmission within twelve months of the decision date of the original manuscript. Please contact the Executive Editor if your resubmission is likely to take longer than this.

Transfers

In some cases, the editorial team of the Journal may offer you the option of transferring your manuscript to an alternative relevant OUP title. If you accept this offer, the manuscript files and any reviewer reports from consenting reviewers will be sent to the recipient journal. The editorial team of the receiving journal may choose to seek additional peer review. A decision will be made on the manuscript based on the feedback from all reviewers and the judgment of the receiving journal’s editorial team.

Acceptance

Following notification of editorial acceptance from the Executive Editor, the Production Editor at Oxford Academic will then send you instructions to complete the following steps:

1. Complete your licence to publish online.
2. Pay your open access charge online. Please note that your manuscript cannot be published without receipt of this.

Proofs

For improved publication speed, the proofs are provided on our Total Online Proof (TOP) system. The corresponding author will receive a link and log-in details and should make all changes within 48 hours after receipt. Any substantial changes and notes added to the proof necessitate the approval of the Executive Editor responsible for the paper. In general, corrections to figures are not permitted at this stage. The corresponding author must ensure that all co-authors agree with any corrections made.

All manuscripts will undergo some editorial modification, so it is important to check proofs carefully.

Post publication commenting

The Journal allows open commenting on published articles. Comments are displayed at the bottom of the article page under the “Comments” section. To comment, users must log-in to their Oxford Academic account or create a new one. Commenter name and affiliations are collected as part of the comment submission process. All comments are reviewed by the editorial team and subject to approval before the comment is published live. During the review stage, the editorial team may contact the authors of either the paper or comment before coming to a decision. The editorial team may also make edits to the comment before publishing.

If a comment is accepted and published, the author of the comment and the corresponding author of the paper are notified of the outcome. If the comment is rejected, the comment author is notified. If you have questions about submitting a comment, contact the editorial office at nar.editorialmanager@oup.com.

Screening for misconduct

Manuscripts may be screened using iThenticate to help detect publication misconduct including plagiarism and redundant publication.

Identity/Activity Detection

The Journal uses ScholarOne Unusual Activity Detection tool to build confidence in the identity of authors and reviewers.

Reviewer Recognition

To promote recognition of the essential work done by reviewers, the Journal offers reviewers the option to have their reviews verified and automatically listed on their Web of Science Researcher profile.

Appeals and complaints

Authors may appeal an editorial decision. To do so, please contact the editorial office at nar.editorialmanager@oup.com, providing as much specific detail as possible about why the original decision should be reconsidered. Every appeal will receive a response within a reasonable timeframe. Please do not resubmit your manuscript in the interim.

To register a complaint regarding non-editorial decisions, the Journal’s policies and procedures, Editors, or staff, please contact Journals.Ethics@oup.com. Complaints are taken seriously and will be carried forward following COPE guidelines and processes.

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Publication and research ethics

Please read specific policies pertaining to the annual Database and Web Server issues.

Authors' responsibilities

Submission of a manuscript implies that it reports unpublished work and is not under consideration elsewhere. At submission, the submitting author confirms on behalf of all authors that they are in complete agreement with the contents of the manuscript and are prepared to abide by NAR’s policies.

If the manuscript was previously rejected by NAR, the cover letter must give the manuscript number of the earlier submission. Authors must upload a response to earlier editorial or referee reports and a summary of the changes that have been made, including changes in authorship.

Authors should promptly notify the Journal if they choose not to revise their manuscript and intend to submit it elsewhere.

The cover letter should provide details of any third-party data which is cited in the manuscript as personal communication(s). The corresponding author must confirm that permission has been obtained for each inclusion.

Authors are responsible for securing written permission to reuse third party content in their work. A copy of the permission must be uploaded with the initial submission. This is particularly important for copyrighted material and for data or software protected by End-User Licence Agreements (EULA) or Software Licence Agreements (SLA).

Authors must inform the journal of any related manuscripts currently under consideration by NAR or any other journal, especially where the related manuscript describes work that may impinge significantly on the results or interpretation of the current NAR submission. A file of the related manuscript should be uploaded into the online submission system.

Authorship

Authorship is limited to those who have made a significant contribution to the design and execution of the work described. Any contributors whose participation does not meet the criteria for authorship should be acknowledged but not listed as an author. The Journal will contact all listed authors at the point of submission to confirm their role. For a detailed definition of authorship, please see the International Committee of Medical Journal Editors (ICMJE) definitions of authors and contributors.

Authorship should be based on (i) substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; (ii) drafting the work or revising it critically for important intellectual content; (iii) final approval of the version to be published; and (iv) agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Persons designated as authors should meet all four of these criteria for authorship. The order of authorship should be a joint decision of the co-authors and should be agreed upon before submission to the journal.

The Journal does not allow ghost authorship, where an unnamed author prepares the article with no credit, or guest/gift authorship, where an author who made little or no contribution is listed as an author. The Journal follows Committee on Publication Ethics (COPE) guidance on investigating and resolving these cases. For more information, please see the OUP Publication Ethics page.

Equal Contribution

It is sometimes necessary to indicate that two or more authors have contributed equally to the manuscript. The joint authors should be identified by a dagger symbol and a footnote containing the statement '† The first X authors contributed equally to this work' should be added. The relative contributions of ALL authors can appear under Acknowledgements if needed.

Joint Corresponding Authors

Corresponding authors take responsibility for the published work on behalf of all authors. The names of joint corresponding authors can appear at any place in the list of authors and will be identified by an asterisk.

Acknowledgements

Any contributors whose participation does not meet the criteria for authorship should be acknowledged but not listed as an author. Because acknowledgment may imply endorsem*nt of the study, the corresponding author should obtain permission from all acknowledged individuals and be prepared to provide this to the journal upon request.

