CASRAI Dictionary

Tag: how to cite biorxiv

  • How to Cite bioRxiv: APA, Vancouver, EndNote

    How to cite bioRxiv in a reference list is straightforward once you know the rule: cite the preprint’s DOI, not a URL alone, mark it explicitly as unreviewed, and — if the content you consulted may differ from the current version — reference the specific version number. bioRxiv preprints receive a DOI (prefix 10.1101/) on posting and are, in the platform’s own words, “citable and part of the scientific record”, but they are not equivalent to a peer-reviewed journal article and most style guides require a disclaimer to say so.

    A preprint is a complete but not-yet-peer-reviewed manuscript posted to an open server — bioRxiv for biology, medRxiv for health sciences — so that findings can be shared, discussed and built upon before formal journal certification. This guide sets out the exact APA and Vancouver formats, how to handle multiple versions, journal-specific quirks, and how to configure EndNote and Zotero so the “not peer reviewed” flag survives into your final manuscript.

    What counts as a citable bioRxiv or medRxiv preprint?

    Every manuscript accepted onto bioRxiv or medRxiv is assigned a DOI at the point of posting, and, per bioRxiv’s own FAQ, “preprints deposited in bioRxiv should be cited using their digital object identifier (DOI)”. The platform is explicit that manuscripts “cannot be removed” once posted, because the DOI is indexed by Crossref, Google Scholar, Europe PMC and the Preprint Citation Index in Web of Science — meaning the preprint is a permanent, citable object regardless of whether it is later published in a journal.

    DOI structure changed part-way through bioRxiv’s history: DOIs assigned before 11 December 2019 use a short six-digit suffix (e.g. 10.1101/123456), while DOIs assigned from that date onward use a longer, date-based suffix (e.g. 10.1101/2023.07.03.123456). medRxiv, co-managed with bioRxiv by the non-profit openRxiv, uses the same 10.1101/ DOI prefix. Neither platform has an Impact Factor, because neither is a journal.

    How do you cite bioRxiv in APA style?

    APA 7th edition treats a preprint as an informally published work, so the citation must name the repository and flag the manuscript’s status in square brackets. There is no separate APA “preprint” reference category — you build it from the general work template.

    Element APA 7th edition rule
    Author Surname, Initials — as listed on the preprint
    Year Year of posting, in parentheses
    Title Italicised, sentence case
    Status flag [Preprint] in square brackets after the title
    Source Repository name (bioRxiv or medRxiv)
    Locator https://doi.org/10.1101/...

    Worked example, adapted from bioRxiv’s official citation model:

    Author, A. N., & Author, B. T. (2013). My article title [Preprint]. bioRxiv. https://doi.org/10.1101/2019.12.11.123456

    In-text citation follows the standard author-date form: (Author & Author, 2013). Do not cite the preprint’s landing-page URL in place of the DOI — the DOI is the stable, version-agnostic locator that Crossref and journal reference-checkers expect.

    How do you cite bioRxiv in Vancouver style?

    Vancouver style, the dominant convention in biomedical journals, follows National Library of Medicine (NLM) guidance for citing preprints, which explicitly reserves a field for the version number and a bracketed “[Preprint]” tag immediately after the title.

    Author FM, Author SM. Title of preprint. Version 2. bioRxiv [Preprint]. 2023 Jul 3 [cited 2026 Jul 3]. Available from: https://doi.org/10.1101/2023.07.03.123456

    In-text citation is numeric, in order of first appearance in the text — for example (1) or a superscript ¹. Journals that follow ICMJE’s Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work permit preprints in the reference list on the same condition APA and NLM apply: the entry must make unambiguous that the work has not been peer-reviewed.

    How do you cite a specific preprint version?

    Unlike a journal article, a preprint can be revised multiple times under one unchanging DOI. If the substance of your citation depends on data, figures or conclusions that changed between versions, cite the version you actually used, not just the DOI.

    • bioRxiv’s own convention: append the version-specific URL — e.g. doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2.
    • APA: add (Version 2) after the title, before the [Preprint] tag.
    • Vancouver/NLM: insert Version 2. as its own sentence element between the title and the repository name.
    • New manuscript vs revision: a genuine revision keeps the same DOI; a substantially different follow-up manuscript is assigned a new DOI and must be treated as a separate reference.

    If a preprint has since been formally published, cite the published version of record wherever possible — bioRxiv automatically links the published article to the preprint page within roughly two weeks of publication, and most journals require you to switch the citation once that link exists.

