Bioinformatics Formatting Requirements: Complete Author Guide

Bioinformatics uses page limits measured in the journal's two-column typeset format.

The guidelines strongly discourage exceeding the stated page limits. They add that manuscripts exceeding the recommended limits may be rejected without review, and that manuscripts which exceed the limit by 20% or more are usually returned by the Editorial Office immediately. Authors can appeal an editorial decision by contacting the editorial office. In manuscript form, 7 pages works out to roughly 5,000 words, not including figures.

Application Notes run up to 4 pages (approx. 2,600 words, or 2,000 words plus one figure) and describe software tools, databases, or web servers rather than new methods. They have their own short structured abstract (Summary / Availability and Implementation / Contact / Supplementary information), and the guidelines say the name of the application should be included in the title. Think of them as extended software announcements that must stand on their own as citable artifacts.

Bioinformatics uses different abstract formats depending on article type.

For Original Papers (structured abstract, a maximum of 150 words is recommended):

• Motivation: The scientific question within the context of the field of study.

• Results: The scientific advance or novel results of the study, and their impact on computational biology.

• Availability and Implementation: Where is the software, and what's needed to run it? (URL, language, OS)

• Contact: Corresponding author email

• Supplementary information: URL or reference to supplements

The structured abstract with Motivation, Results, and Availability sections is distinctive to Bioinformatics. The Availability section in the abstract itself is unusual and reflects the journal's strong emphasis on software and data sharing.

For Application Notes (short structured abstract):

• Four headings: Summary, Availability and Implementation, Contact, and Supplementary information

• The Summary should cover the purpose and novel features of the program in one or two sentences

• No abstract word limit is published for Application Notes

• The complete URL should be given under Availability and Implementation, and the guidelines' examples also mention implementation language and supported platforms

Don't underestimate the importance of the Availability line in the abstract. The guidelines require software to be freely available at stable URLs at the time of submission, so a link that doesn't work puts the paper at risk.

Bioinformatics sets its length limits in journal-template pages, so economy matters.

Figure formatting requirements:

Computational figure conventions: Bioinformatics papers frequently include ROC curves, precision-recall curves, benchmark comparisons, phylogenetic trees, network diagrams, and sequence alignments. For benchmark comparisons, include error bars or confidence intervals. For ROC curves, include AUC values in the legend. For phylogenetic trees, include bootstrap support values at branch nodes.

Table formatting: Tables should be embedded within the main document file, numbered consecutively, self-explanatory, and given a brief descriptive title, with table footnotes indicated by lower case letters. Benchmark comparison tables are most useful when they include runtime, memory usage, accuracy metrics, and the test dataset.

Color figures: Free of charge. The journal does not charge for color, and it is online only.

Supplementary data: Additional figures, tables, benchmark results, and data can go in supplementary material. No limit is published. Supplementary text, figures, and tables should be presented in a single file, separate from the manuscript, and referred to in the main text.

The journal follows Oxford SCIMED style, which uses author-date references. The guidelines ask authors to refer to the Oxford SCIMED requirements when preparing the manuscript after initial review.

In-text citations:

• In-text citation: (Smith 1994)

• List multiple citations chronologically: (Smith 2015, Wong 2015, Patel 2016)

Reference list format:

References are listed alphabetically by author surname.

Kennedy T, Jones R. Effect of obesity on esophageal transit. Am J Surg 1985;149:177-81.

Key formatting details (Oxford SCIMED checklist):

• When there are 4 or more authors, list the first author name followed by et al.

• Page spans are elided (for example 213-5 and 137-87)

• The Latin phrase ibid is discouraged

This is the single most important formatting requirement at Bioinformatics, and it's non-negotiable.

Mandatory requirements:

• All software described in the paper must be freely available to non-commercial users

• Source code must be freely available at stable URLs (for example GitHub or Bitbucket), and the submitted software version and test data should also be archived at a repository such as Zenodo, Figshare, Software Heritage, CRAN, or Bioconductor

• The repository URL must be included in the manuscript (abstract and main text)

• The software must be available at the stated URL at the time of submission

• Encouraged, not required: access through an open source license (see the Open Source Initiative page for examples)

• Documentation sufficient for installation and basic use must be provided

What editors check:

• The URL works and the software is accessible

• The software can be installed following the provided instructions

• The software produces results consistent with what's reported in the paper

• Dependencies are documented

Papers where the software isn't available or doesn't work will be returned. This is enforced consistently. Don't submit until your code is polished, documented, and publicly accessible.

Data availability: Similarly, datasets used for benchmarking or validation should be publicly available or deposited in standard repositories (GenBank, PDB, GEO, ArrayExpress, etc.). Include accession numbers in the manuscript.

1. Software availability is checked. Editors and reviewers actually visit the URL and try the software. Don't submit a URL that doesn't work or isn't yet live.

2. Application Notes are deceptively hard to write. Four pages sounds easy, but fitting a meaningful description of a software tool into about 2,600 words (or about 2,000 words plus one figure) is challenging. Every sentence must count. Skip the extensive background and focus on what the tool does, how it performs, and where to get it.

