Instructions to Authors
Scope
Types of Manuscript
Format-free submissions
Page Charges
General Policies
Open Access Options
Manuscript preparation
Detailed Scope Guidelines
Once you have prepared your manuscript according to the instructions below please visit the online submission website.
Instructions on submitting your manuscript online, along with the Word and LaTex* templates, are available. [*If you use bibtex, please use the bibliography style named natbib.bst]. Further information on inserting figures into the templates.
Bioinformatics allows initial submission of manuscripts to be format-free, however accepted manuscripts will need to be formatted during revision. In order to format your paper after acceptance, please follow these instructions carefully to ensure the publication process is efficient and as rapid as possible.
By submitting an article for publication you confirm that you are the corresponding/submitting author and that Oxford University Press ("OUP") 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 the journal now encourages authors to complete their copyright and licence to publish form online. Upon acceptance of a manuscript at Oxford Journals, authors will be invited to complete an online copyright licence to publish form.
Scope
Bioinformatics provides a forum for the exchange of information in the fields of computational molecular biology and genome bioinformatics, with emphasis on new algorithms and databases that advance the progress of bioinformatics and biomedical research in a significant manner.
Upon submission you will be asked to select one of the following categories for your manuscript:
- Genome analysis
- Sequence analysis
- Phylogenetics
- Structural bioinformatics
- Gene expression
- Genetic and population analysis
- Systems biology
- Data and text mining
- Databases and ontologies
- Bioimage informatics
Types of Manuscript
The following types of paper may be submitted for publication. Please note the page limits for each type of paper formatted in the journal template, as well as the word and figure limitations for papers submitted Format-Free.
Original Papers (up to 7 pages; this is approx. 5,000 words. excluding figures): Original papers that describe new research developments in computational molecular biology, for example: models, algorithms, software involving new methods, biological databases and network information services, and their impact on molecular biology or computer science. Actual biological data, as opposed to purely simulated data, must be used.
Application Notes (up to 2 pages; this is approx. 1,300 words or 1,000 words plus one figure): Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). Software or data must be freely available to non-commercial users. Availability and Implementation must be clearly stated in the article. Authors must also ensure that the software is available for a full two years following publication. Web services must not require mandatory registration by the user. Additional supplementary data can be published online-only by the journal. This supplementary material should be referred to in the abstract of the Application Note. If describing software, the software should run under nearly all conditions on a wide range of machines. Web servers should not be browser specific. Application Notes must not describe trivial utilities, nor involve significant investment of time for the user to install. The name of the application should be included in the title.
Reviews (3-8 pages; this is approx.3000-6000 words excluding figures): Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance submit a draft or abstract/summary no longer than a page.
Letters to the Editor: Bioinformatics publishes "letters to the editors" on the broad range of topics covered by the journal, including political, technical and scientific analyses of issues related to bioinformatics and computational biology. The letters can also include the discussion of papers published by the journal.
Conference Papers: Bioinformatics considers proposals for publishing conference proceeding papers, as supplementary issues or as special sections of the journal. Please be sure to include the following information in your proposal:
- What is the theme of the conference and submitted papers?
- What numbers of papers are expected to be submitted and published?
- What peer review process will be put in place by the conference organisers to recommend papers for publication in the journal?
- How many delegates are expected to attend the conference?
- Assurance that the papers proposed for publication have not and will not be published elsewhere prior to publication in Bioinformatics, or afterwards without the permission of the journal’s publisher.
Format-Free Submission
Bioinformatics manuscripts can be submitted without being formatted into journal style. Manuscripts will need to be formatted for revision, after acceptance. Follow the below guide to ensure your submission will be within page limits.
- Original papers: up to 7 pages, this is approx. 5000 words, not including figures,
- Application notes: up to 2 pages; this is approx. 1300 words or 1000 words plus one figure.
Note that the page count approximation above is based on a) a paper without illustrations (figure/table) b) formatted in Times New Roman font, double-spaced in 12 point font) single column format.
