Tag: biorxiv preprint doi

  • How bioRxiv Versioning Works (v1, v2, v3)

    bioRxiv versioning works by assigning every preprint a version number starting at v1 on first posting; authors can submit revisions at any time before journal acceptance, each becoming v2, v3 and so on under the same DOI, with every prior version preserved and independently citable via the “Info/History” tab. Unlike a journal correction process, there is no editor gatekeeping a revision, and nothing is ever deleted from the record.

    A bioRxiv version is a distinct, permanently archived snapshot of a preprint’s PDF, HTML and XML files, numbered sequentially (v1, v2, v3…) and linked to one persistent DOI that never changes across revisions. Understanding this versioning system — what triggers a new version, what stays fixed, and how to cite a specific one — matters for authors tracking revision history and readers who need to know exactly which version of a claim they are reading.

    What happens when a preprint first posts as v1?

    When a manuscript clears bioRxiv’s screening process — typically within 72 hours of submission, according to bioRxiv’s own FAQ — it is posted as version 1 (v1). The PDF appears first; full-text HTML and XML conversion follows 24–48 hours later.

    Each version, from v1 onward, is independently available in PDF, HTML and XML — the XML format exists for text-mining and machine-readable indexing, a detail most competing explainers omit. Once v1 is live, it is immediately assigned a DOI (via Crossref) and indexed by Google Scholar, Europe PubMed Central and the Preprint Citation Index connected to Web of Science: v1 is citable and part of the permanent scientific record from the moment it posts, not a provisional draft.

    How do authors submit a v2 or later revision?

    Authors submit revisions through the “Submit a Revision” option in their bioRxiv Author Area, locating their existing submission ID and selecting “Submit a revised manuscript.” bioRxiv’s policy states a manuscript “can be revised at any time until it is published in a journal” — there is no fixed revision window and no limit on the number of versions.

    The revision mechanism is intended for substantive changes: new datasets, re-analyses, expanded discussion, or additional supplemental information. A revision is posted under the same DOI, and — critically — the prior version is not overwritten. It remains permanently accessible through the article’s Info/History tab, so a reader can always compare what changed between v1 and v2, or v2 and v3.

    One detail rarely covered elsewhere: if a preprint was originally submitted indirectly via a journal’s own pipeline (journal-to-bioRxiv, or “J2B”), the corresponding author must first register a bioRxiv account using the same email address used at journal submission before they can access the Author Area to file a revision.

    Does the DOI change between versions, and how do you cite one?

    The DOI stays fixed across every version of a bioRxiv preprint. v1, v2 and v3 of the same manuscript all resolve through one DOI — a reader following an older citation lands on whatever version is current, with the option to step back through history.

    To cite a specific version rather than “whatever is current,” bioRxiv appends a version-specific URL to the DOI. Its FAQ gives this exact pattern:

    Element Format Example
    Standard DOI citation doi: 10.1101/[identifier] doi: 10.1101/2019.12.11.123456
    Version-specific citation DOI + version-specific URL doi: 10.1101/2019.12.11.123456 version 2, https://www.biorxiv.org/content/10.1101/2019.12.11.123456v2

    This matters for reference managers such as EndNote: the DOI field should carry the persistent identifier, while the version number belongs in the URL or a note field if the citing author wants to pin the exact revision read, rather than whichever version happens to be live later.

    One exception: if a revision alters the manuscript so substantially that bioRxiv considers it a genuinely different article, the author must submit it as a new manuscript — which receives its own, separate DOI rather than becoming v2 of the original.

    What does NOT require a new version?

    Three specific cases are worth flagging because they trip up first-time bioRxiv authors and are absent from most general explainers:

    • Metadata typos. If the title, author names, affiliations or abstract in the submission form contain an error but the PDF is correct, bioRxiv auto-replaces the site metadata with text extracted from the PDF within roughly 48 hours — authors are told not to submit a full revision solely to fix this.
    • Author name changes. bioRxiv permits a “silent” first/last name update — for example after a legal name change — by direct email request, without a new version or correction notice. This excludes author removal or reordering, which need a standard revision.
    • Supplemental-file-only changes. If only supplemental files change, bioRxiv still requires them submitted together with the article file as part of a new version; a supplemental-only upload cannot be filed alone.

