Skip Navigation

Instructions to Authors

Author Self-Archiving/Public Access policy

For information about this journal's policy, please visit our Author Self-Archiving policy page.

Aims

The aim of Briefings in Bioinformatics is to provide an indispensable resource for the experimental practitioner seeking awareness of the disparate sources of data and analytical tools of contemporary genetics and molecular biology. 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. The journal provides state of the art reviews of new methodologies as they become established.

The Editors, Martin Bishop and Russ Altman, welcome the submission of review papers and case studies for publication. Essential criteria for the publication of papers is that they provide practical guidance to the users of bioinformatics software and databases and do not contain original research results except for illustrative purposes. Reviews are expected to be broad and to cover a variety of approaches to a specified biological problem or research area.

Submission of Manuscripts

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, instructions on how to submit your manuscript online can be found by clicking here.

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

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

  • Review articles (2000-5000 words)
  • Opinion articles
  • Letters to the Editors
  • Software and website reviews
  • Book reviews

All submissions, with the exception of review articles, should be between 500 and 1000 words in length.

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 two referees, who agree to undertake the refereeing within a short period of time.

Licence and permissions

It is a condition of publication that authors grant an exclusive licence to Oxford Journals or the society of ownership. This ensures that requests from third parties to reproduce articles are handled efficiently and consistently, and will also allow the article to be as widely disseminated as possible. In assigning copyright, authors may use their own material in other publications, provided that the journal is acknowledged as the original place of publication, and Oxford Journals is notified in writing and in advance.

On acceptance, copyright licence forms should be returned immediately by fax to us, and a copy must be posted by airmail/first class within 24 hours. Copyright licence forms are available here. If we have not received the form by the time the manuscript arrives, your manuscript may be delayed.

Work submitted for publication must be original, previously unpublished, and not under consideration for publication elsewhere. If previously published figures, tables, or parts of text are to be included, the copyright-holder’s permission must have been obtained prior to submission.

The author bears the responsibility for checking whether material submitted is subject to copyright or ownership rights, e.g. photographs, illustrations, trade literature and data. Where use is so restricted, the Editors and the Publisher must be informed with the submission of the material.

Authorship

All persons designated as authors should qualify for authorship. The order of authorship should be a joint decision of the co-authors. 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. Assurance that all authors of the paper have fulfilled these criteria for authorship should be given in the covering letter.

Competing Interests

At the point of submission, Briefings in Bioinformatics' policy requires that each author 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 mandatory for authors to declare any potential conflicts of interest. You will be prompted to declare these when you make your submission on Manuscript Central.
As the submitting author, it is your responsibility to be aware of your co-authors' conflicts of interest and to declare these. If, however, you are unable to speak on behalf of your co-authors, you and your co-authors will need to complete and return a Conflict of Interest form (Conflict of Interest Form) to the editorial office (fax: +44 (0) 1865 355907). It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy. Please note that your manuscript will not be peer-reviewed until all conflicts have been declared.

If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published paper.

Material Disclaimer

The opinions expressed in Briefings in Bioinformatics are those of the authors and contributors, and do not necessarily reflect those of the editors, the editorial board, Oxford University Press or the organization to which the authors are affiliated.

PREPARATION OF MANUSCRIPTS

General

Papers must be clearly written in English.

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.

Language Editing

Particularly if English is not your first language, before submitting your manuscript you may wish to have it edited for language. This is not a mandatory step, but may help to ensure that the academic content of your paper is fully understood by journal editors and reviewers. Language editing does not guarantee that your manuscript will be accepted for publication. If you would like information about one such service please click here. There are other specialist language editing companies that offer similar services and you can also use any of these. Authors are liable for all costs associated with such services.

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.

Funding & NIH Funding

Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear before the 'Acknowledgements' section.

Oxford Journals will deposit all NIH-funded articles in PubMed Central. See http://www.oxfordjournals.org/for_authors/repositories.html 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.

*NEW*
Briefings in Bioinformatics is happy to announce the launch of free online colour, beginning for all articles accepted after 01/01/2009. All figures submitted to the journal in colour will be published in colour online at no cost. If you do not wish for your figures to be published online in colour, please submit your figures in Black & White.

All figures will be printed in Black and White.

Please make sure the figure captions are understandable for both the colour and black and white version of your figure.

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.

Photographs

Photos can be supplied as good quality black and whites. They must be of 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.

Proofs

All manuscripts will undergo some editorial modification, so it is important to check proofs carefully. PDF page proofs will be sent via e-mail to the corresponding author for checking. To avoid delays in publication, proofs should be checked and returned within 48 hours. Corrections should be returned by annotated PDF, e-mail or fax. Extensive changes to the text may be charged to the author.

Offprints

The corresponding author for all articles will automatically receive a free link to the full text of their article. Corresponding authors may also purchase offprints here.