3. Benchmark comparisons are expected. For Original Papers presenting new methods, reviewers expect quantitative comparisons against existing methods on standard benchmark datasets. A paper that doesn't compare against the state of the art will be sent back.

4. Runtime and memory reporting. Bioinformatics reviewers care about computational efficiency. Report runtime and memory usage on standard hardware. Specify the hardware used for benchmarks (CPU model, RAM, number of cores).

5. Supplementary data for reproducibility. Include parameter files, configuration scripts, and test datasets in supplementary material or the code repository. The goal is complete reproducibility.

6. Category selection. During submission, you'll be asked to select one of the journal's categories (Genome analysis, Sequence analysis, Phylogenetics, Structural bioinformatics, Gene expression, Genetic and population analysis, Systems biology, Data and text mining, Databases and ontologies, or Bioimage informatics). Choose the category that matches the paper's main contribution.

7. Preprint policy. A preprint does not prevent submission to Bioinformatics. Disclose related preprints in your cover letter, and if the paper is accepted, update the preprint with the published paper's DOI.

8. Charges. Bioinformatics has no page charges and no color charges. The journal is fully open access, so an open access charge applies to published papers unless it is waived or covered, for example by a Read and Publish agreement.

The author guidelines ask for Original Papers to be subdivided into this sequence:

1. Title page (title specific to the method/tool, author names, and affiliations)

1. Structured abstract (Motivation, Results, Availability and Implementation, Contact, Supplementary information)

1. Introduction (problem statement, existing approaches, contribution)

1. System and methods

1. Algorithm

1. Implementation

1. Discussion (interpretation, limitations, future directions)

1. References

Acknowledgements go at the end of the text, with a separate Funding section (including grant numbers) first within them, and Supplementary Data goes in a separate file.

The methods, algorithm, and implementation sections should be detailed enough for reimplementation. Include pseudocode for novel algorithms, mathematical derivations for new statistical methods, and architecture diagrams for deep learning models. This level of detail is expected and valued.

For manuscripts targeting Bioinformatics, four patterns generate the most consistent desk-rejection outcomes.

Software not available at submission time. The Bioinformatics author guidelines state explicitly that software must be freely available to non-commercial users at stable URLs at the time of submission. Editors check the repository URL during the review process. Papers where the software is missing, behind a paywall, or returns a 404 error are returned administratively. We regularly see manuscripts in this category: the science is solid, but the code is "coming soon." Bioinformatics will not hold a manuscript while the authors finish the repository.

Leave-one-out cross-validation as the primary validation strategy. The Bioinformatics author guidelines state that papers using leave-one-out will be editorially rejected unless there is a special circumstance in which the procedure can be argued to be meaningful for the problem addressed. They also state that machine learning papers must report performance on an independent test set, and that reporting the average error over the individual cross-validation sets is not sufficient. A manuscript validated only with leave-one-out cross-validation should expect rejection regardless of the algorithm's performance on that dataset.

Simulated or synthetic data as the only validation. Bioinformatics is a biological journal, not a computer science journal. The guidelines require that methods be validated on real biological data. Papers that demonstrate performance exclusively on simulated sequences, synthetic networks, or artificially constructed datasets are regularly returned with requests for real-world validation. Simulation is acceptable as a component of the analysis, not as the primary evidence.

Missing cover letter. The Bioinformatics author guidelines state that all submissions must be accompanied by a cover letter and that submissions omitting one may be editorially rejected. The cover letter should state which article type you are submitting, why the paper is appropriate for Bioinformatics specifically, and confirm that the software is available at the stated URL.

A Bioinformatics pre-submission readiness check evaluates whether your manuscript meets the software availability, benchmark, and structural requirements that determine desk-rejection risk.

These cause the most issues at Bioinformatics:

• Software not available at the stated URL (the most common fatal error)

• Missing structured abstract sections (Motivation, Results, Availability)

• Exceeding the page limit (7 pages for Original Papers, 4 for Application Notes)

• No benchmark comparison against existing methods

• Missing runtime and memory usage data

• Using numbered references instead of OUP author-year style

• Insufficient software documentation in the repository

• Missing license information for the software

• Not specifying the programming language and dependencies

For a complete overview of the journal, see the Bioinformatics journal profile. For more on submission, see our Bioinformatics submission guide and how to avoid desk rejection at Bioinformatics. For journal metrics, check the Bioinformatics JIF page.

For the official guidelines, visit the Bioinformatics author guidelines.

This page was built from the current OUP Bioinformatics author guidelines, the journal's software and machine-learning policy, the page-limit rules for Original Papers and Application Notes, SciRev author-reported timing signals, and Manusights pre-submission review patterns from computational biology manuscripts.

Use this page when the question is "will the submission package pass Bioinformatics formatting and software checks?" For fit and scope, use the Bioinformatics journal profile, Bioinformatics submission guide, and Bioinformatics impact factor.

Bioinformatics formatting is really a reproducibility test. If the repository is not stable, the software cannot run from the stated instructions, the independent test set is missing, or the paper cannot fit into the journal-template page limit, the manuscript is not ready for this journal even if the method itself is promising.