    What happens if an author withdraws a preprint?

    bioRxiv preprints cannot be deleted once posted, because each version carries a DOI and is indexed externally by Google Scholar and Crossref, creating a permanent footprint independent of bioRxiv’s own servers. If authors no longer stand behind their findings, the remedy is a formal withdrawal, not removal.

    To withdraw, the corresponding author uses “Submit a Withdrawal Statement” inside the same Author Area used for revisions. A withdrawal adds a “Withdrawn” watermark to the PDF of every version ever posted and posts an explanatory statement on the article page — but the original manuscript remains viewable via the Info/History tab. It is a labelled correction, not an erasure. bioRxiv notes outright removal happens only in “extremely rare cases,” for legal or safety reasons.

    Once a preprint is published in a peer-reviewed journal, no further author action is usually needed: bioRxiv automatically adds a link to the published version within approximately two weeks, and all preprint versions — v1 through the final revision — remain live alongside it.

    Common questions about bioRxiv versioning

    Can I upload a new version or replace a bioRxiv preprint?

    Authors cannot replace or delete a posted version, but they can add a new one. Using “Submit a Revision” in the Author Area at any point before journal acceptance creates the next sequential version (v2, v3…) while every earlier version stays permanently visible in the Info/History tab.

    Why does bioRxiv take so long to post a new version?

    Both initial posting and revisions go through the same screening step, which usually completes within 72 hours. Delays typically occur over weekends or holidays, or when a submission needs extra scrutiny for scope, plagiarism or safety-related content before the new version is approved.

    Does bioRxiv count as published once it has multiple versions?

    No. Additional versions do not confer peer-reviewed status. bioRxiv is explicit that it “is not a journal” and has no Impact Factor; every version, however many revisions deep, carries the standard disclaimer that the content has not been certified by peer review.

    Are previous bioRxiv versions still readable after a revision posts?

    Yes. Every prior version remains permanently accessible through the Info/History tab on the preprint’s landing page after a new version is submitted, so readers can compare v1 against later revisions rather than losing access to earlier text.

    Implications for research administrators and institutions

    For institutions tracking preprint outputs in repository or CRIS systems, the persistent-DOI-plus-version model means a single DOI can legitimately correspond to several distinct texts over time. Metadata harvesting workflows that snapshot “the” abstract or author list at ingestion risk becoming stale if a later version changes those fields — administrators should record which version number was harvested, not just the DOI.

    For funders, the NIH has stated it “encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work,” and preprints of NIH-funded studies are indexed in PubMed regardless of version count. Citing the version actually reviewed — using the version-specific URL pattern above — gives reviewers an unambiguous audit trail rather than a moving target.

    As preprint volume grows, the version history itself is becoming part of the evidentiary record: it documents how a finding evolved in response to community comment before formal peer review.

  • bioRxiv Link to Published Paper: What the New Linkage Dataset Shows

    A bioRxiv link to published paper is created automatically, usually within two weeks of journal publication, once bioRxiv’s matching system confirms that the preprint and the paper share a title, author list, and DOI. A newly published dataset, PreprintToPaper, has now mapped this process across 145,517 bioRxiv preprints, showing exactly how long that journey takes and how much the underlying science changes along the way.

    The PreprintToPaper dataset is an openly available metadata collection — created by researchers Fidan Badalova, Julian Sienkiewicz, and Philipp Mayr and published in Scientific Data in 2026 — that connects bioRxiv preprints to their eventual journal publications using automated title-similarity, author-similarity, and DOI matching.

    What is the PreprintToPaper dataset?

    PreprintToPaper is a metadata dataset covering 145,517 bioRxiv preprints across two periods: 34,246 preprints from 2016–2018 (pre-pandemic) and 111,271 from 2020–2022 (pandemic era). Records were built by querying the bioRxiv API for preprint metadata and the Crossref API for journal-publication metadata, then linking the two sets algorithmically.

    The dataset sorts every preprint into one of three categories:

    Category Definition Count Share
    Published Formally linked to a journal article on bioRxiv, with a DOI to the version of record 90,614 62.3%
    Preprint Only No matching journal publication identified 35,813 24.6%
    Gray Zone Highly likely published, based on title and author matching, but with no DOI link recorded on bioRxiv 19,090 13.1%

    The Gray Zone category is the dataset’s key methodological contribution. Earlier work — including Abdill and Blekhman’s 2019 analysis in eLife, cited via PubMed Central, which found 42.0% of 15,797 sampled bioRxiv preprints had been formally linked to a published version — relied only on bioRxiv’s own DOI links. PreprintToPaper shows that a further 13.1% of preprints were very likely published but never picked up by that automatic link.

