Author guidelines

What are our aims?

Briefings in Bioinformatics aims to provide an indispensable resource for the experimental practitioner seeking awareness of the disparate sources of data and analytical tools of contemporary biology, biotechnology and medicine based on an explicit molecular description. This includes all areas of genomics, proteomics, lipidomics, glycomics, metabolomics, interactomics and network biology, imaging, systems biology, phenomics, chemoinformatics, computational biology and clinical/medical informatics that have a clear molecular foundation to the study. Large-scale instrumentation and computerisation is reducing the time that needs to be spent in the laboratory. Instead, the rate-limiting step is the analysis and interpretation of data.

How we publish

Briefings in Bioinformatics is a peer-reviewed fully open access journal publishing 6 issues per year online. 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 below.

Once a paper is accepted and the publishing agreement is signed, the Journal will publish the Accepted Manuscript version of the paper (before copyediting and review of the final proof) within one week on the Advance articles page. This will be replaced in Advance articles with the Version of Record of the paper (after copyediting and proof review process) when it is available. The Version of Record will be removed from Advance articles when it is published in the currently open issue. Substantial changes to the published Accepted Manuscript may require a correction notice. The Version of Record requires a correction notice for any changes after it is published, even if it is not yet placed in an issue. See the definitions of the Version of Record and other versions of the paper for more details.

Submitting

After preparing your manuscript according to the guidance in the Preparing your manuscript 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 process. Please contact us with any questions about submitting your manuscript

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 [email protected].

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.

Once a submitted manuscript passes initial assessment by the Journal’s Editor-in-Chief or Deputy Editor-in-Chief, it will then be passed to a handling editor, who will oversee peer review. The Editor-in-Chief or Deputy Editor-in-Chief make the final decision on the submitted manuscript.

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 3 reviewers. 

You may suggest 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. Please do so in your cover letter, along with a brief explanation as to why you want them excluded. However, there is no guarantee these individuals will be excluded by the Journal. 

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.

Volume of submissions and time in the review process

Each year we receive more than 2000 submissions, and publish less than a quarter of these. The acceptance process is highly competitive; the only way to find out whether your manuscript will succeed in that competition is to submit it to us. We aim to communicate with the authors as soon as possible. The average to before first decision is around 20 days. We ask reviewers to report within two weeks, and the time before a decision will depend on their ability to respond in time to our request. We aim, if at all possible, to give a decision within two months in all cases. We aim, so far as possible, to give reasons for a decision not to accept a submission. We do offer authors the opportunity to revise and resubmit in the case that this is recommended by the reviewers.

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

Manuscript transfers

The Journal accepts original submissions as well as transfers from other journals on related topics published by Oxford University Press. Reviewer reports may be included in the transfer with reviewer consent. Transferred manuscripts may be sent out for additional peer review, and a decision will be made on the manuscript based on the feedback from all consenting reviewers and the judgment of the editorial team of Briefings in Bioinformatics.

Screening for misconduct

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

Appeals and complaints

Authors may appeal an editorial decision. To do so, please contact the editorial office at [email protected], 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 [email protected]. Complaints will be taken seriously and will be carried forward following COPE guidelines and processes.

Letters to the Editor and Responses

The Journal welcomes Letters to the Editor from readers offering relevant comments and providing objective and scholarly criticism of recently published articles in the Journal. Contributions should be constructive, professional, and polite. 

At the discretion of the editors, Letters to the Editor being considered for publication may be sent to the authors of the original article to give them the opportunity to submit a Response. If an author does not submit a Response, the Journal may publish a statement indicating this to readers. To enable readers to evaluate the arguments presented, Letters to the Editor and Responses are linked to the original article, are typically published online simultaneously, and may be published together in the same issue.

Submitted Letters to the Editor will undergo an initial assessment by the editors, at which point they may be rejected, sent for revision, or accepted. At the discretion of the editors, Letters to the Editor may be sent for peer review or may be considered without external peer review. Letters to the Editor on the same topic or in response to the same article may be grouped, sent to the corresponding author of the original article for reply, and published at the same time. Authors of Letters to the Editor and Responses may be asked to complete authorship forms, disclose conflicts of interest, and sign publishing agreements (if accepted), as with any manuscript submitted or published in the Journal. The Journal may request revisions to Letters to the Editor and Responses for content, length, clarity, grammar, style, and format.

Publication and research ethics

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. For a detailed definition of authorship, please see the International Committee of Medical Journal Editors (ICMJE) definitions of authors and contributors.

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 ghost, guest, or gift authorship. For more information, please see the OUP Publication Ethics page.

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.

