Instructions to Authors

• About the Journal
• Scope of the Journal
• How to Submit
• Third Party Permissions
• Manuscript Charges
• Detailed Scope Guidelines
• Manuscript Transfer

Bioinformatics Advances allows initial submission of manuscripts to be format-free, however accepted manuscripts will need to be formatted into the two column format 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.

Once you have prepared your manuscript according to the instructions below please visit the online submission website.

About the Journal

Bioinformatics Advances is a fully open access, peer-reviewed journal that publishes continuously into a single online-only volume per year.

All papers published in Bioinformatics Advances are made freely available online under an open access licence, with applicable charges. Please refer to the open access section below.

Once a paper is accepted, Bioinformatics Advances will publish the pre-proofed, pre-copyedited accepted manuscript online within 1 week. This will be replaced by a copyedited, proofed version of the paper in an issue.

Please read these instructions carefully and follow them closely. The Editors may return manuscripts that do not follow these instructions.

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.

Scope of the Journal

Bioinformatics Advances is an interdisciplinary journal on bioinformatics and computational biology. The journal covers bioinformatics methods, such as algorithms, statistics, databases and software as well as biological contributions for which the application of advanced computational methods is an essential factor. The major focus of the journal is on the molecular and cellular levels of biology. The journal covers bioinformatics both for established experimental approaches and for emerging technologies that require innovative computational support. Problems in basic research as well as applications and translational research are covered. The journal also will publish papers that will be of wide interest to the computational community in areas such as education and career development.

The scope is defined in more detail through a series of subject categories. Upon submission you will be asked to select one of these following categories for your manuscript:

• Genome Analysis
• Sequence Analysis
• Phylogenetics
• Structural Bioinformatics
• Gene Regulation
• Genetics and Population Analysis
• Systems Biology
• Data and Text Mining
• Databases and Ontologies
• Bioimage Informatics
• Software
• Data Visualization
• Disease Bioinformatics/Translational Medicine
• Proteomics and Metabolomics
• Computational Neurosciences
• Cancer
• Cheminformatics
• Metagenomics
• Immunoinformatics
• Evolution
• Epigenetics
• Synthetic Biology
• Education

Description of Formal Content

Mathematical, statistical and algorithmic methods are an integral part of most research in bioinformatics and computational biology. Thus, for methodically oriented papers we encourage the inclusion of methodical material into the main text. This also includes the use of formulas and high-level pseudo-code. However, the material should be presented in a fashion that is intelligible for a readership from a wide range of backgrounds. Please do not submit presentations that are directed at a monodisciplinary readership. Specifically, we request the adherence to the following principles:

The definitions of all formal terms except the most basic ones should be described before or upon their first application. This can be done by either presenting the definitions in the text or referring to relevant and easily accessible references.

The readers should be directed at what part of the formal material they are expected to understand and what part of the material is given for completion and directed at only a subgroup of expert readers. That second part of the material should ideally be deferred to the supplementary material.

Special care should be taken to provide an intuitive interpretation of the formal material in the context of the given application to help the more casual reader.

Editorial Policies

Details of Oxford University Press’s editorial policies are available.

Peer Review

This journal uses single blind peer review. Full details about the peer review process are available.

Pre-submission Enquiries

Bioinformatics Advances welcomes pre-submission enquiries from prospective authors who wish to discuss the suitability of their work before sending a formal submission. Please send all enquiries to [email protected].

Appeal Process

Authors may submit a formal appeal for rejected submissions. Appeal requests must be made in writing via email to the Editors in Chief of the journal. Authors must provide detailed reasons for the appeal and point-by-point responses to the reviewers' and/or Associate Editor's comments. Decisions on appeals are final without exception.

Archiving Services

Portico and CLOCKSS are digital archiving/preservation services used to ensure journal content will be accessible to readers in the event of the platform being inaccessible for a significant period of time.

Software and Data Policies

Availability of Data

Bioinformatics Advances requires authors to make data on which the conclusions of the paper rely available to readers. Authors are required to record this availability in a Software and Data Availability Statement in their article.

In general, we require that data be presented in the main manuscript or additional supporting files, or deposited in a public repository. Exceptions to this policy require extraordinary argumentation. Information on general repositories for all data types is available on the research data policy page. A non-exhaustive list of subject specific repositories and global collaborations is shown below.