AI-powered Language Processing Models

Natural language processing tools driven by artificial intelligence (AI) do not qualify as authors, and the Journal will screen for them in author lists. The use of AI (for example, to help generate content or images, write code, process data, or for translation) should be disclosed both in cover letters to Editors and in the Methods or Acknowledgements section of manuscripts. Please see the COPE position statement on Authorship and AI for more details.

Changes in authorship

After manuscript submission, no authorship changes (including the authorship list, author order, and who is designated as the corresponding author) should be made unless there is a substantive reason to do so. The Editor and all co-authors must agree on the change(s), and neither the Journal nor the publisher mediates authorship disputes. If individuals cannot agree on the authorship of a submitted manuscript, contact the editorial office at nar.editorialmanager@oup.com to request withdrawal of the submission. The dispute must be resolved among the individuals and their institution(s) before the manuscript can be accepted for publication. If an authorship dispute or change arises after a paper is accepted, contact OUP’s Author Support team. COPE provides guidance for authors on resolving authorship disputes.

After submission, changing who is designated as the corresponding author will be permitted only where there is a substantive reason to do so. For the avoidance of doubt, changing the corresponding author in order to access Read and Publish funding is not permissible. For more information on Read and Publish funding, refer to the open access charges section.

ORCID

Submitting authors are required to provide an ORCID iD (Open Researcher and Contributor ID) at submission.

All authors are encouraged to provide their ORCID iDs at submission and take advantage of the benefits of participating in ORCID. If you do not already have an ORCID iD, you can register for free via the ORCID website.

As ORCID identifiers are collected, they are included in papers and displayed online, both in the HTML and PDF versions of the publication, in compliance with recommended practice issued by ORCID.

ORCID functionality online allows users to link to the ORCID website to view an author’s profile and list of publications. ORCID iDs are displayed on web pages and are sent downstream to third parties in data feeds, where supported.

If you have registered with ORCID, you can associate your ORCID iD with your submission system account by going to your account details, entering your ORCID iD, and validating your details. Learn more about ORCID and how to link it to your account.

Groups and Consortia

Groups (also known as corporate, organization, or collective names) who meet authorship criteria should be included in the main author list. Every individual in the group should fully meet the criteria for authorship. At least one individual must be designated on behalf of the group as the primary point of contact during the peer-review and production processes, as well as for correspondence following publication. You may list this individual separately in the main author list if desired.

If the group only has a few members, the members should be listed in the author by-line on the manuscript's title page.

If the group has many members, the members should be listed in the Acknowledgements section or in an Appendix at the end of the article.

The group name will be entered for a PubMed citation. The names of the individual members of the group will be entered as collaborator names for PubMed citation, in the order in which they are published in the paper. If an individual is named both in the main author list and as a member of the group, they will appear in PubMed as both an author and a collaborator.

Disclosure of potential conflicts of interest

Authors

The Journal requires all authors to disclose any potential conflict of interest at the point of submission. It is the responsibility of the corresponding author to ensure that conflicts of interest of all authors are declared to the Journal.

A conflict of interest exists when the position, activities, or relationships of an individual, whether direct or indirect, financial or non-financial, could influence or be seen to influence the opinions or activities of the individual. For more information, refer to OUP’s definition of conflict of interest. The Journal follows the COPE guidance for any undisclosed conflict of interest that emerges during peer review, production, or after publication.

The manuscript must include a concise and accurate conflict of interest statement.

Reviewers

Individuals that have a conflict of interest relating to a submitted manuscript should recuse themselves and will not be assigned to peer review the manuscript.

If during peer review an Editor, reviewer, or author becomes aware of a conflict of interest that was not previously known or disclosed they must inform the Editor immediately.

Editors

At initial submission, the corresponding author must declare if an Editor of the Journal is an author of or contributor to the manuscript. Another Editor without a conflict of interest will oversee the peer review and decision-making process.

If accepted, a statement will be published in the paper describing how the manuscript was handled. The statement will read “[Author name] holds the position of Executive Editor for Nucleic Acids Research and has not peer reviewed or made any editorial decisions for this paper."

Privacy policies

OUP’s policy on data and privacy can be foundhere.

Previously published material

You should only submit your manuscript(s) to the Journal if:

• It is original work by you and your co-author(s).
• It is not under consideration, in peer review, or accepted for publication in any other publication.
• It has not been published in any other publication.
• It contains nothing abusive, defamatory, derogatory, obscene, fraudulent, or illegal.

The submitting author must disclose in their cover letter and provide copies of all related or similar manuscripts that are under consideration elsewhere at the time of submission. You must also provide a concise explanation of how the submitted manuscript differs from these related manuscripts and papers. All related previously published papers should be cited as references and described in the submitted manuscript.

For previously published materials including tables and figures, please refer to the Reusing copyrighted materials section.

Preprints

As an author, you retain the right to make an Author’s Original Version (preprint) available through various channels and this does not prevent submission to the Journal. If accepted, the authors are required to update the status of any preprint, including adding your published paper’s DOI. For full details on allowed channels and updating your preprint, please refer to our Author self-archiving policy.

Reusing copyrighted material

As an author, you must obtain permission for any material used within your manuscript for which you are not the rightsholder, including quotations, tables, figures, images, data, or software. In seeking permissions for published materials, first contact the publisher rather than the author. For unpublished materials, start by contacting the creator. Copies of each grant of permission should be provided to the editorial office of the Journal. The permissions agreement must include the following:

• nonexclusive rights to reproduce the material in your paper in NAR
• rights for use in print and electronic format at a minimum, and preferably for use in any form or medium
• lifetime rights to use the material
• worldwide English-language rights

If you have chosen to publish under an open access licence but have not obtained open access re-use permissions for third-party material contained within the manuscript, this must be stated clearly by supplying a credit line alongside the material with the following information:

• Title of content
• Author, Original publication, year of original publication, by permission of [rightsholder]
• This image/content is not covered by the terms of the Creative Commons licence of this publication. For permission to reuse, please contact the rights holder.

