Genome Biology Formatting Requirements: Complete Author Guide

Genome Biology requires a structured abstract for Research articles; Methodology, Software, Database, Brief Report and Review abstracts are unstructured and limited to 100 words.

The three-part Research abstract structure (Background, Results, Conclusions) has no Methods section, so the Results section of the abstract should briefly mention the approach before presenting findings. Software abstracts are unstructured and limited to 100 words, so say what the tool does and how it performs in a few sentences.

A 250-word Research abstract still leaves room to include specific quantitative results. 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 publishes no figure cap for Research articles, and additional files can carry supplementary data.

Figure requirements:

Table requirements:

• Format tables with the Table object function of your word processing program, not as figures or spreadsheet files

• Number tables and cite them in sequence (Table 1, Table 2)

• Table titles up to 15 words above the table and legends up to 300 words underneath

• Color and shading may not be used

• 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 Vancouver reference style, with numbered references.

In-text citations: Numbered, following the Vancouver examples in the journal's instructions.

Reference list format (worked example, with the common wrong form shown for contrast):

Correct (BMC/Vancouver): Smith AB, Jones CD, Brown EF. A comprehensive atlas of chromatin accessibility in human tissues. *Genome Biol.* 2025;**26**:42.
Wrong (APA preset most reference managers default to): Smith, A. B., Jones, C. D., & Brown, E. F. (2025). A comprehensive atlas of chromatin accessibility in human tissues.

Genome Biology, 26, 42.

The difference is what trips auto-exported bibliographies: BMC writes "Smith AB" with no commas or periods inside the name, abbreviates the journal per NLM, and uses the volume:article-number form; the APA form your reference manager exports by default uses "Smith, A. B." and is wrong for Genome Biology.

Key formatting rules:

• Journal abbreviations follow Index Medicus/MEDLINE

• Volume, colon, article number (or page range)

• Dataset references include an accession number or unique identifier such as a DOI

• For books: Smith AB, Jones CD. Title of Book. City: Publisher; Year.

• For preprints: Include the preprint server, DOI, and year

Genome Biology allows citing work that is available through public preprint servers, and BMC editorial policy shows how preprints may be cited in a reference list. If you're citing work posted on bioRxiv or medRxiv, one workable format is:

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

Genome Biology publishes no reference cap for Research articles. Reviews can cite up to 200 references.

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 describes its own policy as a very strict open access, open source and open data policy:

• Sequencing data: BMC mandates deposition of genomic data in a public access repository upon submission; novel DNA, RNA and genome assembly data go to INSDC repositories (for example ENA, SRA or DDBJ) or those working towards INSDC inclusion

• Other datasets: Datasets on which the conclusions rely should be deposited in public repositories (where available and appropriate) or presented in the manuscript or additional files, in machine-readable format

• Code: Source code for in-house scripts must be deposited in a public repository or included in the supplementary materials

• Software tools: Source code for tools described in Methodology or Software articles should be deposited in a public repository with an OSI-compliant license, with the access information and license stated in the manuscript

• Versioned code releases: A static deposition of the described version in a repository that assigns DOIs, cited in the manuscript, is recommended

The Availability of data and materials section is mandatory in every manuscript. Genome Biology expects datasets to be deposited rather than offered on request; its statement templates keep on-request and restricted-access wording for data that cannot be shared publicly, with the conditions for access stated. If your study uses third-party or previously published data, that data must also be available as a condition of publication.

For software papers specifically, the source code must be in a public repository with an OSI-compliant license, and BMC asks that previously unreported software be available for testing by editors and reviewers in a way that preserves their anonymity. Make sure it installs and works as described.

Both are accepted through the Springer Nature submission system linked from the journal's submission guidelines.

Word submissions:

• Standard formatting: double-spaced, line numbers, page numbers

• Figures uploaded in the order they are first mentioned, with multi-panel figures as a single composite file

• Tables under one page can sit in the manuscript; longer tables can go at the end of the document text file

LaTeX submissions:

• The journal encourages the Springer Nature LaTeX template

• A PDF of your manuscript files is compiled during submission using pdfLaTeX and TexLive 2021

• Upload all relevant editable source files; missing source files delay production

The genomics and computational biology community has a strong LaTeX contingent. 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.

