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. In manuscript form (double-spaced), this translates to roughly 4,000-5,000 words of body text plus figures, tables, and references. The page count includes everything, so a paper with 5 complex figures will have less room for text.

Applications Notes are extremely constrained at 2 printed pages. This works out to approximately 1,300 words plus one figure. Applications Notes describe software tools, databases, or web services rather than new methods. They're designed to give the community enough information to find, install, and use your tool. Think of them as extended software announcements.

Discovery Notes are for significant biological findings made through computational analysis. They're shorter than Original Papers and don't require the same level of methodological novelty.

Bioinformatics uses different abstract formats depending on article type.

For Original Papers (structured abstract):

• Motivation: Why is this problem important? (2-3 sentences)
• Results: What did you find or build? (3-4 sentences with specifics)
• Availability: Where can the software/data be found? (URL and license)
• Contact: Corresponding author email
• Supplementary information: URL or reference to supplements
• Total limit: 250 words

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 provide a placeholder link.

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.

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 more on this journal, 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.