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 [email protected]. 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, see the Open access charges section.

ORCiD

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

Policy for Acceptable Use of Large Language Models

The International Society for Computational Biology (ISCB) has created an acceptable use policy for large language models (LLMs), which the journal follows. It is likely that these guidelines will be subject to change in the future as the development of these models continues to change.

Common Acceptable Uses:

• As an aid to correct written text (spell checkers, grammar checkers)
• As an aid to language translation, however, the researcher is responsible for the accuracy of the final text
• As an algorithmic technique for research study
• As an evaluation technique (to assist in finding inconsistencies or other anomalies)
• It is permissible to include LLM generated text snippets as examples in research papers where appropriate, but these MUST be clearly labelled, and their use explained.
• Assist in code writing, however, the researcher is responsible for the correct code
• Create documentation for code, however, the researcher is responsible for the correct documentation

Any acceptable use of LLMs or related technologies to produce, or help to produce, part of the text, figures or other contents of the paper should be explicitly declared and documented with sufficient details in the supplementary materials.

Unacceptable Uses:

• It is not acceptable to use LLMs or related technologies to draft papers (including but not limited to text, figures, tables, and references) from a prompt text. In essence, papers must be written by researchers.
• LLMs cannot be listed as authors as they would not fulfil the requirements of authorship as laid out in the ICMJE guidelines.

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, write code, or process data) 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.

If your usage of LLMs is not covered by any of these use cases, then please contact the Editor of the journal or Editorial Office.

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.

Reviewers

Individuals that have a conflict of interest relating to a submitted manuscript should recuse themselves and will not be assigned to oversee, handle, or 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-in-Chief immediately.

Editors

At initial submission, the corresponding author must declare if the Editor-in-Chief, an editor, or an Editorial Board Member 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 [role] for Briefings in Bioinformatics and has not peer reviewed or made any editorial decisions for this paper."

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 preprints, dissertations, manuscripts, published papers, and reports by the same authors (i.e., those containing substantially similar content or using the same, similar, or a subset of data) that have been previously published or posted electronically or are under consideration elsewhere at the time of manuscript 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.

The Journal does not discourage you from presenting your findings at conferences or scientific meetings but recommends that you refrain from distributing complete copies of your manuscripts, which might later be published elsewhere without your knowledge.

For previously published materials including tables and figures, please see 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, you 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 see 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 Briefings in Bioinformatics
• 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.

Our publisher, 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 the Committee 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 plagiarism as:

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

COPE defines redundant/overlapping publication 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 misconduct 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.

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 the Coalition 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 and images

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 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 C4DISC Guidelines on inclusive language and images.

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.

Availability of data and materials

Where ethically feasible, the Journal strongly encourages authors to make all data and software code on which the conclusions of the paper rely available to readers. Authors are required to include a data availability statement in their paper. When data and software underlying the research article are available in an online source, authors should include a full citation in their reference list. For details of the minimum information to be included in data and software citations see the OUP guidance on citing research data and software.

Whenever possible, data should be presented in the main manuscript or additional supporting files or deposited in a public repository. Visit OUP’s Research data page for information on general repositories for all data types, and resources for selecting repositories by subject area.

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.

Authors may request an exception to the policy due to legal, privacy, ethical, or other limitations or restrictions. Exceptions will be made at the discretion of the Journal. Please notify the editorial office at [email protected] when submitting your manuscript if you wish to request an exception. If an exception is granted, a data availability statement must still be included in your paper specifying what cannot be shared and explaining why.

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.

We suggest you consider these options when choosing your repository:

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

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 would otherwise become permanently unavailable, long-term access to the archives of CLOCKSS and Portico would be triggered. Until such a trigger event were to occur, this content is not available to the public through CLOCKSS and Portico.

Self-archiving

Self-archiving refers to posting a copy of your work on a publicly accessible website or repository. Under certain circumstances, 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.

Publishing agreement and charges

Authors, please read each section on the publishing agreement and charges carefully.

If you have any questions relating to your publishing agreement or charges please contact OUP Support.

Publishing agreement

After your manuscript is accepted, you will be asked to sign a license to publish through our licensing and payment portal, SciPris. The Journal is fully open access, meaning all papers in the Journal are published under an open access license. 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 freely available to all readers immediately upon online publication. 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 Licence
• Crown Copyright
• Open Government Licence

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

Open Government Licence

The Open Government Licence is an open licencing model for content produced by employees of UK Crown bodies allowing users to copy, publish, distribute adapt and transmit the Information for commercial and non-commercial purposes. For additional information visit the gov.uk information on the Open Government Licence.

Charges

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 our licencing and payment portal, SciPris.