Oxford University Press, provides detailed Copyright and Permissions Guidelines, and a summary of the fundamental information.

Misconduct

Authors should observe high standards with respect to research integrity and publication ethics as set out by theCommittee on Publication Ethics (COPE). Falsification or fabrication of data including inappropriate image manipulation, plagiarism, including duplicate publication of the author's own work without proper citation, and misappropriation of work are all unacceptable practices. Allegations of ethical misconduct, both directly and through social media, are treated seriously and will be investigated in accordance with the relevant COPE guidance.

If misconduct has been established beyond reasonable doubt, this may result in one or more of the following outcomes, among others:

• If a submitted manuscript is still under consideration, it may be rejected and returned to the author.
• If a paper has already been published online, depending on the nature and severity of the infraction, either a correction notice will be published and linked to the paper, or retraction of the paper will occur, following the COPE Retraction Guidelines.
• The relevant party’s institution(s) and/or other journals may be informed.

Manuscripts submitted to the Journal may be screened with plagiarism-detection software. Any manuscript may be screened, especially if there is reason to suppose that part or all the of the manuscript has been previously published.

COPE defines plagiarismas “when somebody presents the work of others (data, words or theories) as if they were their own and without proper acknowledgment.”

COPE defines redundant/overlappingpublication as “when a published work (or substantial sections from a published work) is/are published more than once (in the same or another language) without adequate acknowledgment of the source/cross-referencing/justification,
or
when the same (or substantially overlapping) data is presented in more than one publication without adequate cross-referencing/justification, particularly when this is done in such a way that reviewers/readers are unlikely to realise that most or all the findings have been published before.”

COPE defines citation manipulation as “behaviours intended to inflate citation counts for personal gain, such as: excessive self-citation of an authors’ own work, excessive citation to the journal publishing the citing article, and excessive citation between journals in a coordinated manner.”

Data fabrication is defined as intentionally creating fake data or misrepresenting research results. An example includes making up data sets.

Data falsification is defined as manipulating research data with the purpose of intentionally giving a false representation. This can apply to images, research materials, equipment, or processes. Examples include cropping of gels/images to change context and omission of selected data.

If notified of a potential breach of research or publication ethics, the Journal Editor and editorial office staff may inform OUP and/or the author’s institutional affiliation(s).

Ethical research

The Journal follows Committee on Publication Ethics (COPE) guidelines on ethical oversight. We take research integrity seriously, and all research published in the Journal must have been conducted in a fair and ethical manner. Wherever appropriate, the Journal requires that all research be done according to international and local guidelines.

Human subjects

When reporting on human subjects, you should indicate whether the procedures followed were in accordance with the ethical standards of the Helsinki Declaration (1964, amended most recently in 2013), which were developed by the World Medical Association. For non-interventional studies, where ethical approval is not required or where a study has been granted an exemption by an ethics committee, this should be stated within the manuscript with a full explanation. Otherwise, manuscripts must include a statement in the Methods section that the research was performed after approval by a local ethics committee, institutional review board and/or local licensing committee, or that such approval was not required. The name of the authorizing body and any reference/permit numbers (where available) should also be stated there. Please be prepared to provide further information to the editorial office upon request.

Human subjects must give written informed consent, or if they are minors or incapacitated, such consent must be obtained from their parents or guardians. Consent forms should cover not only study participation but also the publication of the data collected. Also, any patient or provider information should be anonymized to the extent possible in accordance with theSafe Harbor method; names and ID numbers should not be used in the text and must be removed from any images (X-rays, photographs, etc.). Please note blanking out an individual’s eyes in a photograph is not an effective way to conceal their identity. In studies where verbal, rather than written, informed consent was obtained, this must be explained and stated within the manuscript. If informed consent is not required or where a study has been granted an exemption, this must be included in the Methods section along with the name of the authorizing body. The Journal does not routinely collect consent forms, but authors should be prepared to provide written consent forms signed by the participants or other appropriate documentation to the editorial office upon request. For further guidance and examples, please refer to COPE’s guidance on consent.

Animal subjects

Studies involving animals require approval from the relevant institutional ethics committee or institutional animal use and care committee, and the research must be conducted in accordance with applicable national and international guidelines. All such manuscripts must include a statement in the Methods section providing details of the name of the committee(s) that approved the study, as well as the permit or animal license numbers where available. Where a study has been granted an exemption, this must be stated in the Methods section along with the name of the authorizing body. Please be prepared to provide further information to the editorial office upon request.

ARRIVE guidelines

You are encouraged to consult the ARRIVE guidelines recommended by the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3R).

Euthanasia or Anesthesia Methods

Where applicable, any euthanasia or anesthesia methods must be carried out in accordance with applicable veterinary guidelines. These methods must be described in detail in the manuscript.

Laboratory Animals

Manuscripts describing research involving laboratory-based animals must include details on housing, husbandry, and steps taken to reduce suffering. In studies where experimental animals were euthanized, details must be provided on humane endpoints. Details on the planned behavioral observations or physiological measurements used to determine the humane endpoint must be described. You are advised to consult the NC3Rs guide on Humane Endpoints and the American Veterinary Medical Association (AVMA) Guidelines for the Humane Slaughter of Animals.