    How does bioRxiv link a preprint to its published paper?

    bioRxiv’s own linking mechanism is largely automatic. According to bioRxiv’s official FAQ, the platform “will usually automatically add a link to the published version within approximately two (2) weeks of journal publication,” after which the corresponding author receives a confirmation email.

    Matching fails occasionally — usually when the title, author list, or venue changes substantially between versions. bioRxiv advises authors to wait two to three weeks after publication before contacting staff directly if no link appears. PreprintToPaper formalises this same matching logic for research purposes, using:

    • A title-similarity score (via Python’s SequenceMatcher, measuring longest common subsequence) with a 0.75 threshold for a probable match;
    • An author-similarity score and an author-count difference to validate borderline cases;
    • Human annotation of 299 borderline records by two independent reviewers, reaching a Cohen’s kappa of 0.86 — a strong agreement level for a manual validation exercise.

    Records with an author-match score above 0.47 were used to reclassify apparent non-publications into the Gray Zone, which is what allows the dataset to correct for bioRxiv’s own linking gaps rather than simply repeating them.

    What publication delays does the dataset reveal?

    Publication rates were not stable across the study window. PreprintToPaper’s authors report that the confirmed publication rate ranged from 71% for preprints posted in 2016 down to 49% for those posted in 2022 — an apparent decline that is substantially narrowed once Gray Zone cases with an author-match score above 0.47 are counted as published rather than unlinked.

    This pattern is consistent with independent findings on preprint-to-publication timing. Earlier tracking studies of bioRxiv preprints reported a pre-pandemic median delay of around 166 days between posting and journal publication, while pandemic-era analyses of COVID-19 preprints found a much shorter median lag, reflecting accelerated peer review for urgent public-health findings. The apparent fall in 2022 publication rates most likely reflects a right-censoring effect — recent preprints simply have not yet had time to complete peer review and appear as “published” in the dataset’s snapshot — rather than a genuine drop in eventual publication.

    How much do titles and abstracts change before publication?

    PreprintToPaper stores both the initial submitted metadata and the final published metadata for each linked record — title, abstract, author list, journal name, and publication date — explicitly to support research on linguistic and structural change between preprint and published versions, including title reformulations and author-order shifts.

    This matters because bioRxiv’s own FAQ already flags a related, more mundane source of variation: metadata such as the manuscript title, author list, and abstract are initially supplied by the author at submission, then replaced with metadata extracted from the PDF once full-text HTML is generated — meaning small differences can appear even before any journal ever sees the paper. Distinguishing that housekeeping-level drift from substantive, peer-review-driven revision is precisely the analytical opportunity the new version-history subset unlocks, and is why the dataset’s authors built author-count-difference and title-similarity fields as first-class, machine-readable variables rather than leaving them buried in free text.

    Answer-first Q&A: common preprint-linkage questions

    For bioRxiv preprints, no manual action is normally required: bioRxiv’s system detects the journal publication and adds the link automatically, typically within two weeks of publication. If no link appears after two to three weeks, authors should contact bioRxiv staff directly so the match can be verified and added manually.

    Does bioRxiv count as published?

    No. A bioRxiv preprint is not peer-reviewed, edited, or certified by a journal, so it does not count as a formal publication. It is, however, a citable, DOI-bearing scholarly record that is indexed by Crossref, Google Scholar, Semantic Scholar, and Europe PMC, and NIH explicitly encourages citing preprints as interim research products.

    Can I cite a preprint in my paper?

    Yes. bioRxiv preprints should be cited by their DOI, in the format “Author AN, Author BT. Year. Title. bioRxiv doi: 10.1101/…”. If citing a specific revision, the version-specific URL should be added, since each preprint version remains permanently accessible under the same DOI.

    How do I update bioRxiv with a published paper if the automatic link fails?

    Authors should first wait two to three weeks past journal publication, since matching runs on a delay. If the link still has not appeared, the corresponding author should email bioRxiv staff or leave a comment on the preprint page; bioRxiv states it will verify all such requests before manually linking the record.