Charges for Reviews, Problem solving protocols, Case Studies, Opinion Articles, Software and website reviews, Book Reviews:

Regular charge: $3,885

Charges for Letters to the Editor, Editorials, Corrections:

Regular charge: $0

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.

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

Colour charges

The Journal does not charge for colour.

Page charges

The Journal does not have page charges.

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.

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. If your paper is published open access, it will always be freely available to all readers, and you can share it without any limitations. Otherwise, use the toll-free link that is emailed to you after publication. It provides permanent, free access to your paper, even if your paper is updated.
• 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. 

Types of Manuscript

Submissions of the following types are accepted for review in the Journal:

• Reviews: surveys of previously published research in specified areas giving an overview and making recommendations for the optimal approaches to problem solving. (2000-7000 words)

• Problem solving protocols: development of methods based on comparison, new software, or new pipeline of existing software for solving a specific bioinformatics problem. Real experimental data must be analyzed. Problem solving protocol papers should demonstrate a new methodological application to a meaningful biological problem. Original algorithms also accepted. (2000-5000 words)

• Case studies: novel applications of methods, pipelines, or software to a specific bioinformatics problem. Significant novelty in the analysis of real experimental data is expected. (2000-5000 words)

• Position articles (by invitation only): discuss a specific bioinformatics topic or issue from a position of authority and present a viewpoint. A position article typically should contain: a clear viewpoint, sufficient background information, evidence to support the viewpoint (including but not limited to facts, data, research findings, reasoning, etc.), presentation of opposing views, and recommendations or solutions. Unsolicited submissions will not be accepted. (2000-7000 words) Interested authors should contact the editorial office and Editor-in-Chief prior to submission.

• Opinion articles: topical or controversial areas that do not warrant a full review (500-1000 words)

• Letter to the Editors: critique of an article previously published in the journal (500-1000 words)

• Software and website reviews: these should be written by authors other than the originators (500-1000 words)

• Book reviews (500-1000 words)

The journal provides topical reviews of new methodologies as they become established. Reviews of the related education and training in the biomedical sciences are included in the scope. The Editors welcome the submission of problem solving protocols and case studies for publication. Subject areas should be clearly defined for both experimental biologists and for bioinformatics specialists. Articles may be broader or more narrowly focused but must cover a variety of approaches to a very well specified biological problem or research area. The underlying concepts must be clearly explained along with the selection of the correct tools for a problem, their limitations, and the interpretation of the results. Descriptions of existing analytical solutions of biological problems should be transparent and user friendly and may include mathematical and statistical methods for high dimensional and high throughput data. Methodological approaches of interest include software comparison and benchmarking, data cleaning and curation, accuracy of predicted and extracted information, ontologies and text-mining, solutions that allow for the large-scale analysis of biological data in reasonable time (high performance computing solutions and cloud systems), standards, training and change management activities, and the determination of causal relationships from data. Ontologies for semantic-based analysis of molecular data and interaction networks, methods and tools for the automatic or semiautomatic annotation of biological data with terms extracted from ontologies, and methods and tools for enrichment analysis are all relevant to the objectives. Articles focusing on illuminating bottleneck problems in important bioinformatics approaches will be especially helpful to readers. There should be more studies focusing on the replicability and reproducibility of bioinformatics methodologies and realistic sample sizes required for this. We encourage papers that provide an independent evaluation of software tools for common tasks. In bioinformatics there are typically multiple different tools and parameter settings that can be selected for a given problem and these should be evaluated and compared to one another using simulation if appropriate and empirical real datasets if available, preferably by authors who are not originators of the software. As the science advances details of what is important changes and the Editors, Editorial Board and Reviewers will be flexible in their policies.

Areas not included

Your article should focus on bioinformatics. If it is purely about genomics you may consider submitting to Briefings in Functional Genomics which publishes high quality peer reviewed articles on the use, development or exploitation of genomic approaches, and their application to all areas of biological research.

If your article is about biological methodology you may wish to consider submitting to Biology Methods and Protocols which publishes papers presenting or using new or improved methods in biological sciences, biomedicine, pre-clinical and translational research.

If your article is concerned with detailed descriptions of databases and database tools a more appropriate place is Database.

Bioinformatics has long provided a place to advance the progress of bioinformatics and biomedical research in a significant manner.

Bioinformatics Advances is a relative newcomer. The journal is published jointly by Oxford University Press and by the International Society for Computational Biology. The journal presents original research articles, reviews, application notes, opinion, perspective and Society features.

Articles which focus on the results of data analysis using existing tools are out of scope as they are biological studies rather than explanations of how to use bioinformatics software. Morphometrics and image analysis without a molecular component are likewise out of scope.