Page Charges
The journal strongly discourages authors from exceeding the page limits. Manuscripts exceeding the recommended limits may be rejected without review - for example manuscripts that exceed the limit by 20% or more are usually returned by the Editorial Office immediately. In the event that a manuscript does exceed the page limits, and the paper is not published under an open access license, we make the following charges:
- Original papers: £100/$190 per excess page (over 7 published pages*)
- Application notes: £100/$190 per excess page (over 2 published pages*)
Orders from the UK will be subject to the current UK 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.
* Please note that the Word and LaTex author templates used for submission to Manuscript Central (ScholarOne) are not an exact reflection of the final typeset article, and therefore cannot be used to estimate exactly how many published pages your final typeset article will be.
General Policies
Previous publication
Submission of a manuscript implies that it reports unpublished work, that it is not under consideration for publication elsewhere and that, if accepted, it will not be published elsewhere in the same form, either in English or in any other language, without the consent of the publisher. Authors should provide the references of similar work that they have already published, or which are currently under consideration by another journal. If the work has previously been presented at a conference, authors should provide details in the covering letter. The journal will consider publication of work that has previously been presented as either a short abstract or poster at a conference, but not as a full paper. If previously published tables, illustrations, or more than 200 words of text are to be included, then the copyright holder's written permission must be obtained. Include copies of any such permission letters with your paper. Please note that plagiarism checking software may be used when reviewing your manuscript during the editorial review process.
Preprint policy
Authors retain the right to make an Author’s Original Version (preprint) available through various channels, and this does not prevent submission to the journal. For further information see our Online Licensing, Copyright and Permissions policies. If accepted, the authors are required to update the status of any preprint, including your published paper’s DOI, as described on our Author Self-Archiving policy page.
Once the manuscript has been accepted the authors must acknowledge that the article has been accepted for publication as follows:
"This article has been accepted for publication in Bioinformatics ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved."
Authorship
All persons designated as authors should qualify for authorship. 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.
Other than in exceptional circumstances the Journal does not allow addition or removal of author names after submission. A satisfactory explanation for any proposed changes in authorship, signed by all authors, will be required. We will also require a letter of consent from any person whose name has been removed indicating that they agree to the removal of their name from the author list. Owing to the complexity of these rules we strongly advise authors to fix the author list before submission and not to attempt to make changes later.
Conflicts of Interest
At the point of submission, 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?
As an integral part of the online submission process, Corresponding authors are required to confirm whether they or their co-authors have any conflicts of interest to declare, and to provide details of these. It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy.
If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published paper.
Availability of Data and Materials
Where ethically feasible, Bioinformatics requires 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 article.
We suggest that data be presented in the main manuscript or additional supporting files, or deposited in a public repository whenever possible. Information on general repositories for all data types, and a list of recommended repositories by subject area, is available on the Research Data Policy page.
Data Availability Statement
The inclusion of a Data Availability Statement is a requirement for articles published in Bioinformatics. Data Availability Statements provide a standardised format for readers to understand the availability of data underlying the research results described in the article. The statement may refer to original data generated in the course of the study or to third-party data analysed in the article. The statement should describe the data and give the information necessary (unique accession or DOI) to retrieve it from a public repository.
The Data Availability Statement should be included in the end matter of your article under the heading ‘Data availability’.
Further information and examples on Data Availability Statements.
ORCID
Bioinformatics requires submitting authors to provide an ORCID iD at submission to the journal. More information on ORCID and the benefits of using an ORCID iD is available. If you do not already have an ORCID iD, you can register for free via the ORCID website.
Software
If the manuscript describes new software tools or the implementation of novel algorithms, the authors must:
• provide a self-contained and easy-to-use implementation of the software together with appropriate test data and detailed documentation on how to acquire, install, and run the software. This includes information on the purpose and values of all optional parameters.
• make the software and the source code freely available at stable URLs (e.g. github, bitbucket) without request to non-commercial users at the time of submission (availability must be clearly stated in the manuscript)
• ensure that the submitted software version and test data are archived at dedicated repositories such as Zenodo, Figshare, Software Heritage, CRAN, and Bioconductor.