C4DISC partnership

The Journal and OUP aim to create a community that fosters diversity, equity, and inclusion. As part of our commitment to these principles, OUP is a proud partner of theCoalition for Diversity & Inclusion in Scholarly Communications (C4DISC). C4DISC works with organizations and individuals within the scholarly communications landscape to foster equity, inclusion, diversity, and accessibility across the publishing industry and its published outputs.

Inclusive language

As defined by the Linguistic Society of America, “Inclusive language acknowledges diversity, conveys respect to all people, is sensitive to differences, and promotes equal opportunities”. We encourage you to consider using inclusive language and images when preparing your manuscript. For guidelines, please see the inclusive language guidelines.

Accessibility

Written, visual, and audio content in your submission should be accessible to all. Please see the C4DISC guidelines for making text, images, charts, tables, and audio and video accessible.

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Availability of data and materials

Please consult the Journal’s full Data Deposition policy.

Authors are required to include a data availability statement in their paper.

Data and codes: where ethically possible, authors must provide access to all data and software code underlying the results presented in their article at submission. For details of the minimum information to be included in data and software citations see the OUP guidance on citing research data and software.

Research materials: including strains, clones, cell lines, hybridomas, and genetically modified organisms that are described in publications in the Journal should be made available to any qualified investigator promptly upon request. Materials must be available freely or at reasonable cost to members of academic institutes for a minimum of 5 years from publication.

Synthetic oligomers: manuscripts that describe the application of synthetic nucleic acids or nucleic acid mimics to modulate gene expression must include a complete description of the base sequence and chemical modification pattern of the oligomers.

The Editors are prepared to deny further publication rights in the Journal to authors unwilling to abide by these principles.

Whenever possible, data should be presented in the main manuscript or additional supporting files or deposited in a public repository. Please consult the Journal’s full Data Deposition policy for information on general repositories for all data types, and resources for selecting repositories by subject area.

Computational Resources

NARhas strong policies regarding the accessibility and longevity of the computational resources that it publishes. The journal requires that any published database, webserver, webservice, stand-alone program, or dataset be:

• freely available over the internet, without login or registration, and
• updated or at least maintained in a fully functional form, ideally at the same URL for at least 5 years.

Additional rules pertain to:

Databases

• If any part of the database (e.g. the one that deals with the user-submitted data) needs to be password-protected, only the freely available part will be considered by the reviewers.
• Authors are encouraged, but not required, to make the contents of their databases freely available as flat or relational files upon request.

Webservers

• Any third-party software employed by the website that has more restrictive usage terms must be listed.

Software

• Software must be freely available to users at the time of submission, either as executable versions for multiple, common platforms (Linux, Windows and MacOS) or as source code or as a web server.
• Authors must ensure that the software is available for a full 5 years following publication, preferably through a download link on a stable URL or in a public code repository such as GitHub. Please note that you will be required to deposit the code to Zenodo or FigShare and provide the permanent DOI in the Data Availability statement at revision or acceptance. These repositories will retain the version of the code that was used in your paper. They will also link back to Github so that readers can benefit from any newer versions.
• Authors are encouraged, but not required, to make their source code available through an open-source license (seeOpenSourcefor examples)

Data availability statement

The inclusion of a data availability statement is a requirement for papers published in the Journal. Data availability statements provide a standardized format for readers to understand the availability of original and third-party data underlying the research results described in the paper. The statement should describe and provide means of access, where possible, by linking to the data or providing the required unique identifier.

More information and example data availability statements.

Choosing where to archive your data

Authors are highly encouraged to select a repository that issues DOIs as this helps to facilitate persistent linking to the dataset from the research article. You may refer to online resources such as FAIRsharing.org and re3data.org for lists of data repositories, including information on certification status and services offered.

By order of preference, authors should:

1. Deposit the data in a subject-specific public repository.

2. If there is no such repository, deposit the data in a generic repository that issues DOIs as this helps to facilitate persistent linking to the dataset from the research article. You may refer to online resources such as FAIRsharing.org and re3data.org for lists of data repositories, including information on certification status and services offered. We suggest you consider these options when choosing your generic repository:

• Code Ocean (for data and code)
• Dryad Digital Repository
• Figshare
• Harvard Dataverse
• Open Science Framework
• Zenodo

3. If options 1-2 above are not possible, provide the data as supplementary files.

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Submitting your bioRxiv preprint to the journal

You can submit your bioRxiv preprint directly from the bioRxiv server to NAR. To do this, visit the Author Area in bioRxiv and select NAR from the list of options.

This will transfer all manuscript files and author information to NAR. You will then receive an email with a link to your submission in NAR, where you will need to answer some additional questions and approve the manuscript for submission.

Authors submitting their bioRxiv preprint to NAR should refer to the section on Preprints. In particular, you should note the following:

• The preprint that you submit to NAR must be the Author’s Original Version before any peer review.
• You should not submit your preprint to more than one journal simultaneously.
• If your paper is accepted for publication in NAR, you are responsible for ensuring that the preprint is updated with the DOI of and a link to the published paper. bioRxiv does this automatically for most papers, but the process is imperfect, particularly if the preprint and paper titles are different.

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Digital preservation

Content published in the Journal will automatically be deposited into digital preservation services, including CLOCKSS, the Global LOCKSS Network, and Portico. This ensures the long-term preservation of your work. Through LOCKSS, participating institutions can sustain access to content if the Journal were to otherwise be unavailable, even for a short period of time. Should the Journal ever cease to publish, or content otherwise become permanently unavailable, long-term access to the archives of CLOCKSS and Portico would be triggered. Until such a trigger event occurs, content is not available to the public through CLOCKSS and Portico.

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Self-archiving

Self-archiving refers to posting a copy of your work on a publicly accessible website or repository. Under certain circ*mstances, you may self-archive versions of your work on your own webpages, on institutional webpages, and in other repositories.