For new data resources that are published in the journal we encourage authors to submit to one or more of the available database listings such as:

Database Commons - https://ngdc.cncb.ac.cn/databasecommons/

FairSharing - https://fairsharing.org/

Availability of 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) at the time of submission (availability must be clearly stated in the manuscript)

•    make the software available using an open source license (see Open Source Initiative page for examples)

If the manuscript describes a web server or online database, the authors must:

•    ensure that the web server described is 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

•    provide the source code freely available at stable URLs (e.g. github, bitbucket) at the time of submission

•    provide help pages and a tutorial on how to use the resource and how to interpret the results

•    provide support / maintenance for at least three years after publication.

The name of the web server or web database should be included in the title of the manuscript.

Software and Data Availability Statement

The inclusion of a Software and Data Availability Statement is a requirement for articles published in Bioinformatics Advances. Software and Data Availability Statements provide a standardized format for readers to understand the availability of software and data underlying the research results described in the article. A link to the open source software and open license must be included within the statement. 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 and provide means of access, by linking to the data or providing the required unique identifier. Further information and examples of Data Availability Statements can be found on the research data policy page.

The Software and Data Availability Statement should be included in the end matter of your article under the heading 'Software and Data availability'.

Authorship

Authorship is confined 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 investigating and resolving these cases. For more information, please see the OUP Publication Ethics page.

After manuscript submission, no authorship changes (including the authorship list, author order, and who is designated as the corresponding author) should be made without the approval of the editor. All co-authors must agree on the change(s), and neither the Journal nor the publisher mediates such disputes. If individuals cannot agree on the authorship of a submitted manuscript, contact the editorial office. 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.

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.

ORCID information

Bioinformatics Advances 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.

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.

bioRxiv (B2J)

Bioinformatics Advances participates in B2J, which means it is set up to accept direct transfers from bioRxiv. This may help authors save time in submission as manuscript files and metadata can be transmitted directly from bioRxiv to the submission system.

Conflict of Interest

When submitting a paper, you and your co-authors must declare any potential conflicts of interest. You must do this by including a Conflict of Interest statement in your submitted manuscript. See the Conflict of Interest section of the Ethics page for more information. 

Members of the editorial staff of the journal should include the following COI disclosure in their article: [Author initial] holds the position of [Editor-in-Chief/Associate Editor/Editorial Board Member] for Bioinformatics Advances and is blinded from reviewing or making decisions for the manuscript.​

Ethics policy

Authors should observe high standards with respect to publication best practice. Analyzed personal data must have been collected adhering to the ethical standards for data collection in accordance with the Declaration of Helsinki. For data taken from other resources, a reference to those resources documenting adherence to ethical data collection suffices. Falsification or fabrication of data, plagiarism, including duplicate publication of the authors’ own work without proper citation, and misappropriation of work are all unacceptable practices.

If data have been collected specifically for the study, adherence to ethical data collection standards must be given by reference to the ethics committee that approved the study and the reference number, where appropriate. If a study has been granted an exemption from requiring ethics approval, this should also be detailed in the manuscript (including the name of the ethics committee that granted the exemption). Further information and documentation to support this should be made available to the Editor on request.

For all research involving human subjects, informed consent to participate in the study should be obtained from participants (or their parent or legal guardian in the case of children under 16) and a statement to this effect should appear in the manuscript. Please also confirm that you have followed national guidelines on data collection and release in the place the research was carried out. Please also state the year in which approval was granted.

Figures should faithfully represent the original data. Manipulation to obscure any features of the image is unacceptable. Any cases of ethical or publication malpractice are treated very seriously and will be managed in accordance with the Committee on Publication Ethics (COPE) guidelines. Further information about OUP’s ethical policies is available on the Publication Ethics page. The journal reserves the right to reject papers where the ethical practices are, in the Editors’ opinion, open to doubt.

Submission

We will consider your manuscript as long as:

• it is your own original work and does not duplicate any previously published work, including your own;
• it is not under consideration, in peer review, or accepted for publication in any journal other than Bioinformatics Advances;
• it has not been published in any other journal; and
• it contains nothing abusive, defamatory, libelous, obscene, fraudulent, or illegal.

Authors should observe high ethical standards and obey publication best practices. The following are all unacceptable:

• data falsification or fabrication
• plagiarism, including duplicate publication of your own work without proper citation
• misappropriation of work

We treat any case of ethical or publication malpractice very seriously. We will address them in accordance with the Committee on Publication Ethics (COPE) guidelines. Further information about OUP’s ethical policies is available.

Plagiarism

Manuscripts submitted to Bioinformatics Advances may be screened with iThenticate anti-plagiarism software in an attempt to detect and prevent plagiarism. Any manuscript may be screened, especially if there is reason to suppose part or all of the text has been previously published. Prior to final acceptance any manuscript that has not already been screened may be put through iThenticate. More information about iThenticate can be found iThenticate page.