We encourage authors to provide access through an open source license (see Open Source Initiative page for examples) and to implement the software using a non-proprietary programming language. We encourage authors to provide information on how to reproduce results/figures described in the manuscript. The name of the software should be included in the title of the manuscript wherever possible.
If the study relies on already published methods, the corresponding software used must have its code open and accessible to allow for reproducibility of the results described in the manuscript.
If the manuscript describes a web server or web service, the authors must:
• ensure that web servers described are accessible without login credentials, except in exceptional cases
• ensure that it is fully functional at the time of submission
• ensure that the HTTPS protocol is used (the URL must be clearly stated in the manuscript)
• include test data (e.g. through loading buttons) that can be easily used for formatting requirements
• provide the source code freely available at stable URLs (e.g. github, bitbucket) without request to non-commercial users at the time of submission
• provide help pages and a tutorial on how to use the web server and how to interpret the results
• provide support / maintenance for at least 3 years after publication.
The name of the web server or web service should be included in the title of the manuscript wherever possible.
Machine learning
Machine learning as technology has implications for many application areas but in all cases, the application of machine learning methods Papers using machine learning must contain a dedicated subsection clearly describing the composition of the training dataset. This should include information on the preparation of the cross-validation sets and of an independent test set that is not used in the training process. For data originating from biological sequences the description must furthermore address how homology between sequences is taken into account to ensure that the training and independent test sets do not have identical or near identical examples. Papers using leave-one-out will be editorially rejected unless there is a special circumstance in which it can be argued that this procedure is meaningful for the problem addressed in the paper. Machine learning papers must report the performance on an independent test set. It is not sufficient to report the average error over the individual cross-validation sets. For Original papers this subsection should appear in the methods section and for Application notes in the supplementary material.
Supporting Data
Bioinformatics is aligned with the general movement towards open FAIR data. All data on which the conclusions given in the publication are based must be publicly available in stable public repositories. Bioinformatics fully supports the recommendations of the National Academies regarding data sharing (see Board on Life Sciences, Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences). If the analysis is based on new datasets, authors must submit these to appropriate public repositories. All data must be made available to the journal for the purpose of peer review.
Supplementary Data
Only directly relevant material should be included in the full text of manuscripts. Supporting materials and Appendices which are not essential for inclusion in the full text, but would nevertheless benefit the reader, can be published as online-only Supplementary Data. Supplementary Data should be submitted for review, in a separate file or files from the manuscript. Authors should make sure that all additional text, figures and tables are presented in a single file. Authors should ensure that the Supplementary Data is referred to in the main manuscript at an appropriate point in the text. Supplementary Materials cannot be altered or replaced after the paper has been accepted for publication. For the purpose of long-term preservation of this information, we require supplementary material to be published and stored on our website. It is acceptable for authors to post supplementary material on their own website in addition to this, but not in place of this.
Pre-screening
At present the journal accepts ~30% of manuscripts that are submitted. To increase the efficiency of the publication process, manuscripts received in the Bioinformatics office therefore undergo a pre-screening process. Papers that are considered to be of less significance to the readership of the journal are returned without review.
The review process
At least four suggested reviewers must be provided by the author at the submission stage. A manuscript will not be assigned to an Associate Editor until this information has been provided. Following this, the manuscript will be sent to two or more referees, who agree to undertake the refereeing within a short period. Authors should normally carry out any revision within four weeks including formatting the manuscript into journal style. Revisions that are not received within 90 days will be treated as new submissions.
Acceptance
When accepted by the editors, authors may be asked to send the files of the final manuscript to the editorial office. These files are used for typesetting and should be either Word or LaTex files.
Because accepted manuscripts are published online following acceptance, it is important that the final version of the manuscript supplied by the author contains no information regarding the citation information (volume, issue, year) or a copyright line as this will mislead readers.
Licence to Publish
It is a condition of publication in Bioinformatics that authors grant an exclusive licence to Oxford University Press. 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. As part of the licence agreement, Authors may use their own material in other publications provided that Bioinformatics is acknowledged as the original place of publication and Oxford University Press as the Publisher. Information about the Creative Commons licence.
Scientific Misconduct
When dealing with potential cases of misconduct the journal follows the guidelines provided by the Committee on Publication Ethics (COPE).