Data and code must be public by publication. This isn't a polite suggestion. Third-party or previously published data used in the study must be available as a condition of publication, and BMC mandates that data of the types it lists be released to the public on publication. Start the deposition process at submission, not after acceptance.

There is no separate Benchmark article type. If you're comparing tools or methods, check the article types in the submission guidelines and ask the editors through a presubmission enquiry which one fits.

Reviewer-visible software testing. BMC asks that previously unreported software be available for testing by editors and reviewers in a way that preserves their anonymity. Make sure your README is clear, your dependencies are documented, and your test data is included. A reviewer who can't install your tool is likely to say so.

Transparent peer review is permanent policy. In a November 2018 editorial the journal announced that after 1 January 2019 all submissions would be reviewed transparently, with reviewer reports published anonymously alongside the article; recent articles also show the author comments. If your paper is accepted, your reviewer correspondence is likely to be published. Write your responses accordingly.

Preprints are allowed. BMC editorial policy says posting a preprint is not considered prior publication and that preprints may be cited in a reference list; Genome Biology is also an affiliate journal of the Review Commons preprint peer review platform.

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).

Restrictive code licenses create friction. For tools described in Methodology or Software articles, Genome Biology asks for source code in a public repository with an OSI-compliant license, and its Availability section for software asks you to state any restrictions on use by non-academics. If your institution requires a restrictive license, resolve that before submitting rather than during production.

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

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

Tool or software papers without real-data evidence. Genome Biology's criteria for Methodology and Software articles ask for a clear advance over existing tools in a side-by-side demonstration, benchmarked on synthetic or ground-truth data where possible, with utility shown on real data. A new alignment algorithm or peak caller that shows impressive speed and accuracy on simulated reads only is at risk of desk rejection if the paper does not show what the tool does on real data.

The journal says such an article need not provide novel biological insights, but a real biological application can help to show the method's utility. For new tools, lead with the demonstrated advance, then explain the method that made it possible.

Non-commercial or restrictive code license. For tools described in Methodology or Software articles, Genome Biology asks for source code in a public repository with an OSI-compliant license, and the access information and license must be clearly stated in the manuscript. Licenses that restrict commercial use, such as CC BY-NC or academic-only licenses, generally do not satisfy the Open Source Definition behind that request. If your institution's technology transfer office is involved in the license, begin that conversation at submission, not at acceptance.

Specialist findings without demonstration of broad relevance to the genomics community. Genome Biology competes with Nature Genetics and Genome Research for the highest-impact genomics papers. The editors apply a "who cares?" filter at the desk: would a researcher working on a different organism, tissue, or disease model find this result meaningful? A study that identifies a novel chromatin remodeler in a specific cell type must make the case that the mechanism is broadly relevant. Papers that read as specialist characterization without broader biological implications are returned before review.

Data or code not deposited at submission. BMC mandates that genomic data such as nucleic acid sequences be deposited in a public access repository upon submission, available to editors and reviewers during peer review and released to the public on publication. "Data will be deposited upon acceptance" does not meet that policy. For sequencing data, this means repository accession numbers (with private reviewer access if the data are not yet public) should be in the manuscript when you submit. For code, BMC asks that it be archived in a repository with a DOI or other unique identifier, and recommends Zenodo for software on GitHub, so a GitHub URL pointing to a private or under-construction repository is not sufficient. The journal also says submissions received without the elements of the BMC Minimum Standards of Reporting Checklist may be returned to the authors as incomplete.

A Genome Biology pre-submission readiness check evaluates whether your manuscript meets the data availability, code licensing, and scope requirements before submission.

This page uses Genome Biology's Springer Nature submission guidelines, article-type guidance, figure and table preparation rules, data/code availability instructions, Clarivate JCR metrics, SciRev community timing reports, and Manusights pre-submission review patterns from genomics and computational biology manuscripts.

This page is for authors checking the manuscript package before upload; the Genome Biology submission guide, review-time page, APC page, and journal profile cover venue fit and logistics.

The failure pattern we see is treating data and code availability as a production task. For Genome Biology, accession numbers, archived code, licenses, and installability are part of formatting readiness. If those pieces are not ready, the manuscript can look polished and still be unready for submission.