How to Submit

You must submit your paper via our web-based submission system, which may be found at http://mc.manuscriptcentral.com/bioadv. Bioinformatics Advances allows initial submission of manuscripts to be format-free, however accepted manuscripts will need to be formatted into the two column format 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.

If you have not published with Bioinformatics Advances before, you will need to create an account. More information is available on the ScholarOne Manuscripts FAQ and help page.

Questions about submitting can be sent to the editorial office at [email protected].

Article Types

This journal publishes several different article types, as described below.

Original Article

These are articles that present original research contributions in the areas described in the scope statement. Criteria for publication are described in the subject category texts available within the scope statement.

• length - up to 8 pages
• abstract—maximum word count: 200
• keywords—maximum keywords: 5. Journal keywords are preferred.
• references—maximum references: 50
• tables and figures—maximum of 6 figures and 6 tables

Each submission must contain the following sections: Abstract, Introduction, Methods, Discussion, References. The following sections may be appropriate in some cases: Algorithm, Implementation.

Application Note

These articles present openly accessible software systems and their use. Criteria for publication include usefulness of the software for a sizeable user community – as documented in the article, e.g. via use cases – software quality and ease of use as well as providing tutorial material and documentation of the software.

• length - up to 4 pages
• abstract—maximum word count: 200
• keywords—maximum keywords: 5. Journal keywords are preferred.
• references—maximum references: 10
• tables and figures—maximum of 3 figures or tables

Each submission must contain the following sections: Abstract, text, References.

Scientific Data

These articles present innovative and useful openly accessible data sets and their use. Criteria for publication include being a substantial novel contribution, usefulness of the dataset for a sizeable user community – as documented in the article, e.g. via use cases – barrier-free access and adequate searchability of the dataset, as well as sufficient explanation of the dataset generation. In general, we expect the data to be deposited in an acknowledged data repository such as those listed in the paragraph on data availability in this document.

length - up to 4 pages

abstract—maximum word count: 200

keywords—maximum keywords: 5. Journal keywords are preferred.

references—maximum references: 10

tables and figures—maximum of 3 figures or tables

Each submission must contain the following sections: Abstract, text, References.

Discovery Notes

These articles present novel biomedical insights for whose discovery bioinformatics techniques are essential. Criteria for publication are described in the subject category texts available within the scope statement.

• length - up to 6 pages
• abstract—maximum word count: 200
• keywords—maximum keywords: 5. Journal keywords are preferred.
• references—maximum references: 10
• tables and figures—maximum of 5 figures or tables

Each submission must contain the following sections: Abstract, Introduction, Methods, Results, and Conclusion.

Review

These articles represent up-to-date overview of the state of the art on a certain topic in computational biology.

• length - up to 8 pages
• abstract—maximum word count: 200
• keywords—maximum keywords: 5. Journal keywords are preferred.
• tables and figures—maximum of 6 figures or tables

May be in a format best suited to subject matter, but should include Abstract, Text, References. For clarity the main body of text should be sub-divided into sections. Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance email a draft or abstract/summary no longer than a page to the editorial office.

Opinion

These article present opinions by the author on a certain controversial or underexposed topic in the field.

• length - up to 5 pages
• abstract—maximum word count: 100
• keywords—maximum keywords: 5. Journal keywords are preferred.
• tables and figures—maximum of 3 figures or tables

Perspective

These articles present the perspective of where the authors see a field going or challenges with which the field is confronted and approaches to meet those challenges.

• length - up to 5 pages
• abstract—maximum word count: 200
• keywords—maximum keywords: 5. Journal keywords are preferred.
• references—maximum references: 20
• tables and figures—maximum of 4 figures or tables

Letter to the Editor

These short articles present points of a diverse nature that the author wants to make to the editors and reader of the journal.

Feature

The articles contain content commissioned by the journal editors. They can comprise personality features on outstanding researcher in the field, such as award winners, features on issues pertaining to politics and research funding, or societal issues such as those pertaining to ethics, diversity, and more.

Third-Party Permissions

If you wish to reproduce any material for which you do not own the copyright—including quotations, tables, or images—you must obtain permission from the copyright holder. The permissions agreement must include the following documents:

• nonexclusive rights to reproduce the material in your article in Bioinformatics Advances
• both print and electronic rights, preferably for use in any form or medium
• lifetime rights to use the material
• worldwide English-language rights

Further information on obtaining permissions is available.