Bioinformatics Advance Access
Bioinformatics Advanced Access articles are initially published in their 'Accepted Manuscript' form as soon as possible post acceptance. Subsequently, a copyedited, typeset, corrected version of the 'Corrected Proof' is also published on the Advanced Access page. More information, including how to cite Advance Access papers, can be found on the Advance Access Page.
Complimentary ISCB memberships for authors
Bioinformatics is a journal of the ISCB and as part of our partnership with the Society we have 200 complimentary ISCB memberships to offer our authors each year. If you are the corresponding author of a Bioinformatics paper and would like to request this, please contact the ISCB after your article has been published.
Open Access Option for Authors
Bioinformatics offers the option of publishing under either a standard licence or an open access licence. Please note that some funders require open access publication as a condition of funding. If you are unsure whether you are required to publish open access, please do clarify any such requirements with your funder or institution.
Should you wish to publish your article open access, you should select your choice of open access licence in our online system after your article has been accepted for publication. You will need to pay an open access charge to publish under an open access licence.
Details of the open access licences and open access charges.
ISCB members are entitled to a 15% discount on the open access fee to publish in Bioinformatics. In order to receive this discount, ISCB members must claim this discount prior to signing a license to publish. Please do so by contacting the production editor at OUP (BIOINFORMATICS@oup.com) and informing them that you are an ISCB member.
OUP has a growing number of Read and Publish agreements with institutions and consortia which provide funding for open access publishing. This means authors from participating institutions can publish open access, and the institution may pay the charge. Find out if your institution is participating.
Extra page and colour figure charges will not be levied when publishing under an Open Access license, as the APC covers the full cost of publishing in the journal.
Third-Party Content in Open Access papers
If you will be publishing your paper under an Open Access licence but it contains material for which you do not have Open Access re-use permissions, please state this clearly by supplying the following credit line alongside the material:
- Title of content
- Author, original publication, year of original publication, by permission of [rights holder]
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.
Manuscript Preparation
Papers must be clearly and concisely written in English and within the recommended length. In the interests of speed, manuscripts are not extensively copyedited and authors are requested to check their texts carefully before submitting them so that proofs will require only correction of typographical errors.
Cover letter
All submissions must be accompanied by a cover letter explaining the suitability of the paper for Bioinformatics. Submissions omitting a cover letter may be editorially rejected. If the submitted manuscript deviates from the requirements listed in the Instructions to Authors, the reasons for this must be clearly explained. For example, machine learning papers deviating from the listed requirements must explain why this is necessary and specifically suited to the problem addressed.
How to prepare text and figures
Guidelines on the types of documents that can be uploaded to the online submission system.
Prepare your figures at publication quality resolution, using applications capable of generating high-resolution .tif files (1200 d.p.i. for line drawings and 350 d.p.i. for colour and half-tone artwork). The printing process requires your figures to be in this format if your paper is accepted and printed. Useful information on preparing your figures for publication. For online submission, please also prepare a second version of your figures at low-resolution for use in the review process; these versions of the figures can be saved in .jpg, .gif, .tif or .eps format. For INITIAL submission, it is preferable that you insert the low-resolution versions of the figures and tables into the word processing but you can also upload these versions as separate files.
Sections of the manuscript
Please subdivide manuscripts into the following sequence of sections, according to the type of paper:
- Original papers: Title page, Structured Abstract, Introduction, System and methods, Algorithm, Implementation, Discussion, References.
- Reviews: May be in a format best suited to subject matter, but should include Title page, Structured Abstract, Text, References. For clarity the main body of text should be sub-divided into sections.
- Applications notes: Title page, Short Structured Abstract, Text.
Title page
The title should be short, specific and informative, avoiding if possible version number and the words: tool, package, application, software (and similar). If novel software is being described, the name of the software should be included in the title. The surname and initials of each author should be followed by his/her department, Institution, city with postal code and country. Any changes of address may be added to the footnotes.