    What are the implications for institutions and publishers?

    For research administrators tracking outputs, PreprintToPaper’s Gray Zone category is a practical warning: relying solely on bioRxiv’s own “published” flag will undercount real publication rates by roughly 13 percentage points in this sample. Institutional repositories and research-information systems that harvest bioRxiv metadata directly should therefore treat unlinked-but-matched preprints as a distinct, reviewable category rather than as simply unpublished.

    For publishers and editors, the dataset’s version-history subset offers a reusable framework for auditing how much a manuscript’s core claims shift between preprint and version of record — separating genuine post-review revision from routine metadata clean-up. That distinction is directly relevant to authorship practice, where author-order and contributor-list changes between preprint and publication are common but rarely tracked systematically, and to broader definitional work maintained in the CASRAI Dictionary of scholarly-communication terms.

    The dataset itself, along with its code, is openly deposited on Zenodo, giving any institution the means to replicate or extend the analysis against its own output list rather than treating bioRxiv’s publication status as a black box.

  • bioRxiv Template: LaTeX & Word Formatting Guide

    A bioRxiv manuscript template is a formatting scaffold — in LaTeX or Word — that arranges title page, abstract, figures, and references to match bioRxiv’s posting system, but bioRxiv itself mandates no single template. Authors may submit a plain PDF, a Word file with separate figures, or a LaTeX-derived PDF built from one of several community templates. This guide walks through each formatting field so a manuscript is ready for upload on the first attempt, rather than repeating the general submission-guidelines overview already covered elsewhere on this site.

    bioRxiv is the preprint server for biology, operated by Cold Spring Harbor Laboratory, that posts unpublished research manuscripts after a basic screening step rather than peer review.

    Does bioRxiv Require a Specific Manuscript Template?

    No. bioRxiv’s own guidance states that it “does not require a particular article format/style,” and submission formats can therefore vary considerably between manuscripts. The bioRxiv Submission Guide describes the simplest route as uploading a single PDF containing the full text, figures, and tables.

    This absence of a mandatory template is precisely why community-built templates exist: authors want the discipline of a fixed structure — title page order, figure placement, reference formatting — even though bioRxiv will accept a manuscript without one. The trade-off is that a template also signals to co-authors and affiliates conducting screening that the manuscript is complete and properly ordered.

    Which LaTeX Template Should You Use for bioRxiv?

    For LaTeX users, Overleaf hosts several bioRxiv-tagged templates that compile directly to a submission-ready PDF. Two are widely used within the biology preprint community, and both descend from the same lineage: the HenriquesLab bioRxiv template, itself a modification of the PNAS journal template.

    The quantixed/manuscript-templates repository extends this further: a single manuscript source can generate either a typeset preprint layout (\documentclass[twocolumn]{bioRxiv}) or a line-numbered journal-submission layout (\documentclass[submit]{bioRxiv}) by commenting one line in a merge file, avoiding two parallel documents. It also adds native \orcidlink support so ORCID iDs render correctly on the title page.

    Template Format Platform Notable field-level feature
    arXiv/bioRxiv template LaTeX Overleaf General-purpose preprint layout with figure embedding
    HenriquesLab bioRxiv template LaTeX Overleaf PNAS-derived styling built specifically for bioRxiv
    quantixed/manuscript-templates LaTeX GitHub / Overleaf Switchable preprint vs. journal-submission layout; ORCID support
    chrelli/bioRxiv-word-template Word (.docx) GitHub Styled headings and figure captions for non-LaTeX authors
    finkelsteinlab/BioRxiv-Template Word (.docx) GitHub Reader-friendly layout aimed at readability over journal mimicry

    Whichever LaTeX template is used, the .tex source must still be compiled and converted to PDF before upload — bioRxiv’s submission system does not accept raw .tex files.

