Genome Biology Formatting Requirements: Complete Author Guide

Genome Biology is notably flexible with word limits, trusting authors to calibrate length to content.

The lack of a rigid word limit doesn't mean anything goes. Editors expect papers to be concise and well-organized. A 15,000-word Research article is possible but only if the scope genuinely demands it. Method papers tend to be longer because they need detailed benchmarking and comparison sections. Software papers should be shorter and focused on demonstrating the tool's utility.

Genome Biology's Benchmark articles are a distinctive format. They systematically compare tools, pipelines, or methods in a specific area (variant callers, single-cell analysis pipelines, etc.). These are highly cited and valued by the community. If you're doing a fair, thorough comparison, this format is worth considering.

Genome Biology requires structured abstracts for Research, Method, and Software articles.

• Word limit: Approximately 350 words (not rigidly enforced but editors will ask you to trim excess)
• Required headings: Background, Results, Conclusions
• No citations in the abstract
• Keywords: Not required separately (keywords are embedded in the BMC system)

The three-part structure (Background, Results, Conclusions) omits a Methods section, which is unusual. This means your Results section in the abstract should briefly mention the approach before presenting findings. For software papers, the Results section describes what the tool does and how it performs.

The 350-word abstract gives you room to include specific quantitative results and methodological detail. For genomics papers, include key numbers: sample sizes, genome coverage, variant counts, accuracy metrics. Reviewers and readers scan the abstract for these specifics.

Genome Biology doesn't impose a strict figure cap. Most Research articles include 5-10 main figures with additional files for supplementary data.

Figure requirements:

Table requirements:

• Word or LaTeX table format
• Every column needs a header
• Horizontal rules only
• No vertical lines
• Large supplementary tables should be submitted as Additional Files in CSV or Excel format

Genomics-specific figure expectations:

• Genome browser screenshots should include track labels, coordinates, and scale bars
• Manhattan plots should include genome-wide significance line and chromosome labels
• Heatmaps should include dendrograms (if clustered) and color scale bars
• Benchmarking figures should include all tested tools with clear labeling
• Multi-panel comparison figures should use consistent axis scales across panels
• Violin plots or ridge plots preferred over bar charts for distributions

For bioinformatics and genomics papers, the quality of data visualization matters enormously. Genome Biology reviewers will flag overcrowded plots, missing axis labels, and inconsistent formatting. Use consistent color schemes across related figures. If you're comparing methods, use the same data presentation format for all methods.

Genome Biology uses the BMC numbered reference style.

In-text citations: Square brackets: [1], [2, 3], [4-7]. Place before punctuation.

Reference list format (numbered):

1. Smith AB, Jones CD, Brown EF. A comprehensive atlas of chromatin accessibility in human tissues. Genome Biol. 2025;26:42.

Key formatting rules:

• All authors listed (no "et al." in the reference list for articles with fewer than 30 authors)
• For 30+ authors, list first 29 followed by "et al."
• Journal titles abbreviated per NLM standards
• Volume, colon, article number (or page range)
• DOI typically not in the formatted reference (BMC adds links automatically)
• For books: Smith AB, Jones CD. Title of Book. City: Publisher; Year.
• For preprints: Include the preprint server, DOI, and year

Genome Biology is one of the few high-impact journals that explicitly welcomes preprint citations. If you're citing work posted on bioRxiv or medRxiv, format it as:

12. Smith AB, Jones CD. Title of preprint. bioRxiv. 2025. doi:10.1101/2025.01.01.000000.

There's no strict reference cap. Research articles typically cite 50-80 references. Review articles can go well over 100.

Genome Biology uses "Additional Files" for supplementary material, following BMC convention.

Common additional file types:

• Extended data tables (CSV, Excel)
• Additional figure files (Figure S1, S2, etc.)
• Supplementary methods
• Raw benchmark results
• Code documentation
• Extended statistical analyses

Data and code availability (critical):

Genome Biology has one of the strictest data availability policies among genomics journals:

• Sequencing data: Must be deposited in GEO, SRA, ENA, or DDBJ
• Processed data: Must be available for download (via Additional Files or public repository)
• Code: Must be on a public platform (GitHub, GitLab, Bitbucket, or Zenodo)
• Software tools: Must include documentation and test datasets
• Versioned code releases: Zenodo DOIs for specific code versions are encouraged

The Data Availability section is mandatory. Don't write "Data available upon request." Genome Biology requires public access to all data and code. Papers have been rejected at the revision stage for failing to make data publicly available.

For software papers specifically, the tool must be freely available, documented, and installable. Reviewers will test your software. If it doesn't install or work as described, the paper will be rejected regardless of the algorithm's merit.

Both are accepted through the BMC submission system.

Word submissions:

• BMC Word template available from the journal website
• Standard formatting: double-spaced, line numbers, page numbers
• Figures embedded or at end of manuscript
• Tables within the manuscript

LaTeX submissions:

• BMC LaTeX template (bmc_article class)
• Available on the BMC website and Overleaf
• Submit source files and compiled PDF
• BibTeX supported with BMC bibliography style

The genomics and computational biology community has a strong LaTeX contingent. Many Genome Biology authors use LaTeX, and the journal's production system handles it well. For software and method papers with code snippets or mathematical notation, LaTeX is a natural choice.

Word is fine for experimental genomics papers. There's no penalty for either format.

Genome Biology has several practices that distinguish it from other genomics journals.

1. Data and code must be public before publication. This isn't a polite suggestion. Genome Biology will hold your paper in production until data is deposited and code is publicly available. Start the deposition process at submission, not after acceptance.

2. Benchmark articles are a specific, valued format. If you're comparing tools or methods, consider the Benchmark format rather than a standard Research article. Benchmark articles are among the most-cited papers in Genome Biology because the community uses them for tool selection.

3. Reviewer-visible software testing. For Software papers, reviewers are asked to install and test the software. Make sure your README is clear, your dependencies are documented, and your test data is included. A reviewer who can't install your tool in 30 minutes will give a negative review.

4. Transparent peer review option. Genome Biology offers transparent peer review where the reviewer reports, author responses, and editorial decision letters are published alongside the paper. It's opt-in but encouraged.

5. Preprint citation welcomed. Unlike some journals that are ambiguous about preprint citations, Genome Biology explicitly supports citing preprints and has a preprint-to-journal transfer pathway.

6. Methods must be reproducible. The journal has a strong emphasis on reproducibility. Provide enough methodological detail that another group could replicate your analysis. For computational work, this means sharing not just code but also the computational environment (Docker containers, Conda environments, or equivalent).

7. Community standards compliance. For specific data types, follow community standards: MINSEQE for sequencing experiments, MIAME for microarrays, FAIR principles for data management.

Frequent issues with Genome Biology submissions:

• Data not deposited in public repositories
• Code not on a public platform (or repo is private)
• Software papers without installation documentation
• Missing structured abstract headings (Background, Results, Conclusions)
• Reference format inconsistencies (mixing BMC and other styles)
• Genome browser screenshots at insufficient resolution
• Missing scale bars or labels on genomic visualizations
• "Data available upon request" instead of public deposition

For quick answers to the most common Genome Biology formatting questions, see the FAQ section at the top of this page.