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 Briefings in Bioinformatics can be found below.

Papers must be clearly written in English.

All articles should be submitted with a title page. The title page should include the following: (1) the title, (2) the name(s) of authors, (3) the authors' institutional affiliations (4) the telephone number, fax number, and e-mail address of the corresponding author.

All review articles and software/website reviews should be accompanied by a short abstract, outlining the aims and subject matter, up to 5 key points (see below) and up to six keywords should be provided for indexing purposes.

All papers, articles and reviews should be accompanied by a short (about 30 words) description of the author(s) and, if appropriate, the organisation of which he or she is a member.

Authors should avoid the use of language or slang which is not in keeping with the academic and professional style of the Journal. Authors should not also seek to use the Journal as a vehicle for marketing any specific product or service.

Authors should follow the conventions of the CSE Style Manual (Council of Science Editors, Reston, VA, 2006). Chemical Abstracts and its indices should be followed for chemical names. For biochemical terminology the recommendations issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published in 1992 by the Biochemical Society, UK should be followed. For enzymes, the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1992 should be used. Wherever possible, the recommended SI units should be used. Genotypes should be italicised. Phenotypes should not be italicised. For bacterial agents nomenclature Demerec et al. (1966) Genetics, 54, 61-76 should be followed and The Trends In Genetics Nomenclature Guide (1998), Elsevier, Cambridge. Titles of organisations etc should be written out first in full followed by the organisation's initials in brackets, eg. Food and Drug Administration (FDA) and thereafter the initials only should be used.

Text abstracts

Text abstracts must be written in English.

Graphical abstracts

A graphical abstract is a single figure prepared by the authors that summarizes the key point(s) of an article and serves as a visual introduction to encourage interest in the content. When preparing your graphical abstract, keep in mind that they are ideally suited for promoting your article on social media, so text should be large enough to be read in that context and the image should be oriented in landscape format.

Please also consider the accessibility of your graphical abstract to all readers. See OUP's Guidelines for making figures accessible.

Your graphical abstract should be submitted as a separate file, selecting the appropriate file type designation in the online submission system. The file should be named “graphical_abstract”. Please see OUP's guidance on appropriate file format and resolution for graphics.

References

All references must be cited in the text and should be denoted using numbers in square brackets before the punctuation., e.g. [1, 3–5]. References should be numbered consecutively in the order in which they appear.

Style in the References section should be as follows (this is to be consistent with PubMed):

1. Attwood T.K. The role of pattern databases in sequence analysis. Brief Bioinform 2000;1:45–59.
2. Long HC, Blatt MA, Higgins MC et al.. Medical Decision Making. Boston: Butterworth-Heinemann, 1997.
3. Manners T, Jones R, Riley M. Relationship of overweight to haitus hernia and reflux oesophagitis. In: Newman W (ed). The Obesity Conundrum. Amsterdam: Elsevier Science, 1997,352–74.
4. Hou Y, Qiu Y, Vo NH et al. 23-O derivatives of OMT: highly active against H. influenzae. In: Programs and Abstracts of the Forty-third Interscience Conference on Antimicrobial Agents and Chemotherapy, Chicago, IL, 2003. Abstract F-1187, p.242. American Society for Microbiology, Washington, DC, USA.
5. Public Health Laboratory Service. Antimicrobial Resistance in 2000: England and Wales. http://www.hpa.org.uk./infections/topics_az/antimicrobial_resistance/amr.pdf (7 January 2004, date last accessed).

If there are four or more authors, then use the first three followed by et al.
Papers in preparation or submitted for publication should not be in the reference list.

Authors are asked to ensure the references to named people and/or organisations are accurate and without libellous implications.

Key Points

Key Points are displayed at the end of the article, and should consist of 3-5 brief sentences. Key Points are an opportunity to summarise the key messages of the article and can include anything that is felt to be important for the reader to particularly note.

Study funding

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

Oxford Journals will deposit all NIH-funded articles in PubMed Central. See Author Resources for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines below.

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].’

Figures

Figures should be supplied in an electronic format at a suitable size for printing with the following resolutions: 600 dots per inch (dpi) for line drawings and combinations; 300 dpi for greyscale. Please ensure that the prepared electronic image files print at a legible size and are of a high quality for publication. Online colour figures are free of charge.

Figures should be referred to in the text and numbered consecutively. They should be supplied separately from the main body of the text, with their approximate final positions, and legends marked within the main text. Figure legends should describe the figure content and should be understood independently from the text. Abbreviations should be avoided in figures. If abbreviations or symbols are used in the figures they should be explained in the figure legend, if they have not been explained in a key.