Manuscript Preparation: Format, Structure, and Style

Word Submissions

Please use the journal's Word template for information on what to include and how to structure an article for submission.

LaTeX Submissions

If you wish to use LaTeX to write your manuscript before submitting, please use the OUP LaTeX template available at overleaf.com by following this link. For useful information on preparing your manuscript for publication, go to this page. Please read the online instructions carefully and select the layout and formatting options indicated for this journal. Bioinformatics Advances uses a Modern Large template, and an author-year reference style. When submitting your manuscript, please submit the PDF in the first instance for review featuring any tables, figures and references alongside the main text; if your article is accepted for publication you will be asked to supply source files at this stage.

Pre-submission Language Editing

If you are not confident in the quality of your English, you may wish to use a language-editing service to ensure that editors and reviewers understand your paper. Language editing is optional and does not guarantee that your manuscript will be accepted. Edited manuscripts will still undergo peer review by the journal.

Title Page

Please include the following:

• the title of your paper
• all author names and affiliations
• mailing address and email address of one corresponding author
• a short running head of 50 characters or less

Abstract

Abstracts have a maximum length of 200 words and must not contain reference citations or abbreviations.

Please add keywords after the abstract Journal keywords are preferred.

Style

Please refer to these requirements when preparing your manuscript after initial review. More information is available on the style guide. Consistent US or UK spelling should be used throughout, except in quotations and in references. 

Abbreviations

Please define nonstandard abbreviations at the first occurrence.

Tables

You must number all tables (e.g., table 1, table 2, table 3) and reference them in the text. You must place all tables at the end of the main text. Tables should be in an editable format, and not embedded as an image file.

References

You may format references in any readable style at submission. You are responsible for the accuracy of reference information. References follows the style of author - date shown below:

• 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.

Acknowledgements and Funding

Acknowledgements and funding information should be included at the end of your manuscript. Please fully cite any relevant funding information, including specific grant numbers. 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

You must include figure titles and legends within the manuscript file—they should not be included in the image file.

You must submit each figure as an individual image file. Submit all panels of a multipanel figure on a single page as one file. For example, if the figure has 3 panels, the figure should be submitted as one file. Each panel should be labelled as a letter (A, B, C, D, etc.) in the upper-left corner of each panel.

Images of photographs or paintings can be provided as raster images. Common examples of raster images are .tif/.tiff, .raw, .gif, and .bmp file types. The resolution of raster files is measured by the number of dots or pixels in a given area, referred to as “dpi” or “ppi.”

• minimum resolution required for printed images or pictures: 350dpi
• minimum resolution for printed line art: 600dpi (complex or finely drawn line art should be 1200dpi)
• minimum resolution for electronic images (i.e., for on-screen viewing): 72dpi

Images of maps, charts, graphs, and diagrams are best rendered digitally as geometric forms called vector graphics. Common file types are .eps, .ai, and .pdf. Vector images use mathematical relationships between points and the lines connecting them to describe an image. These file types do not use pixels; therefore, resolution does not apply to vector images.

Figures prepared as .doc/.docx or .jpeg/.jpg files will not be accepted.

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. 

Supplementary Material

You must submit supplementary data or supplementary material at the same time as the main manuscript.

• Supplementary material must be cited in the text of the main manuscript.
• Supplementary material will be available online only and will not be copyedited or typeset.
• Style and formatting of supplementary material should be consistent with that of the manuscript.
• Supplementary material should be formatted to function on any internet browser.
• Supplementary material files should be no larger than 15MB each.

Licence to Publish and Open Access Options

Bioinformatics Advances is a fully open access journal and depends upon open access publication fees for its operation. After your manuscript is accepted, you must sign a licence to publish form on our Author Portal.

If your paper is accepted, you will be charged an open access fee. See the Charges section below for more information. All papers are freely available online upon publication under an open access licence.

Manuscript Charges

Author Portal

You can pay open access charges on the same Author Portal site you used to sign your licence to publish. You can pay immediately online or request an invoice by email or post. Any applicable discounts can also be applied prior to payment.

You can pay your open access charges immediately after you sign your licence.

CC BY licence (non-member): $2,726

ISCB member discount: 20%

Charges for Letters to the Editor, Editorials, Corrections, Memoriam papers: $0

Free developing country charge*: $0

*Visit our APC waiver policy page for more information on eligibility for geographic-based waivers.  

Your funding agencies may have specific requirements for what type of open access licence to use, so please check before selecting a licence. Please see Creative Commons licences for more information. Please check with your funding body if you are unsure of any licence requirements.