    How do you handle bioRxiv and medRxiv in EndNote and Zotero?

    Reference managers diverge sharply on preprint support, which is the step most researchers get wrong even after they have the correct written format.

    Zotero has offered a dedicated Preprint item type since 2019, with discrete fields for Repository, DOI and Archive ID — importing a bioRxiv record via its DOI or the browser connector populates these automatically, and the “not peer reviewed” status is preserved in the item type itself rather than relying on free text.

    EndNote has no equivalent native preprint type in most current libraries. The practical workaround is:

    1. Create the reference as Unpublished Work or Journal Article, whichever your output style maps most cleanly to a preprint field set.
    2. Enter “bioRxiv” or “medRxiv” as the publisher/journal field, and paste the full DOI (not the landing-page URL) into the DOI field.
    3. Add “Preprint, not peer reviewed” to the Notes or Type of Work field so it survives into any custom output style you build.
    4. If you cite a specific version, record it in the Edition or Notes field, since EndNote has no dedicated version field for preprints.

    Whichever manager you use, verify the exported reference against the APA or Vancouver template above before submission — auto-generated preprint references are the most common source of missing DOIs and dropped “[Preprint]” tags in manuscript reference lists.

    Frequently asked questions

    Is it okay to cite bioRxiv?

    Yes. bioRxiv states that manuscripts posted to the server “receive DOIs and thus are citable and part of the scientific record.” Citing is acceptable across most disciplines and funders, provided the reference clearly discloses that the work is a preprint and has not completed peer review.

    Does bioRxiv have a DOI?

    Yes. Every preprint deposited on bioRxiv is assigned a DOI under the 10.1101/ prefix at the point of posting, and this DOI remains stable across revisions of the same manuscript, resolving by default to the latest version.

    Is bioRxiv considered published?

    No. bioRxiv preprints are not formally “published” in the peer-reviewed sense — they have not been certified, edited or typeset by a journal. They are nonetheless a permanent, indexed part of the scientific record and cannot be withdrawn from the server once posted, only marked as withdrawn.

    Can I cite a preprint in my paper?

    Yes, in most journals and grant applications. Guidance aligned with ICMJE recommendations and publisher policy (e.g. Springer Nature) requires the reference to carry a “[Preprint]” note, the DOI, and standard bibliographic details, so readers cannot mistake it for a peer-reviewed source.

    What this means for authors, editors and institutions

    Funders have moved from tolerating preprint citation to actively encouraging it: the US National Institutes of Health states that it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and NIH-funded preprints are indexed directly in PubMed. That policy signal, combined with Crossref and Europe PMC indexing, means a correctly formatted preprint citation is no longer a stylistic afterthought — it is a discoverability and compliance requirement.

    Research offices, editors and reference-management teams should standardise on three checks before submission: the DOI (not a bare URL) is present, the cited version matches the version consulted, and the “[Preprint]” disclaimer appears in the visible reference text, not only in a database field. As preprint volume grows, these checks keep a reference list accurate and consistent with the style guide a target journal enforces.

  • bioRxiv Preprint DOI: How Versions Are Cited

    Every bioRxiv and medRxiv preprint receives a single, permanent DOI that stays constant across all revisions — the DOI always resolves to the newest version, and a specific version (v1, v2, v3) is cited by appending the version number to the DOI-based URL, not by requesting a new identifier.

    A bioRxiv preprint DOI is a Crossref-registered digital object identifier assigned to a manuscript once openRxiv’s screening team approves it for posting, and it serves as the manuscript’s permanent citation handle for the life of the record. Understanding how that identifier behaves across revisions — and how it eventually connects to a journal’s version of record — is essential for anyone citing, tracking, or administering preprint outputs.

    What is a bioRxiv preprint DOI?

    A bioRxiv or medRxiv DOI is issued the moment a submission clears openRxiv’s screening process, which bioRxiv’s Submission Guide states typically takes 24–72 hours. The identifier is deposited with Crossref, the DOI registration agency used by both servers, and it is what makes a preprint “citable and part of the scientific record” rather than a private working draft.

    Since December 1, 2025, all newly posted bioRxiv and medRxiv articles use the prefix 10.64898, replacing the legacy 10.1101 prefix used throughout the Cold Spring Harbor Laboratory (CSHL) era. According to openRxiv’s own explainer, published November 18, 2025, articles posted before that date keep their existing 10.1101 DOIs unchanged — nothing needs to be re-cited or updated by authors or readers; only new submissions carry the new prefix.

