# GENERAL POLICIES OF THE JOURNAL

New – Please note that the journal now encourages authors to complete their copyright licence to publish form online.

Open Access charges are now payable using our Author Services site. This will enable you to pay online with a credit/debit card, or request an invoice by email or post.

Authors' responsibilities
Submission of a manuscript implies that it reports unpublished work and that it is not under consideration elsewhere. All files, including figures, must be original. The submission process must be carried out by the corresponding author. The corresponding author checks the relevant boxes during online submission on behalf of all authors to indicate that they are in complete agreement with the contents of the manuscript and are prepared to abide by the general policies of NAR as listed below. If the corresponding author is not the senior author, then full contact details of the latter must be included in the submission. Under certain circumstances the journal may need to communicate with the senior author of the manuscript. The email addresses of all co-authors must also be provided.

During submission, authors are requested to upload a cover letter containing additional information which will aid the processing of the manuscript. This must include details of any previous submission of the work to NA, either partial or in entirety, which has been rejected, regardless of any changes in authorship. The manuscript number of the earlier submission must be provided, together with a file containing the responses to any editorial or referee reports and a summary of the changes that have been made. The cover letter should also contain details of any data obtained from other groups which is cited in the manuscript as a personal communication(s). The corresponding author must confirm that permission has been obtained for each inclusion.

Authors must also advise 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.

Conflicts of Interest
NAR policy requires that EACH author of all manuscripts reveal any financial interests or connections, direct or indirect, or other situations that might raise the question of bias in the work reported or the conclusions, implications, or opinions stated - including pertinent commercial or other sources of funding for the individual author(s) or for the associated department(s) or organization(s), personal relationships, or direct academic competition. When considering whether you should declare a conflicting interest or connection please consider the conflict of interest test: Is there any arrangement that would embarrass you or any of your co-authors if it was to emerge after publication and you had not declared it?

It is the responsibility of the corresponding author to ensure that all co-authors adhere to this policy and to confirm whether they have any conflicts to declare. The corresponding author should then, during the submission process, complete the conflict of interest field on behalf of all co-authors.

If the corresponding author is unable to do this, then each co-author must complete and return an individual copy of the form available at the following link (Conflict of Interest Form). It is the corresponding author's responsibility to co-ordinate the completion and return of written forms. The forms should be faxed to the Senior Editorial Office (+44 (0)1252 240 001) before the manuscript is accepted.

In the event of one or more co-authors declaring a conflict of interest, details should be provided either online during the submission process or in the faxed form, and a prominent paragraph included in the submitted manuscript. If the manuscript is published, this information will be communicated in a statement in the published paper.

If you are in any doubt as to what constitutes a conflict, please read the FAQs or contact the Senior Editorial Office.

Ethical conduct
NAR expects that authors will observe high standards with respect to publication ethics. For example, the following practices are unacceptable: (1) falsification or fabrication of data, (2) plagiarism, including duplicate publication of the authors' own work, in whole or in part without proper citation, (3) misappropriation of the work of others such as omission of qualified authors or of information regarding financial support. Allegations of unethical conduct will be discussed initially with the corresponding author. In the event of continued dispute the matter will be referred to the author's institution and funding agencies for investigation and adjudication.

NAR regularly uses plagiarism detection software on submitted manuscripts. The journal reserves the right to decline submissions suspected of plagiarism at any time. In addition, the journal reserves the right to report any suspicion of plagiarism to the lead author's institution.

In addition to proper ethical conduct regarding authorship practices, the journal also requires that all research, especially those that utilize animal experiments or or samples derived from individual human subjects and patients, adhere to the OUP Ethical Research Guidelines and to all institutional review and national legal requirements.

Oxford Journals, publisher of NAR, is a member of the Committee on Publication Ethics (COPE), and the journal strives to adhere to the COPE code of conduct and guidelines. For further information see http://publicationethics.org/about.

Prior publication and preprint policy
NAR allows authors to deposit preprints in community preprint servers such as ArXiv.org, provided that entries are updated to acknowledge that the article has been accepted/published by NAR. Please click here for our full self-archiving policy. Our policy towards such archives is kept under review, but we currently do not consider articles that have already been posted in Nature Precedings or PLoS Currents. Authors are encouraged to contact the editorial office if they are in any doubt about prior submission.

Upon receipt of accepted manuscripts at Oxford Journals authors will be invited to complete an online copyright licence to publish form.

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 the New Creative Commons licence can be found here.