    Formatting a bioRxiv Manuscript in Word

    Authors who do not use LaTeX can format directly in Microsoft Word using a template such as the chrelli or finkelsteinlab bioRxiv templates on GitHub, both designed to visually approximate a typeset preprint while remaining fully editable. The practical field order to follow is:

    • Title page: full title, author list, institutional affiliations, ORCID iDs, and the corresponding author’s contact details.
    • Abstract: a single unstructured paragraph summarising rationale, method, and findings.
    • Main text: Introduction, Results, Discussion, and Methods — bioRxiv does not enforce a fixed section order, so discipline-specific conventions (e.g. Methods-first for some biology sub-fields) are acceptable.
    • Figures and tables: either embedded in-line at first citation or supplied as separate files.
    • Author Contributions: a statement of who did what, increasingly expressed using the CRediT contributor role taxonomy.
    • Competing interests and funding: brief declarations, matching journal norms.
    • References and, where applicable, a separate Supplementary Information reference list.

    On the Author Contributions field: CASRAI originated the CRediT contributor role taxonomy in 2014. The standard is now stewarded by NISO as ANSI/NISO Z39.104-2022, and mapping each author to a defined CRediT role gives the statement a machine-readable structure that a free-text sentence lacks.

    What File Formats and Figure Rules Does bioRxiv Require?

    bioRxiv’s accepted formats are narrower than they first appear, and mismatched file types are a common cause of upload failure.

    • Main text: PDF, Microsoft Word, or WordPerfect.
    • Figures and tables submitted separately: GIF, TIFF, EPS, or JPEG.
    • Supplemental files: posted largely as-is, so a wider range of file types is tolerated.
    • LaTeX source: must be compiled to PDF before submission; the system does not ingest .tex directly.

    bioRxiv also offers a print-friendly, in-line-figure PDF generated automatically from the full-text HTML of a posted preprint — a feature introduced in February 2022 specifically so readers are not limited to the author’s originally submitted figure placement.

    Article type matters as much as file type. bioRxiv categorises submissions as New Results, Confirmatory Results, or Contradictory Results; narrative reviews, commentaries, opinion pieces, and step-by-step protocols are not considered appropriate for the server. New manuscripts reporting clinical trial results must go to medRxiv instead of bioRxiv.

    How Does bioRxiv Assign a DOI, and How Should a Preprint Be Cited?

    Every bioRxiv preprint receives a Crossref DOI under the 10.1101/ prefix as soon as it clears screening and posts — no separate application step is required from the author. This DOI remains stable through subsequent revised versions of the same preprint.

    For citation, most style guides treat a bioRxiv preprint as a standard journal-style reference carrying a DOI instead of (or alongside) volume and page numbers; Wikipedia maintains a dedicated {{Biorxiv}} citation template for exactly this purpose. Once a preprint is later published in a peer-reviewed journal, citing conventions typically shift to the journal DOI, with the preprint DOI retained as a historical record of priority.

    Frequently Asked Questions About bioRxiv Submission

    Can anyone submit to bioRxiv?

    Yes. Any author may deposit a manuscript on bioRxiv provided it covers a relevant scientific field, is unpublished at the time of submission, and all co-authors have consented to its deposition. Authors must first register on the submission site before uploading a manuscript.

    How much does it cost to submit to bioRxiv?

    There is no fee to submit an article to bioRxiv. This distinguishes it from many journals’ article-processing charges and from some other preprint servers that levy optional support fees, making template correctness — not payment — the main barrier to a smooth first submission.

    Can you put a paper on bioRxiv after submitting it to a journal?

    Yes. A manuscript can be posted to bioRxiv at any point before a journal formally publishes it, and new revised versions can be posted at any time up to journal publication or assignment of a journal DOI, provided the target journal’s own preprint policy permits it.

    When should you submit to bioRxiv?

    There is no fixed submission window: a manuscript can go to bioRxiv at any stage before journal publication, including alongside or ahead of journal submission. Once a paper has already been formally published by a journal, it can no longer be submitted to bioRxiv.

    What This Means for Authors and Institutions

    The lack of a mandatory bioRxiv template shifts formatting risk onto the author rather than the platform. Choosing a maintained LaTeX template, such as one built to switch between preprint and journal-submission layouts, or a Word template with pre-styled headings, reduces reformatting work twice: once for the preprint and again when the manuscript is later reshaped for a target journal.

    For research offices and library preprint-support teams, standardising on one or two vetted templates — and requiring CRediT-tagged Author Contributions statements — creates consistency across a department’s preprint output without waiting for bioRxiv itself to impose a house style. As preprints increasingly carry citable, versioned DOIs from the moment of posting, formatting discipline at submission time has become part of an institution’s research-integrity record, not just a cosmetic step.

  • 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.