Structured Abstract (see recent issues of journal for examples)
Original papers
Abstracts are structured with a standard layout such that the text is divided into sub-sections under the following five headings: Motivation, Results, Availability and Implementation, Contact and Supplementary Information. In cases where authors feel the headings inappropriate, some flexibility is allowed. The abstracts should be succinct and contain only material relevant to the headings. A maximum of 150 words is recommended. If internet hyperlinks are available for any part of the abstract, then this should be given in the form of 'clickable text', i.e.{{http://www...}}.
- Motivation: This section should specifically state the scientific question within the context of the field of study.
- Results: This section should summarize the scientific advance or novel results of the study, and its impact on computational biology.
- Availability and Implementation: This section should state software availability if the paper focuses mainly on software development or on the implementation of an algorithm. Examples are: 'Freely available on the web at http://www.example_url.org.' Website implemented in Perl, MySQL and Apache, with all major browsers supported'; or 'Source code and binaries freely available for download at URL, implemented in C++ and supported on Linux and MS Windows'. The complete address (URL) should be given. If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users. Authors must also ensure that the software is available for a full two years following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see Open Source Initiative page for examples).
- Contact: Full email address to be given, preferably an institution email address.
- Supplementary information: Links to additional figures/data available on a web site, or reference to online-only supplementary data available at the journal's web site.
Applications Notes
Abstracts for Applications Notes are much shorter than those for an Original Paper. They are structured with four headings: Summary, Availability and Implementation, Contact and Supplementary Information.
- Summary: This section should summarize the purpose/novel features of the program in one or two sentences.
- Availability and Implementation: See above for advice and examples for this section.
- Contact: Full email address to be supplied, preferably an institutional address.
- Supplementary information: Links to additional figures/data available on a web site, or reference to online-only Supplementary data available at the journal's web site.
Acknowledgements
These should be included at the end of the text and not in footnotes. Please ensure you acknowledge all sources of funding, see funding section below.
Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear first in the 'Acknowledgements' section.
Funding information
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].’
Oxford Journals will deposit all NIH-funded articles in PubMed Central. See Depositing articles in repositories – information for authors for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines above.
Crossref Funding Data Registry
In order to meet your funding requirements authors are required to name their funding sources, or state if there are none, during the submission process. For further information on this process or to find out more about the CHORUS initiative please click here. For further information on this process or to find out more about CHORUS, visit the CHORUS initiative.
References
These should conform to standard scientific reporting style. Previous work in the field should be mentioned. Sufficient information should be given so that an application can be re-implemented. A test data set and results must be provided (where appropriate).
Authors are responsible for the accuracy of the References. Published articles and those in press (state the journal which has accepted them) may be included. In the text, a reference should be cited by author and date and enclosed by round brackets; not more than two authors may be cited per reference; if there are more than two authors use et al. References must not be numbered. At the end of the manuscript, the citations should be given in alphabetical order, with the author's surname followed by the initial. References should include in the following order: author, year, paper title, journal title, volume number, inclusive page numbers. The name of the journal should be abbreviated according to the World List of Scientific Periodicals. Book references should also include the editors and the name and address of the publisher. References should therefore be listed as follows:
Personal communications (J.Smith, personal communication) should be authorized by those involved in writing, and unpublished data should be cited as (unpublished data). Both should be used as sparingly as possible and only when the unpublished data referred to is peripheral rather than central to the discussion. 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 References section. References to manuscripts accepted for publication but not yet published should be included in the reference list as 'in press'.
Examples are given here:
- Myasnikova,E. et al. (2000) Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics, 17, 3-12.
- Schäfer,J. and Strimmer,K. (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics, 21, 754-764.
Tables
Tables should be embedded within the main document file and be numbered consecutively. Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables should be indicated by lower case letters but should not include extensive experimental detail.
Figures
All figures should be embedded within the text inside the main document file and referred to in the text as Figure 1 etc. All figures should be formatted to fit into, or be reduced to, a single (86 mm) or double (178 mm) column width. Figure legends should appear adjacent to the relevant figure.
- Web screen dumps: The editors prefer tables or figures instead of web screen dumps. All figures should have a white background to increase the contrast between the illustration and the background, so that the figure is easy to read.