    The DOI suffix is not arbitrary. Since December 11, 2019, it has embedded the date the author approved the submission for posting (e.g., 2026.01.01.123456), which lets a reader estimate an article’s age directly from the citation string, much as a volume and year do for a journal article. DOIs assigned before that date used a simple six-digit suffix instead.

    How do bioRxiv and medRxiv assign DOIs across versions?

    openRxiv assigns exactly one DOI per article, and that single DOI covers every subsequent version. When an author submits a revision, the new version posts under the same DOI; the identifier’s landing page always resolves to the most recent version, while earlier versions remain permanently accessible via the article’s Info/History tab.

    This is a deliberate design choice, not a technical limitation. openRxiv has stated that “opinions differ on whether each version of a preprint should have its own DOI,” and different repositories take different approaches — but for bioRxiv and medRxiv, version-specific DOIs are not issued. A revision is only assigned a brand-new DOI if its content has changed so substantially that the author submits it as an entirely new manuscript rather than a revision.

    Because Crossref registration is not instantaneous, a newly posted preprint’s DOI URL can take up to 24 hours to resolve. During that narrow window, linking directly to the bioRxiv or medRxiv article page — rather than the DOI — is the more reliable option for time-sensitive sharing.

    Attribute Detail
    Current DOI prefix (from 1 Dec 2025) 10.64898
    Legacy DOI prefix (CSHL era, pre-Dec 2025) 10.1101
    Suffix format (post 11 Dec 2019) YYYY.MM.DD.###### — embeds author-approval date
    DOIs per article One; always resolves to the latest version
    Version-specific citation Append version number to the article URL, e.g. …/10.1101/2019.12.11.123456v2
    bioRxiv ISSN (electronic) 2692-8205 (NLM Catalog / ISSN Portal)
    medRxiv launch June 2019, spun off from bioRxiv for clinical and health-science research
    Registration agency Crossref

    How do you cite bioRxiv v1 vs v3 correctly?

    Because a single DOI serves every version, citing “v3” requires more than the bare DOI. bioRxiv’s own FAQ gives the format directly: cite the DOI, then append the version-specific URL if a particular version matters to the claim being made.

    The standard citation format is: Author AN, Author BT. Year. Title. bioRxiv doi: 10.1101/2019.12.11.123456. To pin the citation to version 2 specifically, this becomes: doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2. The same logic applies to medRxiv and to articles carrying the newer 10.64898 prefix.

    Version specificity matters most when:

    • A reviewer or reader needs to see exactly what was public at the time a claim was made or a decision was taken
    • An earlier version contained results, figures, or conclusions later revised or retracted
    • A funder, journal, or regulator requires a dated, auditable snapshot of the manuscript (relevant to research administration compliance workflows)

    Most citations across preprint servers are not version-specific — the majority of preprints only ever have a single version — so appending a version tag is the exception, applied only when precision genuinely matters. The National Institutes of Health (NIH) explicitly encourages citing preprints in grant applications, stating in its policy on Reporting Preprints and Other Interim Research Products that it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work.”

    How does the preprint DOI link to the published journal article?

    When a preprinted manuscript is subsequently accepted by a journal, openRxiv’s matching algorithms detect the connection and update the preprint’s Crossref DOI metadata to point to the journal article’s DOI. This link typically appears within approximately two weeks of formal journal publication, and the corresponding author receives a confirmation request by email.

    This bidirectional metadata relationship is what allows citation trackers, institutional repositories, and CRIS systems to treat the preprint and the published article as related outputs of the same research rather than duplicate records. Ideally the journal’s own DOI record reciprocally references the preprint, though bioRxiv’s FAQ notes this does not always happen in practice — a gap that research administrators should check for when auditing an author’s output list.

    A related, often underappreciated fact: roughly two-thirds of bioRxiv preprints go on to be published in a peer-reviewed journal, according to meta-research published in eLife (Abdill & Blekhman, 2019) — meaning the DOI-linking mechanism is relevant to the majority of postings, not a rare edge case.

    Common questions about bioRxiv and medRxiv DOIs

    Does bioRxiv have a DOI?

    Yes. Every bioRxiv and medRxiv preprint is assigned a DOI registered with Crossref once it clears screening. This makes preprints citable and part of the permanent scientific record, indexed by Google Scholar, Crossref, Semantic Scholar, Europe PMC, and the Preprint Citation Index in Web of Science.