For information about the Journal's policy, and to learn which version(s) of your paper are acceptable for self-archiving, please see our Author self-archiving policy.

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Publishing agreements and charges

Publishing agreement

After your manuscript is accepted, you will be asked to sign a licence to publish through the SciPris portal. The Journal is fully open access, meaning all papers in the Journal are published under an open access licence. The corresponding author will need to arrange payment of an open access charge to publish in the Journal. This charge allows all published papers to be immediately and freely available to all readers immediately upon online publication, as part of a long-term archive, without subscription barriers to access. Editorial decisions occur prior to this step and are not influenced by payment or ability to pay. Papers can be published under the following:

• Creative Commons Attribution licence (CC BY)
• Creative Commons Attribution Non-Commercial licence (CC BY-NC)
• United States Government Open Licence
• UK Open Government Licence

Please see the OUP guidance on licences, copyright, and re-use rights for more information regarding these publishing agreement options.

Open Access Charges

Please see the details of open access licences and charges. As the Journal is fully open access, you must pay the open access charge or request to use an institutional agreement to pay the open access charge through the SciPris portal.

The current open access charges are:

CC BY/CC BY-NC - $3,802

OUP has a growing number of open access agreements with institutions and consortia, which provide funding for open access publishing (also known as Read and Publish agreements). This means corresponding authors from participating institutions can publish open access, and the institution may pay the charge. Find out if your institution has an open access agreement.

To be eligible for one of OUP’s Read and Publish agreements, the corresponding author must provide their qualifying institution as their primary affiliation when they submit their manuscript. After submission, changing the corresponding author in order to access Read and Publish funding is not permissible.

In order to access a Read and Publish deal, your institution must be verified within the ScholarOne system. To verify your institution, please select from the drop-down list of institutions displayed in Step 4: Authors & Institutions of the submission process.

NAR asks authors to state the source of funding used to pay the Open Access publication charge, after having a manuscript accepted. This provides transparency for readers, funding bodies, and the publisher. If appropriate the information will be added to the Acknowledgement section of the article. It is not compulsory to provide this information, but we encourage all authors to do so.

The Journal does not charge for colour.

The Journal does not have page charges.

Waivers

Corresponding authors based in countries and regions, that are part of the developing countries initiative receive a full waiver of their open access charges. For further details, please see our APC Waiver Policy.

For queries relating to waiver requests, please contact OUP’s Open Access team openaccess@oup.com.

Copyright Licence

Upon receipt of accepted manuscripts at Oxford Journals, authors will be invited to complete an online copyright licence to publish. If the form has not been received by the time we receive author corrections, publication of your manuscript will be delayed.

As part of the licence agreement, authors may use their own material in other publications provided that the Journal is acknowledged as the original place of publication and Oxford University Press as the Publisher. Information about theNew Creative Commons licences.

Please note that by submitting an article for publication you confirm that you are the corresponding/submitting author and that Oxford University Press may retain your email address for the purpose of communicating with you about the article. You agree to notify OUP immediately if your details change. If your article is accepted for publication OUP will contact you using the email address you have used in the registration process. Please note that OUP does not retain copies of rejected articles.

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Changes to published papers

The Journal will only make changes to published papers if the publication record is seriously affected by the academic accuracy of the published information. Changes to a published paper will be accompanied by a formal correction notice linking to and from the original paper.

As needed, we follow the COPE guidelines on retractions.

For more information and details of how to request changes, including for authors who wish to update their name and/or pronouns, please see OUP’s policy on changes to published papers.

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Promoting your work

As the author, you are the best advocate for your work, and we encourage you to be involved in promoting your publication. Sharing your ideas and news about your publication with your colleagues and friends could take as little as 15 minutes and will make a real difference in raising the profile of your research.

You can promote your work by:

• Sharing your paper with colleagues and friends. As your paper is published open access, it will always be freely available to all readers, and you can share it without any limitations.
• Signing up for an ORCID iD author identifier to distinguish yourself from any other researchers with the same name, create an online profile showcasing all your publications, and increase the visibility of your work.
• Using social media to promote your work. To learn more about self-promotion on social media, see our social media guide for authors.

Find out how Oxford University Press promotes your content.

Press releases

If you would like to arrange an embargo date so that a press release can be issued simultaneously with the publication of your paper, please contact us as soon as possible. Once published, the paper cannot be temporarily withdrawn. If your paper has already been accepted, contact the Author Support Team. If your manuscript is still under review, please contact the editorial office (nar.editorialmanager@oup.com).

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Preparing your manuscript

General guidelines on preparing your manuscript for publication can be found on OUP’s Preparing and submitting your manuscript page. Specific instructions for NAR can be found below.

Please see specific instructions for submitting to the annual Database and Web Server issues.

Data Deposition

Authors must provide access to the data underlying the results presented in their article at submission. For more information on where and how to deposit your data, please visit the Data Deposition and Standardization page.

Pre-submission language editing

Manuscripts must be clearly and concisely written in English. The Editors reserve the right to reject without review those that cannot adequately be assessed because of a poor standard of English. If you are not confident in the quality of your English, you may wish to use a language-editing service before submitting to ensure that Editors and reviewers understand your manuscript. Oxford University Press, partners with Enago, a leading provider of author services. Through the OUP-Enago partner page, prospective authors are entitled to a discount for language editing, abstract and layperson summary writing, rejected manuscript editing, and creation of graphical abstracts, illustrations, and videos.

Enago is an independent service provider, which will handle all aspects of this service, including payment. As an author you are under no obligation to take up this offer. Language editing and other services from Enago are optional and do not guarantee that your manuscript will be accepted. Edited manuscripts will undergo the regular review process of the Journal. For more details and a list of additional resources, please see OUP’s page on language services.