Author Self-Archiving/Public Access policy

Authorisations
If previously published tables, illustrations or more than 200 words of text are to be included in an article in NAR, then the copyright holder's permission must be obtained, and copies of such permission letters should be forwarded to the production office upon acceptance of the manuscript. Authors must obtain authorisation for all personal communications.

Authorship
All persons designated as authors should qualify 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. Each author should have participated sufficiently in the work to take public responsibility for the content. Authorship credit should be based on substantial contribution to conception and design, execution, or analysis and interpretation of data. All authors should be involved in drafting the article or revising it critically for important intellectual content, and must have read and approved the final version of the manuscript.

All authors must be from a recognised institution. Personal postal addresses are not acceptable.

Errors in author names cannot be corrected after publication and will affect the author's record in PubMed.

Joint First Authorship
Such a footnote is allowed. The joint first authors must be the first names appearing in the list of authors. A footnote containing the statement: "The authors wish it to be known that, in their opinion, the first x authors should be regarded as joint First Authors" will be added. Other statements concerning joint authorship will not be published. Joint senior/last authorship is not permitted.

Joint Senior/Corresponding Authors
Corresponding authors, also referred to as senior authors, take responsibility for the published work on behalf of all authors. NAR allows up to three corresponding authors to be marked per script. One of the joint corresponding authors MUST be the submitting author. The names of joint corresponding authors can appear at any place in the list of authors and will be identified by an asterisk. All other symbols, combinations of authors or footnotes will be removed.

Groups and Consortia
Groups and Consortia can be included in the list of Authors. The full list of members does not have to be provided but if it is, the points below apply:

• If the group only has a few members, the members should be listed in a footnote 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.

For articles where only the group is listed as Author (i.e. no individuals are listed), the corresponding email address must link to a named individual not a generic email address. The name and institution of the individual must be provided. Acronyms in the list of Authors are acceptable as long as they are unambiguous.

Proofs
Corresponding authors will be sent proofs in PDF format by email. It is the authors' responsibility to check proofs thoroughly.

Post-publication corrections
Corrections are made if the publication record is seriously affected by the accuracy of published information. NAR operates a rapid online publication model, 'Advance Access'. Advance Access publication constitutes definitive publication and is not subject to informal changes. However if a significant error is discovered after publication of an Advance Access article, which necessitates correction to the online version, a new version will be published online with a footnote to outline the changes made. Both versions will continue to be available online. Corrections to articles more than 2 years old will only be considered under exceptional circumstances.

Corresponding authors who wish to have considered the publication of a correction that materially affects the data or conclusions of their already published paper should contact the editor who handled their manuscript.

Page charges
ALL papers are made freely available under an Open Access model at the NAR website http://www.nar.oxfordjournals.org and also at PubMed Central (http://www.pubmedcentral.nih.gov/) immediately upon publication.

The charge for authors at institutions with NAR membership will be £710/$1385/1065 euros. The charge for authors at institutions without NAR membership will be £1420/$2770/2130 euros.

There are no excess page charges for papers that occupy 9 pages or less. Papers that occupy more than 9 pages will incur an additional charge of \$195/£100/150 euros for each page in excess of 9.

Under NAR’s Open Access model the journal’s costs are covered primarily by author publication charges (rather than subscription fees). NAR has a small budget for waiving open access charges for authors in developing countries and others in genuine financial hardship. Funds for waivers are limited, however, as the journal would not be sustainable without income from author charges to cover its costs.
The NAR Editors hope that contributors to NAR will support the journal’s open access model by paying the publication charges if they are able to do so. An NAR Author Loyalty Discount may also be available. Further information is available at

Offprints
The publisher will provide free online access to the full text (both HTML and PDF) of the article. Print offprints, including online-only papers, are available for a charge. Offprints can be ordered using the Oxford Journals Author Services site. Once your paper is accepted, you will receive an email from OUP to access this site.

Orders from the UK will be subject to a 20% VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

Availability of materials

• Research materials: including strains, clones, cell lines, hybridomas, genetically modified organisms, X-ray and NMR co-ordinates 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.
• Software: If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to users at the time of submission (either as executable versions for multiple, common platforms or as source code). Availability must be clearly stated in the article. Authors must ensure that the software is available for a full TWO YEARS following publication, preferably through a download link on a stable URL or in a public code repository such as GitHub or SourceForge. Authors are encouraged to make their source code available through an open source license (see www.opensource.org for examples).
• Databases: must be freely available to all via the web and not be password protected. Authors are encouraged to make the contents of their databases freely available as flat or relational files upon request.
• Web servers: must be freely available to all with no login requirement. Authors are encouraged to make the underlying code and data for their web tools available upon request.