    How do you cite a bioRxiv preprint?

    Cite the author list, posting year, title, and the DOI — for example, “bioRxiv doi: 10.1101/2019.12.11.123456.” To cite a specific version, append the version-specific URL after the DOI, following the format published on bioRxiv’s official FAQ page.

    Is it okay to cite bioRxiv preprints?

    Yes, with a caveat: bioRxiv states plainly that manuscripts “receive DOIs and thus are citable,” but they are not peer-reviewed at the time of posting. Readers and citers should note the preprint status explicitly and check whether a peer-reviewed version now exists before relying on it as a final source.

    Do all preprint versions have their own DOI?

    No. openRxiv assigns one DOI per article, shared by every revision. The DOI resolves to the newest version by default; earlier versions stay accessible through the article’s history tab and are cited by adding a version tag to the URL, not by obtaining a separate identifier.

    Why this matters for research administrators

    For institutions managing CRIS records, REF-style output audits, or funder compliance reporting, the DOI-prefix transition and the single-DOI-per-article model both have practical consequences. Output lists built before December 2025 will show 10.1101 DOIs; anything posted afterward will show 10.64898 — both are equally valid, permanent identifiers, and neither supersedes the other. Automated deduplication or metadata-harvesting scripts that pattern-match on the “10.1101” prefix should be updated to also recognise 10.64898, or they risk silently dropping newly posted preprints from institutional repositories.

    The version-tracking model also has implications for research integrity workflows: because withdrawal notices and corrections are recorded against the same DOI rather than issued as a new identifier, institutions monitoring compliance should check an article’s Info/History tab — not just its DOI — before citing it in a report. As preprints continue to be formally recognised in NIH and UKRI reporting frameworks, treating the DOI as a static citation string, disconnected from its version history, is no longer sufficient practice for accurate scholarly record-keeping.

  • Does bioRxiv Count as a Publication? A Guide for Tenure and Promotion Committees

    Does bioRxiv count as a publication? No — not on its own. A bioRxiv preprint is a citable, DOI-registered scientific manuscript that has not been through peer review, and bioRxiv’s own FAQ states plainly that the server “is not a journal so it has no Impact Factor.” Tenure and promotion (P&T) committees should treat it as a genuine, citable research output — evidence of productivity, priority, and open-science practice — but list and weigh it separately from peer-reviewed publications.

    A preprint is a complete scientific manuscript that authors make publicly available before, or independently of, certification by journal peer review.

    What Is a bioRxiv Preprint?

    bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by the non-profit openRxiv. Manuscripts are screened for plagiarism and inappropriate content but are posted online within roughly 72 hours, without editorial peer review, copyediting, or typesetting.

    Every posted manuscript receives a Crossref-registered DOI, which is what makes it citable and part of the permanent scientific record. bioRxiv preprints are indexed by Google Scholar, Crossref, Europe PMC, Semantic Scholar, and the Preprint Citation Index connected to the Web of Science; preprints reporting NIH-funded research are also indexed in PubMed.

    Because it distributes preprints rather than certified, edited articles, bioRxiv does not carry an ISSN — the identifier reserved for ongoing serial (journal) publications. There is no equivalent of a “bioRxiv issue” or “bioRxiv volume”; each preprint stands alone under its own DOI, which is the correct locator to use in citations, CVs, and grant applications.

    Does bioRxiv Count as a Formal Publication?

    No. bioRxiv’s FAQ is direct on this point: preprints “have not been finalized by authors, might contain errors, and report information that has not yet been accepted or endorsed in any way by the scientific or medical community.” A preprint is a manuscript in circulation, not a certified publication.

    This has two immediate, practical consequences for committees:

    • No journal metrics apply. bioRxiv has no Impact Factor because it is not a journal — the metric does not exist for it, and any “bioRxiv impact factor” figure circulating online is not authoritative.
    • No peer-review certification exists unless a journal or independent review service has posted its reviews alongside the preprint via bioRxiv’s public review dashboard, which some — but not most — preprints carry.

    The distinction matters most in biomedical fields, where the International Committee of Medical Journal Editors (ICMJE) recommends that journals not treat prior posting on a recognised preprint server as prior publication that would bar later submission — preprints and journal articles are understood as different stages of the same research, not competing outputs.