Line charts, bar charts and pie charts should be two-dimensional, with single categories, a generous margin, and grey-scaled backgrounds (with a 25% tint). Appropriate scales should be used and sources should be quoted. Bar charts should have two categories or more and at least five observations; otherwise the data should be presented in a table. Horizontal lines should be used to mark the major values on the y-axis. Line charts should show changes over long time spans and should have at least ten observations. Pie charts should be used to show proportions and have a minimum of four segments, and a maximum of twelve.

Figure accessibility and alt text

Incorporating alt text (alternative text) when submitting your paper helps to foster inclusivity and accessibility. Good alt text ensures that individuals with visual impairments or those using screen readers can comprehend the content and context of your figures. The aim of alt text is to provide concise and informative descriptions of your figure so that all readers have access to the same level of information and understanding, and that all can engage with and benefit from the visual elements integral to scholarly content. Including alt text demonstrates a commitment to accessibility and enhances the overall impact and reach of your work.  

Alt text is applicable to all images, figures, illustrations, and photographs. 

Alt text is only accessible via e-reader and so it won’t appear as part of the typeset article. 

Detailed guidance on how to draft and submit alt text.

Photographs

Photos can be supplied as sufficient quality with respect to detail, contrast and fineness of grain to withstand the unavoidable loss of contrast inherent in the printing process. Their approximate final positions should be indicated in the text. Electronic copies of photos should be provided, where possible, as GIF, TIFF or BITMAP files (minimum acceptable resolution 300 dpi).

Internet Screen Dumps

Internet screen dumps must be provided in greyscale and should have a white background to increase the contrast between the illustration and the background. They should be provided electronically as BITMAP, with a minimum acceptable resolution of 300 dpi. Their approximate final positions should be indicated in the margin of the text. Authors should be aware that graphics supplied with low resolution are not guaranteed to reproduce well and should be avoided whenever possible.

Tables

Tables should be submitted in electronic form, preferably in MS Word or Excel. Tables should be referred to in the text and numbered consecutively. They should be supplied separately from the main body of the text, with their approximate final positions indicated in the text. Each column should have a short heading and, where appropriate, the units should be stated. Table legends should describe the content and should be understood independently from the text. Data columns should be right-hand aligned, or aligned by decimal place, where appropriate; data should be sorted where possible. Footnotes should be included on the same pages as the tables themselves and should be used to explain any abbreviations used in the table and denote them by letter. Footnotes should also be used to quote sources.

Pre-Submission Technical Checks

In partnership with Cactus, we are offering authors free usage of their Paperpal Preflight tool pre-submission. This is an AI-driven tool that performs technical checks tailored to Briefings in Bioinformatics. Authors are given a markup of suggested corrections to match their paper to journal requirements. Before submission, we encourage authors to run their paper through this tool. Please note that this is not mandatory and suggested corrections are optional.

Authors also have the option to pay for additional language checking – again, this is not mandatory and all suggested corrections are optional.

Pre-submission language editing

You may wish to use a language-editing service before submitting to ensure that editors and reviewers understand your manuscript. Our publisher, 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.

Submission

All material to be considered for publication in Briefings in Bioinformatics must be submitted in electronic form via the journal's online submission system at Manuscript Central. New authors should create an account prior to submitting a manuscript for consideration. Once you have prepared your manuscript according to the instructions below, here are instructions on how to submit your manuscript online.

Submissions should be typewritten, double-spaced, on A4 or US letter paper and supplied electronically as Word or rich-text files.

This journal is supported by the OUP LaTeX template. If you are using LaTeX to write your paper, please see the ‘OUP LaTeX template’ section on this page to find instructions and to access the template.

Articles received by the Editors will undergo a pre-screening process to increase the efficiency of the publication process. Papers that are considered to be of minor importance to the readership of the Journal are not reviewed. Papers selected for review are sent out to three referees, who agree to undertake the refereeing within a short period of time.

Format-Free Submission

Briefings in Bioinformatics manuscripts can be submitted without being formatted into journal style. Manuscripts will need to be formatted for revision, after acceptance.

The journal strongly discourages authors from exceeding suggested word limits on different manuscript types. Manuscripts that exceed the limit by 1000 words or more are usually returned by the Editorial Office immediately.

Contact us

For questions regarding submission and review, including appeals, you can reach the editorial office by email at [email protected].

After your paper has been sent to production, you can contact [email protected] for questions regarding publishing agreements and charges, the production process, or publication. Please see Changes to published papers if you need to request a substantive change to your published paper.