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

Guidelines for ChIP-Seq experiments and related whole genome assays
For experiments that strive to determine and analyze genome-wide sites of genetic or epigenetic modifications or trans-factor binding sites (using high-throughput approaches such as such as ChIP-Seq experiments) NAR expects that researchers will follow published ENCODE guidelines and corresponding best practices (see Landt et al. (2012) "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia" Genome Research 22: 1813 - 1831; doi 10.1101/gr.136184.111). These guidelines include recommendations that investigators:

1. Test and report antibody reactivity and specificity using both a primary test (immunoblot or immunofluorescence) and at least one secondary test (see the above reference for further details).

2. Perform measurements and sequencing on at least two independent replicates, and analyze the resulting data for overall agreement and significance thresholds.

3. Generation and use of appropriate control samples, such as sequencing of samples not subjected to immunoprecipitation or of samples subjected to a mock ChIP reaction with an irrelevant control antibody.

Deposition of sequence and structural data
Sequence information, co-ordinates used to create molecular models described in a manuscript, and structural data must be submitted in electronic form, prior to acceptance, to the appropriate database for release no later than the date of publication of the corresponding article in the Journal. Deposition numbers and/or accession numbers provided by the database should be included in the manuscript and entered into the relevant boxes during online submission or communicated to the Executive Editor handling the manuscript as soon as received. In cases where there may be no appropriate database, authors must make their data available on request. Atomic co-ordinates may be included in the publication as supplementary material. Manuscripts will not be published until the Journal is in receipt of the deposition number.

For papers reporting novel nucleic acid sequences
Nucleic acid sequence information must be deposited with one of the three major collaborative databases (EMBL/GenBank/DDBJ). For sequences obtained from a public or private web site, it is the author's responsibility to ensure that any sequence used within the manuscript is deposited before publication. It is necessary to submit sequences to one database only since data are exchanged between EMBL, GenBank and DDBJ on a daily basis. New sequence names and their accession numbers should be listed at the beginning of the Materials and Methods section to aid searches by readers. In order to allow new methods of data search, NAR encourages authors to cite GenBank accession numbers when referring to established sequences within their manuscript. Contact details for submission to databases.

For papers reporting novel three-dimensional structures
Atomic co-ordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited with a database. Authors must agree to release the atomic coordinates and experimental data when the associated article is published.
The Cambridge Crystallographic Data Centre (CCDC) is appropriate for deposition of data on nucleosides, nucleotides and other small molecules.
A member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), MSD-EBI (www.ebi.ac.uk/msd), PDBj (www.pdbj.org), or BMRB (www.bmrb.wisc.edu) is appropriate for deposition of data on proteins determined by X-ray crystallography and for all macromolecules determined by NMR methods.
The Nucleic Acid Database (NDB) is appropriate for atomic co-ordinate and structure factor data for crystal structures of nucleic acids.
Contact details for submission to databases.

For papers reporting novel protein sequences
Protein sequences, which have been determined by direct sequencing of the protein, must be submitted to UniProt (i.e. TrEMBL, Swiss-Prot and PIR) using the interactive submission tool SPIN. Please note that they do not provide accession numbers, IN ADVANCE, for protein sequences that are the result of translation of nucleic acid sequences. These translations will forwarded automatically from the nucleotide sequence databases (EMBL/GebBank/DDBJ) and assigned UniProt accession numbers on incorporation into UniProt. Results from characterization experiments should also be submitted to UniProt: for novel sequences, these should be included with the sequence submission. Existing UniProt entries should also be updated. This can include information such as function, subcellular location, subunit, etc. Contact details for submission to databases.

For papers reporting new ChIP-Seq data
New ChIP-Seq data must be deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/), with accession numbers at or before acceptance for publication.

Microarray data All authors must comply with the 'Minimal Information About a Microarray Experiment' (MIAME) guidelines published by the Microarray Gene Expression Data Society, which can be found at http://www.mged.org/Workgroups/MIAME/miame_checklist.html. NAR also requires submission of microarray data to the GEO (http://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) databases, with accession numbers at or before acceptance for publication.

Quantitative PCR Authors are encouraged to follow the 'Minimal Information for Publication of Quantitative Real-Time PCR Experiments' (MIQE) guidelines, if appropriate. The guidelines are published by the Real-Time PCR Data Markup Language Consortium and can be found at http://www.rdml.org/miqe.php

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