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. Contributions should  display significant improvements in method and/or new biological insight. 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 localization; 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. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze 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. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Structural Bioinformatics

This category includes: New methods and tools for prediction, analysis and comparison of molecular structures; 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. Contributions should  display significant improvements in method and/or new biological insight.  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 progress 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 Regulation

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), and RNA-seq. 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. Contributions should  display significant improvements in method and/or new biological insight. 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 signaling 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 signaling 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 behavior will be also considered. Contributions should display significant improvements in method and/or new biological insight.  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 analyses 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 modeling 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 data sets that include images as a component, and development of bioimage-related ontologies and image retrieval methods.

We will consider manuscripts that describe straightforward application of established computational methods to biological data sets, nor those that report incremental improvements in performance on benchmark data sets 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.

Software

This category includes novel methods and software systems for enabling bioinformatics analyses, including workflow models, web-services, high-performance computing, data gathering, crowd sourcing etc.

We will not consider manuscripts that describe straightforward application of established computational methods, nor those that report incremental improvements in performance on benchmark data sets without a substantial advance in methodology. New methods MUST be compared to existing state-of-the-art methods, using real biological data. 

Data Visualization

This category includes novel methods for visualizing biological data such as high-dimensional data, data submitted to statistical analysis, graphs and networks and data on dynamical systems.

We will not consider manuscripts that describe straightforward application of established computational methods, 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. 

Disease Bioinformatics/Translational Medicine

This category includes novel methods and data analyses furthering the diagnosis, prognosis and therapy of diseases as well as helping to elucidate the molecular basis of disease. In this category we require a particular disease or a group of diseases to be in the focus of attention. Both associations and causal relationships between molecular aspects and the disease are of interest. For papers in this category we require substantial and convincing validation of the contribution based on real biological data and argumentation of significant progress by the contribution.

Proteomics and Metabolomics

This category includes novel methods for analyzing proteomic and metabolomic mass spectrometry data.  Contributions should  display significant improvements in method and/or new biological insight. 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. 

Computational Neurosciences

This category includes novel methods for analyzing molecular, electrophysiological and image data pertaining to questions in neuroscience. Contributions should  display significant improvements in method and/or new biological insight. 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. 

Cancer

This category includes novel methods and data analyses furthering the diagnosis, prognosis and therapy of cancer as well as helping to elucidate the molecular basis of disease, including tumor evolution. Both associations and causal relationships between molecular aspects and the disease are of interest. For papers in this category we require substantial and convincing validation of the contribution based on real biological data and argumentation of significant progress by the contribution.

Cheminformatics

This category includes novel methods for drug design, drug screening and drug optimization based in 1D-, 2D- or 3D data. Contributions should  display significant improvements in method and/or new biological insight. 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. 

Metagenomics

This category includes novel methods for analyzing metagenomic data, i.e. sequence data on microbial communities taken from complex samples. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Immunoinformatics

This category includes novel methods and data analyses pertaining to immunity and infectious diseases. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Evolution

This category includes novel methods and data analyses pertaining to evolutionary processes and evolutionary history of biological molecules and systems, in general. Specific issues like tumor evolution, microbial resistance development and ancestral human migration, which fit into specific other categories, do not belong in this category. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Epigenetics

This category includes novel methods and data analysis pertaining to epigenetic issues such as DNA methylation, histone modification, chromatin structure and transcriptional gene regulation, in general. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Synthetic Biology

This category includes novel methods for the computational support of synthetic biology, e.g., the optimization of genomes and/or genetic or molecular networks. Contributions should  display significant improvements in method and/or new biological insight. 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 analyze existing sequence data will only be considered if novel biological insight is obtained.

Education

This category includes: Bioinformatics education and training, syllabus and program development, standards and assessment, online learning, teaching methods and guidance of best practice. In addition, topics related to challenges and opportunities in bioinformatics education, and efforts towards equity and diversity in bioinformatics education are within scope

Articles should be of interest to a broad audience. We would recommend that you send a presubmission enquiry to the editors for specific advice on articles and which article type may be most suitable. We generally do not consider training manuals or protocol articles to lie within the scope of this category.

Manuscript Transfer

Bioinformatics Advances receives transfers from other journals on related topics published by Oxford University Press. All transfers are sent according to the choice of the authors. Unless a reviewer declines to have their feedback shared, reviewer reports and the original decision letter are included in the transfer, but the reviewer identities are not shared.

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 reviewers and the judgment of the editorial team.