File Types

Authors are encouraged to use the NAR Word and OUP LaTeX templates.

LaTeX

If you have prepared your manuscript using TeX or LaTeX please create a PDF version to upload. This should be the complete manuscript (text with figures appearing at the end of a paper).

Please note that only the PDF is required on submission and LaTeX files will be requested at revision stage.

For creating manuscripts in LaTeX, NAR recommends the use of the OUP LaTeX template. The template is available online at Overleaf and also as a downloadable package via OUP's Preparing and submitting your manuscript page. Please use the 'Modern Large' design.

Overleaf is a free, collaborative online LaTeX editor that allows you to write your manuscript in a TeX or rich text environment, to generate PDF outputs as you write, and to share your manuscript with co-authors and collaborators. Overleaf also allows you to submit your manuscript files directly into our online submission system, without needing to upload files manually, as well as to make updates to those files if preparing a revised submission.

Initial submission

For the initial submission, we encourage you to submit a single .pdf file which includes the main text, references, tables, and figures. All figures and tables should be embedded in the text to facilitate reviewing.

Please upload supplementary data as separate file(s).

Do

• Number all pages.
• Use embedded TrueType fonts in your Word document. (Select 'Tools> Options' from the top menu bar, select 'Save' tab and then check the box to Embed TrueType fonts and click OK. For word 2007, click 'Save as> Tools> Save Options> Preserve Fidelity'. Select 'Embed Fonts', tick the first box and untick the second box.)
• Insert special characters using the Symbol font.
• Use single-column and single-spaced text (unless using LaTeX)

Don’t

• Use line-numbering.
• Use footnotes.

Revision

Please ensure that you provide the following files, carefully labelled so that their content is clear. Please provide all source files in their native editable format.

• Your responses to Referee or Editor comments specifying all changes made.
• Graphical Abstract: see guidelines below.
• Revised manuscript: .docx, .rtf or LaTeX file format but NOT PDF format. Changes made in response to Referee or Editor comments must be writtenin red. Embed tables, figures, and their respective captions in the text to facilitate reviewing.
• High-resolution figure files: For a simple guide to preparing figure files, please see ourshort guidelines. These guidelines cover recommended file formats, resolution, sizing, and colour management options, to help you achieve the best outcomes online and in print.
• Tables: any editable format (such as Microsoft Word, PowerPoint or Excel), not as an image file.
• Supplementary data: must submitted in a separate file to the main article, preferably in PDF format.

Detailed guidelines are also provided below.

Article structure

Manuscripts should be ordered as follows:

Title

The title must be clearly intelligible to a non-specialist. The use of jargon and non-standard abbreviations is not permitted.

Authors and affiliations

List the names of all author(s) in the following format: first name followed by initial(s) and last name – e.g. John Smith or John E. Smith.

Affiliations of all authors: must include as a minimum Department/Division/Unit, Institution, Town, Postal Code, Country.

Email address(es) of corresponding author(s).

Graphical abstract

We require graphical/video abstracts for all article types, preferably with the original submission, butno later than at revision. A video/graphical abstract is a visual representation of the central finding or methodology of the paper. It will be displayed in the table of contents and will be published as part of the article online and in the PDF. Authors should strive to make the video/graphical abstract informative, interesting, visually appealing, and straightforward. The graphical/video abstract should be submitted for peer review as a separate file, selecting the appropriate file-type designation in the journal’s online submission system. The file should be clearly named e.g., graphical_abstract.tif, video_abstract.mp4. SeeOUP's Preparing and submitting your manuscript pagefor guidance on appropriate file format and resolution for graphics and videos. Videos should be submitted as an .mp4 file-type, at the highest possible resolution, and include a still image to represent the video in the print PDF.

Technical Requirements:

• Size: 5:2 aspect ratio, 127x50mm or 5x2in minimum
• Orientation: landscape
• Please see our short guidelines to preparing figures. These guidelines cover recommended file formats, resolution, sizing, and colour management options, to help you achieve the best outcomes online and in print.
• Font: Use a sans serif font such as Arial, 12–16 points

The graphical abstract should:

• be simple
• be original i.e. not an existing main or supplementary figure
• importantly, not include trademarked or copyrightedimages or logos. For example, you could use the text UniProt, but not thelogo
• use colour
• use text sparingly, mainly for labels
• consist of a drawing, diagram, graph, etc. illustrating a main point or methodology of the paper
• read from top-down or left-to-right

Seeexamples from previous issues.

Text Abstract

• Text abstracts must be written in English.
• Single paragraph, not exceeding 200 words.
• URLs, references to figures or schemes, reference citations or non-standard abbreviations should NOT be included. However, note that URLs MUST be included in the abstract of manuscripts submitted to the Database and Web Server issues.

Introduction

Present the objectives of the work and provide an appropriate background, avoiding a detailed examination of the literature or a description of the results.

Materials and Methods

As experimental reproducibility is essential to support data and derived conclusions, NAR places the Materials and Methods Section before the Results Section in all submission types and insists that all essential experimental procedures are detailed in the main manuscript text and not relegated to supplemental files. We, nonetheless, encourage the use of supplemental files for additional information and/or data, but notin lieuof a detailed Materials and Methods Section.Methods derived from unpublished sources must be explicitly described and cannot be simply referenced back to bioRxiv or related preprints for replication, validity, and proof of reliability.

For further clarity of experimental designs, we also request a list of essential sub-headings under the Materials and Methods Section, for availability of reagents, deposited data, programs, web sites, etc. These Materials and Methods descriptors apply to all manuscripts, regardless of whether they are Standard research or METHODS submissions.

