Bioinformatics Formatting Requirements: Complete Author Guide

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

The 7-page limit for Original Papers is firm, and the editorial office, not reviewers, enforces a hard rule: manuscripts exceeding the limit by 20% or more are returned administratively before they reach a scientific reviewer. There is no appeal path described in the guidelines. In manuscript form, 7 typeset pages works out to roughly 5,000 words of body text plus figures, tables, and references.

Applications Notes run up to 4 printed pages (~2,600 words) and describe software tools, databases, or web servers rather than new methods. They require their own structured abstract (Summary / Availability and Implementation / Contact / Supplementary Information) and must include the software name in the title, an unusual hard rule specific to this journal. 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, 150 words max):

• Motivation: Why is this problem important? (2-3 sentences)
• Results: What did you find or build? (3-4 sentences with specifics)
• 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 Applications Notes (unstructured):

• 150 words maximum
• Single paragraph
• Must include the URL where the tool is available
• Must state the programming language and operating system

Don't underestimate the importance of the Availability line in the abstract. Bioinformatics editors check that the software is accessible at the stated URL during the review process. If the link doesn't work, the paper will be held.

Bioinformatics figures count toward the page limit, 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: Editable tables with headers for every column. Benchmark comparison tables should include runtime, memory usage, accuracy metrics, and the test dataset. Horizontal rules at top, below header, and bottom. No vertical rules.

Color figures: Free for online publication. Print color may incur charges, but most Bioinformatics readers access articles online.

Supplementary data: Additional figures, tables, benchmark results, and data can go in supplementary material. No strict limit. Submit as a single PDF with additional data files as needed.

Bioinformatics uses the OUP reference style, which is an author-year system.

In-text citations:

• Single author: Author (Year)
• Two authors: Author1 and Author2 (Year)
• Three or more: Author1 et al. (Year)
• Parenthetical: (Author, Year) or (Author1 et al., Year)

Reference list format:

Alphabetical by first author's last name.

Author,A.B., Author,C.D. and Author,E.F. (Year) Title of article. Journal Abbreviation, Volume, Pages.

Key formatting details:

• Author names: Last name, initials (no space between initials)
• "and" before last author (not "&")
• Year in parentheses after author list
• Article title in sentence case
• Journal name abbreviated and in italics
• Volume in bold
• DOI included when available

Example:

Zhang,Y., Chen,L. and Patel,W.R. (2026) A deep learning approach for protein structure prediction from cryo-EM data. Bioinformatics, 42, 1234-1240.

Note the OUP convention of no space between initials in author names (Zhang,Y. not Zhang, Y.). This is a small detail that production editors check.

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 for academic use
• Source code must be deposited in a public repository (GitHub, GitLab, Bitbucket, SourceForge)
• The repository URL must be included in the manuscript (abstract and main text)
• The software must be functional at the stated URL at the time of review
• License must be clearly stated (GPL, MIT, BSD, Apache, etc.)
• 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
• The license is clearly stated
• 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. Applications Notes are deceptively hard to write. Two pages sounds easy, but fitting a meaningful description of a software tool into 1,300 words with a 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. Associate Editor selection. During submission, you'll select a track (Genome Analysis, Sequence Analysis, Systems Biology, etc.) that determines which Associate Editor handles your paper. Choose carefully because the wrong track can delay the assignment process.

7. Preprint policy. Bioinformatics doesn't penalize preprints. If your paper is on bioRxiv or arXiv, that's fine. Include the preprint DOI in the manuscript for transparency.

8. Page charges. Bioinformatics doesn't charge page fees for standard papers. Open access APCs apply if you choose the OUP open access option.

A standard Bioinformatics Original Paper follows this structure:

1. Title (specific to the method/tool and its application)
2. Author names and affiliations
3. Abstract (structured: Motivation, Results, Availability, Contact, Supplementary Information)
4. 1. Introduction (problem statement, existing approaches, contribution)
5. 2. Methods (algorithm description, mathematical formulation, implementation details)
6. 3. Results (benchmark comparisons, validation, real-data applications)
7. 4. Discussion (interpretation, limitations, future directions)
8. Acknowledgements
9. Funding (separate section with grant numbers)
10. Conflict of Interest
11. References
12. Supplementary Data (separate file)

The Methods section 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.

In our pre-submission review work with 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 for academic use and accessible at a working URL at the time of review. 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. Bioinformatics reviewers consistently flag leave-one-out cross-validation (LOOCV) as insufficient for method validation papers. The journal expects holdout test sets, cross-validation on independent benchmark datasets, or comparison against established benchmarks with published performance data. A manuscript validated only with LOOCV on a single dataset will generate reviewer pushback 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 submission system explicitly requires a cover letter, and the editorial office returns manuscripts submitted without one. 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 missing cover letter is an administrative return, not a scientific rejection.

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, 2 for Applications 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 impact factor page.

For the official guidelines, visit the Bioinformatics author guidelines.

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.