    Criterion bioRxiv preprint Peer-reviewed journal article
    Peer review None (screening only) Completed by journal referees
    Persistent identifier DOI (Crossref) DOI (Crossref)
    ISSN Not applicable Carried by the journal
    Impact Factor None — not a journal May apply, per journal
    Citable and indexed Yes — Google Scholar, Crossref, Europe PMC Yes, plus journal-specific indexes
    Counts as REF output (UK) Not an eligible output type alone Yes, as version of record or AAM

    How Should Research Offices and P&T Committees Weigh Preprints?

    Institutional guidance is converging on a middle position: preprints are legitimate, citable evidence of research activity, but they are not substitutes for peer-reviewed publication in a promotion dossier. The San Francisco Declaration on Research Assessment (DORA) recommends that institutions “value the full range of research outputs” and stop leaning on journal-level metrics as a proxy for quality — a principle that supports counting preprints as evidence of output, provided their unreviewed status is disclosed, not concealed.

    Funder policy reinforces this. The US National Institutes of Health states that it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and explicitly permits citing preprints in grant applications and progress reports.

    In the UK, the position is narrower for one specific purpose: the Research Excellence Framework (REF) requires submitted outputs to be the version of record or the author’s accepted manuscript of a peer-reviewed work. A bioRxiv preprint is not, by itself, an eligible REF output type — it can evidence timeliness and priority in a narrative CV, but the REF-returnable output remains the eventual peer-reviewed article.

    These decisions typically sit with the research administration office coordinating the promotion dossier, working alongside the candidate and department. Research offices advising P&T committees should:

    1. Confirm whether the department’s or institution’s promotion policy names preprints explicitly, rather than assuming silence means exclusion.
    2. Ask candidates to separate preprints from peer-reviewed publications on the CV, never blend the two lists.
    3. Treat preprint citation counts and altmetrics as supplementary evidence of impact, not a replacement for peer-review certification.
    4. Check REF, funder, and journal eligibility rules before assuming a preprint alone satisfies an output requirement.

    How to Cite and List bioRxiv Preprints

    bioRxiv’s own citation guidance is the authoritative format: cite the preprint using its DOI, in the style Author AN, Author BT. Year. Title. bioRxiv doi: 10.1101/xxxxxx. If a specific version needs citing, add the version-specific URL alongside the DOI, since revisions post under the same DOI but remain individually accessible in the article’s version history.

    On a CV or narrative CV, best practice is to follow the same disclosure standards used for other authorship and contribution records:

    • Create a clearly labelled “Preprints” or “Working Papers” heading, separate from “Peer-Reviewed Publications.”
    • Include the DOI for every entry, since bioRxiv preprints are permanently archived (via Portico) and citable indefinitely, even if later withdrawn.
    • Note the eventual journal placement once available — bioRxiv automatically links a preprint to its published version within about two weeks of journal publication.
    • In funding applications, cite preprints exactly as NIH and comparable funders permit: as interim research products, with the DOI as the locator.

    bioRxiv preprints cannot be withdrawn from the record once posted; authors may only append a formal withdrawal statement, and the original manuscript stays accessible. This permanence is precisely why the DOI, not the manuscript title alone, is the correct and durable citation anchor for any P&T dossier.

    Preprint FAQs for Promotion Committees

    Is bioRxiv considered published?

    No. bioRxiv preprints are unpublished manuscripts distributed before or independent of journal peer review. They carry a DOI and are part of the citable scientific record, but bioRxiv itself states they have not been “accepted or endorsed” by the scientific community through peer review.

    Can you cite a bioRxiv paper?

    Yes. Every bioRxiv preprint receives a Crossref DOI, making it citable in manuscripts, CVs, and grant applications. The NIH explicitly permits citing preprints in funding applications as interim research products, and most journals now accept prior preprint posting.

    What qualifies as a publication?

    A formal publication is a manuscript that has completed editorial peer review and been accepted, edited, and released by a journal or publisher, typically carrying an ISSN (journal) and article DOI. A preprint, lacking peer review, does not meet this threshold on its own.

    Is bioRxiv a journal?

    No. bioRxiv is a preprint archive and distribution service operated by the non-profit openRxiv, not a journal. It has no editorial board issuing acceptance decisions and, per its own FAQ, “no Impact Factor” because that metric applies only to journals.

    For promotion committees, the practical takeaway is definitional discipline: a bioRxiv preprint is real, citable, DOI-anchored research evidence — but it is not a peer-reviewed publication, has no Impact Factor or ISSN, and should be evaluated on its own terms, alongside institutional, funder, and (in the UK) REF-specific rules, rather than folded silently into a publication list.