• Reagents: This sub-heading should include enzymes, antibodies, kits, specialized commercial instruments, non-standard chemicals, peptides, recombinant proteins,et al. with reference to company name, location, and catalog #.
• Biological Resources: This sub-heading should list all cell lines, organisms and strains, plasmid vectors,et al. Each resource should include its repository with location and resource #, web link, and reference, if appropriate.
• Statistical Analyses: Details to mathematical evaluations for quantifying accuracy, sensitivity, and reproducibility should be included, indicating equation choice and numbers of replicates.
• Novel Programs, Software, Algorithms:Each new resource presented in the manuscript should be detailed with appropriate links and availability for free (non-password) access to codes/scripts.
• Web Sites/Data Base Referencing:Every site or program used in the manuscript should be listed with its most recent and useful reference.

Nomenclature conventions

Restriction enzymes, DNA methyltransferases and homing endonucleases should be named or referred to using the conventions described in Roberts,R.J. et al. (2003)Nucleic Acids Res., 31, 1805-1812. Note that restriction enzyme names should NOT be italicized.

Computer programs

For papers that describe a computer program, the authors should either make the program accessible as a web server with no login requirements, deposit the source code in a public repository such as Zenodo or Figshare, or upload an executable version of the program and instructions as supplementary data. Any costs associated with a reader acquiring the program must be specified in the text. Note that in general any complicated mathematics needed to explain an algorithm should be included as supplementary material.

NMR papers

Resonance assignments should be reported relative to DSS and not to HOD.

Statistical analyses

Materials and Methods, and corresponding descriptions of actual experiments should contain, anywhere relevant:

1. The exact sample size (n) for each experimental group/condition, given as a number, not a range.
2. A precise description of the sample collection allowing the reader to understand whether the samples represent technical or biological replicates (including how many animals, litters, cultures, laboratory replicates, etc.)
3. If comparisons are made between groups, a clear description of the method used for statistical inference must be stated:

   For the analysis of categorical outcomes, exact methods or asymptotic methods with appropriate adjustments for small sample size should be used when the numbers of events are small. Standard chi-squared or difference in proportions tests can be used when the sample sizes and numbers of events are sufficiently large.

   For comparisons of continuous data that are normally distributed data, t-tests are appropriate for comparisons of two groups, whereas Analyses of Variance (ANOVA) are generally required for comparisons between for three or more groups. Such tests are also robust when applied to non-normal distributions with sufficiently large sample sizes. When the sample size is small, and prior evidence suggests that the measurements are unlikely to be normally distributed, appropriate nonparametric methods are usually preferable.

4. If p-values are presented, one-sided or two-sided should be specified. If one-sided, justification should be provided. Confidence intervals should also accompany the parameter for which statistical significance is being tested.
5. If multiple comparisons are made, there should either be appropriate adjustments to the p-values or a justification provided for why no adjustments were made.
6. Describe continuous data using averages, and specify if using the mean or median. Also specify measure of variation (for continuous data) as either standard deviation or standard error of the mean. If describing binary data, include numerator and denominator, not just percentage. For estimates of proportions and means, also provide confidence intervals.

There are a variety of online resources to assist Authors with proper statistical choices and approaches, that can be found through simple internet searches for statistical tests in the biological sciences. Examples include:

A biologist's guide to statistical thinking and analysis

Handbook of Biological Statistics

Results

Results and Discussion may be combined.

Results should be clear and concise.

Discussion

Results and Discussion may be combined.

This should focus on the significance of the results of the work, not repeat them. Avoid lengthy citations and discussion of published literature.

Data Availability

Authors must provide access to the data underlying the results presented in their article at submission. Access details must be provided in a ‘Data Availability’ statement at the end of the manuscript. For more information on where and how to deposit your data, please visit theData Deposition and Standardizationpage.

Supplementary Data statement

Authors must add the following statement if their manuscript includes supplementary material for publication: ‘Supplementary Data are available at NAR Online’.

Please see also Supplementary Data guidelines below.

Acknowledgements (including Dedications)

The Editors will consider requests for dedications. Ordinarily, requests will be granted only for dedications to recently deceased scientists.

Funding

You must fully declare all funding information relevant to the study, including specific grant numbers, under a separate subheading following the acknowledgements.

If the funder is listed in theCrossref funder registry, the funder name should appear exactly as it appears in that database. Seethis pagefor more information on funding agency requirements.

The following rules should be followed:

• The sentence should begin: ‘This work was supported by …’
• The full official funding agency name should be given, i.e. ‘National Institutes of Health’, not ‘NIH’ (full RIN-approved list of UK funding agencies). Grant numbers should be given in brackets as follows: ‘[grant number xxxx]’
• Multiple grant numbers should be separated by a comma as follows: ‘[grant numbers xxxx, yyyy]’
• Agencies should be separated by a semi-colon (plus ‘and’ before the last funding agency)
• Where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number 'to [author initials]'.

An example is given here: ‘This work was supported by the National Institutes of Health [AA123456 to C.S., BB765432 to M.H.]; and the Alcohol & Education Research Council [hfygr667789].

Conflict of Interest Disclosure

Please see Disclosure of potential conflicts of interest above.