- Line illustrations: These must be of sufficient quality for publication as submitted, i.e. clear, sharp, clean and of even density. Figures will NOT be redrawn or relabelled. Any lettering or text should be in proportion with the rest of the figure.
- Photographs: These 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.
- Colour figures: Inclusion of colour figures is subject to a special charge (£350/US$600/€525 to print a figure in colour). Online colour figures are free of charge. Orders from the UK will be subject to the current UK 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.
Please note that extra page and colour figure charges will not be levied when publishing under an Open Access license, as the APC covers the full cost of publishing in the journal.
Conventions
In general, the journal follows the conventions of the CBE Style Manual (Council of Biology Editors, Bethesda, MD, 1983, 5th edition). Follow Chemical Abstracts and its indices for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published by the Biochemical Society, UK. For enzymes, use the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1980. Where possible, use the recommended SI units. Genotypes should be italicized. Phenotypes should not be italicized. For bacterial agents nomenclature follow Demarc et al. (1966) Genetics, 54, 61-76.
LATEX
TEX-based manuscripts should be produced using the LATEX article style format only. The document style options used must indicate two-column text with 86 mm column widths.
English Language Editing
If English is not your first language, you may want to consult a list of optional services on the Language services page. Language editing does not guarantee that your manuscript will be accepted for publication. Authors are liable for all costs associated with such services.
Proofs
Authors are sent page proofs by email. These should be checked immediately and returned to the publishers by email (further details are supplied with the proof). A charge may be made to authors who insist on amendment within the text at the page proof stage.
Graphical abstracts
Authors are encouraged to submit a graphical abstract as part of the article, in addition to the text abstract. The graphical abstract should clearly summarize the focus and findings of the article, and will be published as part of the article online and in PDF. The graphical 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.tiff. See Preparing and submitting your manuscript page for guidance on appropriate file format and resolution for graphics. Please ensure graphical abstracts are in landscape format.
Note that graphical abstracts will be subject to any print reproduction charges that the journal levies for colour figures.
Detailed Scope Guidelines
Genome analysis
This category includes: Comparative genomics, genome assembly, genome and chromosome annotation, identification of genomic features such as genes, splice sites and promoters.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method.
Sequence analysis
This category includes: Multiple sequence alignment, sequence searches and clustering; prediction of function and localisation; novel domains and motifs; prediction of protein, RNA and DNA functional sites and other sequence features.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. Papers that analyse existing sequence data will only be considered if novel biological insight is obtained.
Phylogenetics
This category includes: novel phylogeny estimation procedures for molecular data including nucleotide sequence data, amino acid data, whole genomes, SNPs, etc., simultaneous multiple sequence alignment and phylogeny estimation, phylogenetic approaches for any aspect of molecular sequence analysis (see Sequence Analysis scope), models of molecular evolution, assessments of statistical support of resulting phylogenetic estimates, comparative methods, coalescent theory, approaches for comparing phylogenetic trees, methods for testing and/or mapping character change along a phylogeny.
We will consider algorithms, applications, databases, data repositories, and representation tools in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real or simulated biological data with a preference towards the combination of both approaches. Improvements in capabilities and/or speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. Papers that analyse existing sequence data will only be considered if novel biological insight is obtained.
Structural Bioinformatics
This category includes: New methods and tools for structure prediction, analysis and comparison; new methods and tools for model validation and assessment; new methods and tools for docking; models of proteins of biomedical interest; protein design; structure based function prediction.
We will consider algorithms, applications and databases in any of the above areas relating to Protein, RNA or DNA. We will consider papers related to new methods for organizing structural information, and for its representation. Small improvements or modifications of existing algorithms will generally not be suitable. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Papers that report three-dimensional models of macromolecules, molecular dynamics simulations and docking results will not be considered. Descriptions of repositories of automatically generated models will only be published if it can be demonstrated that they provide significant advantages over existing ones.
If your manuscript describes a three-dimensional model of a protein that has been manually built, you should deposit it in the PMDB database (see also NAR 34, 306-309). The database will return a unique identifier which you can include in your manuscript, thereby allowing readers to have access to your model.