References

• Cited in the text by sequential number only, in order of appearance, and listed numerically in the References section.
• Personal communications, unpublished results, manuscripts submitted or in preparation, statistical packages, computer programs and web sites should be cited in the text only, NOT included in the Reference list. For example: (unpublished data).
• Authors should check all references carefully and ensure that all references in the Reference section are cited in the text. Note that multiple references or page spans under one number are not allowed.
• You can download the current reference style for this journal at EndNote's website.
• Journal names should be abbreviated in the style of Chemical Abstracts.
• Where the list of Authors is extensive it is acceptable to list the first 10 Authors followed by et al.
• Full titles of journal articles must be provided.
• References should conform to the following examples

1. Journal article:Schmitt,E., Panvert,M., Blanquet,S. and Mechulam,Y. (1995) Transition state stabilisation by the 'high' motif of class I aminoacyl-tRNA synthetases: the case of Escherichia coli methionyl-tRNA synthetase. Nucleic Acids Res., 23, 4793-4798.
2. Book:Maniatis,T., Fritsch,E.F. and Sambrook,J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
3. Book chapter:Huynh,T.V., Young,R.A. and Davies,R.W. (1988) Constructing and screening cDNA libraries in lambdagt10 and lambdagt11. In Glover,D.M. (ed.), DNA Cloning - A Practical Approach. IRL Press, Oxford, Vol. I, pp. 49-78.
4. Online journal article:Capaldi,S., Getts,R.C. and Jayasena,S.D. (2000) Signal amplification through nucleotide extension and excision on a dendritic DNA platform. Nucleic Acids Res., 28, e21.
5. Preprints:Fan,X., Yang,Y. and Wang,Z. (2018) Pervasive translation of circular RNAs driven by short IRES-like elements. biorXiv doi: https://doi.org/10.1101/473207, 18 November 2018, pre-print: not peer-reviewed.

Tables

• All tables and their captions should be embedded in the text to facilitate reviewing.
• If needed, individual tables should also be submitted in an editable format (such as Microsoft Word, Excel, or PowerPoint), not as an image file.
• Avoid excessive formatting, such as the use of colour and shading, which are not replicated in the published web version, and the use of tabbed spacing to indicate alignment.
• Ensure that any formatting or superscript symbols such as asterisks are explained in the table footnote.
• Provide units in column or row headers, rather than in the table body.
• All tables provided should be cited within the article text.

Figures

• All figures and their captions should be embedded in the text to facilitate reviewing.
• In addition, you are required to submit high-resolution images, preferably with your initial submission but no later than revision stage.Detailed guidelines are available.
• Please ensure that the figure is clearly labelled with its figure number.
• The captions should be highly detailed and nearly sufficient to comprehend each panel without extensive reliance on the main text.

Representation of experimental data as computer images:

If primary experimental data are presented in the form of a computer-generated image (such as those from a PhosphorImager or digital camera), any editing must be described in detail. A linear (rather than sigmoidal) relationship between signal and image intensity is assumed. Unless stated, it is assumed that the image is unedited.

Inappropriate manipulation of images to highlight desired results is not allowed.Please read thisarticlefor detailed guidance. As you prepare your figures, please adhere to the following guidelines to accurately present your data:

• No specific feature within an image may be enhanced, obscured, moved, removed, or introduced.
• The grouping of images from different experiments or from different parts of the same experiment, whether they are gels, blots, photos, micrographs, or any other type of image (i.e. the creation of a 'composite image') must be made absolutely explicit by the arrangement of the figure (i.e.using dividing lines) and by the text of the figure legend.
• Adjustments of brightness, contrast, or colour balance are acceptable if they are applied to the whole image and as long as they do not obscure, eliminate, or misrepresent any information present in the original, including the background. Non-linear adjustments (e.g.changes to gamma settings) must be disclosed in the figure legend. Alteration of brightness or contrast that results in the disappearance of any features in a gel (either bands or cosmetic blemishes) or similar alterations in other experimental images is strictly forbidden.

Supplementary Data

Manuscripts may include supplementary data to be made available by the publisher as online-only content, linked to the online manuscript. Such data should consist of electronic files and should not merely be a link to another web site. Manuscripts accompanied by online Supplementary data are designated with an ' S ' in the Table of Contents in the print edition.

For a definition of Supplementary data and the guidelines for submitting it, please visit this page.

All Supplementary data MUST be referred to in the main manuscript at an appropriate point in the text.

Please note that Supplementary Material is considered as published material and is regulated by the same copyright and permissions rules as the published article to which it belongs.

Cover Figures

Authors are encouraged to submit colour figures to be considered for use of the cover of NAR. If you would like to submit a cover image for consideration, please visit this page for details.

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Contact Us

If you experience any problems during the online submission process, please consult the Author’s User Guide which provides more detailed submission instructions and ‘movie tutorials’ explaining how to submit your manuscript. You will find this under ‘User Tutorials’ on the Login screen of ScholarOne Manuscripts.

If your problems are purely technical (i.e. failure of files to be uploaded or converted), contact the ScholarOne support team using the 'Get Help Now' link in the top right-hand corner of every screen.

For questions regarding submission and review, including appeals, you can contact the editorial office by email at nar.editorialmanager@oup.com.

After your paper has been sent to production, you can contact oupsupport@scipris.com for questions regarding the production process or publication. Please see Changes to published papers if you need to request a substantive change to your published paper.

Open Access queries and waiver request should be sent to openaccess@oup.com.

For queries about payments and licensing, please contact jnls.author.support@oup.com.

For queries about Standard articles, contact the Senior Executive Editors:
Dr J. Sale (jesnar@mrc-lmb.cam.ac.uk) or Dr B. Stoddard(stoddnar@fhcrc.org)

For queries specifically about Methods articles, contact:
Dr A. Kimmel(ark.nar@gmail.com)or Dr G. Sczakiel(nar@imm.uni-luebeck.de)

For queries specifically about Critical Reviews and Perspectives, contact:
Dr D. Corey (david.corey@utsouthwestern.edu)and David Rusling (david.rusling@port.ac.uk)

For queries specifically about Database issue articles, contact:
Dr D. Rigden
Email:nardatabase@gmail.com

For queries specifically about Web Server issue articles, contact:
Dr D. Seelow
Email:nar@bihealth.de

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