Gene Expression
This category includes a wide range of applications relevant to the high-throughput analysis of expression of biological quantities, including microarrays (nucleic acid, protein, array CGH, genome tiling, and other arrays), RNA-seq, proteomics and mass spectrometry. Approaches to data analysis to be considered include statistical analysis of differential gene expression; expression-based classifiers; methods to determine or describe regulatory networks; pathway analysis; integration of expression data; expression-based annotation (e.g., Gene Ontology) of genes and gene sets, and other approaches to meta-analysis.
We will consider novel algorithms and applications in the above areas that constitute significant advances. Applications (including databases and web resources) will only be considered if significantly innovative. Measures of significance include anticipated impact on broad community and replacement of heuristics with principled approaches. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Development in areas with established approaches, such as normalization or classification, must represent a conceptual advance and show more than marginal improvement over existing methods.
Genetics and Population Analysis
This category includes: Segregation analysis, linkage analysis, association analysis, map construction, population simulation, haplotyping, linkage disequilibrium, pedigree drawing, marker discovery, power calculation, genotype calling.
We will consider algorithms and applications in any of the above areas. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Improvements in speed of methods may be considered if it is demonstrated that this will significantly widen the application of the method. We consider statistical methodology only when there is significant bioinformatics content such as new algorithms or software. We do not consider software that implements methods recently published elsewhere by the same authors.
Systems Biology
This category includes whole cell approaches to molecular biology. Any combination of experimentally collected whole cell systems, pathways or signalling cascades on RNA, proteins, genomes or metabolites that advances the understanding of molecular biology or molecular medicine will be considered. Interactions and binding within or between any of the categories will be considered including protein interaction networks, regulatory networks, metabolic and signalling pathways. Detailed analysis of the biological properties of the systems are of particular interest.
We will consider algorithms, applications, databases, data repositories, and visualization and representation tools in any of the above areas. Systems for the simulation of dynamics and/or spatial behaviour will be also considered. Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. New methods MUST be compared to existing state-of-the-art methods, using real biological data. The inclusion of experimental data is very much encouraged.
Data and Text Mining
This category includes: New methods and tools for extracting biological information from text, databases and other sources of information. Description of tools to organize, distribute and represent this information. New methods for inferring and predicting biological features based on the extracted information. The submission of databases and repositories of annotated text, computational tools and general methodology for the work in this area are encouraged, provided that they have been previously tested.
The journal requires that methods, systems and data to be made public. Strong emphasis should be placed on the biological applicability of the methods and the application to realistic biological scenarios. The main interest of the journal is the application to problems in molecular biology, but we also encourage submissions related with the relation between molecular and other type of data such as clinical, epidemiological, evolutionary, genomics, and others. Combination of information extraction technologies from heterogeneous sources and the combination with various computational approaches is also encouraged. The journal is not primarily interested in publishing analysis related with the sociological aspects of publications. The use of standard data sets for the evaluation of the methods is strongly advised, as well as the comparison with previous methods using common data sets.
Databases and Ontologies
This category includes: Curated biological databases, data warehouses, eScience, web services, database integration, biologically-relevant ontologies.
We will consider applications in any of the above areas. Descriptions of databases will not be published if they have been previously described unless there have been substantial changes or enhancements that represent a fundamental change in the database. We encourage Application Notes describing programmatic interfaces to biological data and services.
Bioimage Informatics
This category includes novel methods for the acquisition, analysis and modelling of images produced by modern microscopy, with an emphasis on the application of innovative computational methods to solve challenging and significant biological problems at the molecular, sub-cellular, cellular, and tissue levels.
This category also encourages large-scale image informatics methods/applications/software, joint analysis of multiple heterogeneous datasets that include images as a component, and development of bioimage-related ontologies and image retrieval methods.
We will not consider manuscripts that describe straightforward application of established computational methods to biological datasets, nor those that report incremental improvements in performance on benchmark datasets without a substantial advance in methodology. New methods MUST be compared to existing state-of-the-art methods, using real biological data. Manuscripts describing methods that rely on substantial user intervention are also discouraged.