CASRAI Dictionary

Tag: biorxiv citation

  • 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.

  • bioRxiv License Update: What Changed for Authors and Reuse

    bioRxiv’s licence update, live via the platform’s Author Area since January 2026, lets authors request a change to a less-restrictive Creative Commons licence on a preprint already posted — without submitting a new version. The change can only move in one direction, towards more permissive reuse, and it exists chiefly to help authors bring older preprints into line with funder mandates that require CC BY.

    bioRxiv is a free preprint server for the life sciences, operated by the non-profit organisation openRxiv, which also runs the companion server medRxiv for health-sciences preprints.

    Contents

    What is the bioRxiv licence update, and why was it introduced?

    The bioRxiv licence update is a self-service feature that lets a preprint’s corresponding or submitting author switch its Creative Commons licence to a less restrictive option after posting, without triggering a full revision. openRxiv documented the mechanics in a step-by-step guide published on 7 January 2026, and followed up with a policy explainer on 20 May 2026 setting out the rationale.

    The trigger is compliance drift. Openrxiv’s own explainer states that a growing number of funders “require their grantees to apply specific licenses to their preprints, typically CC BY,” but that “many authors are unaware of this” and post under a more restrictive option by default. Before this update, the only remedy was submitting an entirely new version of the preprint and re-selecting a licence — a heavier process that also generates a fresh revision record. This is distinct from an earlier, smaller change in January 2025, when bioRxiv and medRxiv reordered their licence-selection menus to place CC BY at the top of the list; the 2026 update is the first mechanism that lets authors retroactively fix the licence on preprints they have already posted.

    How do authors request a licence change?

    The workflow runs entirely through the bioRxiv submission system’s Author Area and does not require re-uploading a manuscript. It applies only to the most recent version of a preprint, and only to preprints posted within the past two years.

    • Log into the Author Area from the bioRxiv submit page.
    • Locate the “Request License Update” box on the right-hand side of the page.
    • Select “Update license choice on previously posted papers.”
    • Choose the eligible preprint by its manuscript ID (only papers where the requester was corresponding or submitting author are listed).
    • Select a new, less restrictive licence and submit the request; a confirmation email follows.

    Two constraints apply strictly. First, the feature is unavailable if an incomplete revision is already in the submission system, or if a previous licence request is still pending. Second, a request can even be made after the preprint has been formally published in a journal, since the licence sits on the preprint record independently of the journal’s own copyright terms.

    Licence options compared: what actually changed

    bioRxiv preprints have long offered a choice of Creative Commons licences plus a “no licence” (all rights reserved) default, and a CC0 public-domain option for US federal employees such as NIH intramural researchers. What changed in 2026 is not the menu of options — it is that authors can now move an already-posted preprint from a more restrictive option to a less restrictive one after the fact.

    Licence Commercial reuse Attribution required Text-and-data mining / AI training Typical funder fit
    CC BY Permitted Yes Unrestricted, including commercial use HHMI, Gates Foundation, most cOAlition S funders
    CC BY-ND Permitted (no derivatives) Yes Mining permitted; no adapted/derivative outputs distributed Rarely funder-compliant
    CC BY-NC Not permitted Yes Restricted to non-commercial use Non-compliant with CC BY mandates
    CC BY-NC-ND Not permitted Yes Most restrictive; non-commercial, no derivatives Rarely funder-compliant
    CC0 Permitted (public domain) No Unrestricted US federal/NIH intramural authors only
    No licence selected Not permitted without separate permission N/A Reuse requires author permission Non-compliant with most funder mandates

    Because Creative Commons licences are irrevocable once attached to a public copy of a work, the update only runs in the permissive direction. An author can move from CC BY-NC to CC BY; the system rejects a request to move from CC BY to a more restrictive licence, since existing downloaded and archived copies would remain under the original, broader terms regardless.

    What this means for CC-BY reuse, text-and-data mining, and AI training

    bioRxiv’s baseline terms of use already permit text-and-data mining of posted content, which is the legal hook that has made preprint corpora attractive training data for machine-learning systems. The licence attached to an individual preprint then determines the scope of onward reuse beyond that baseline — and this is where the 2026 update has practical bite.

    Under CC BY, any party — including a commercial AI developer — may reproduce, adapt, and redistribute the work, provided the original authors are credited. Under CC BY-NC or CC BY-NC-ND, commercial reuse (which covers most AI model training conducted by for-profit developers) is not licensed, regardless of the platform-level text-mining consent. That gap is precisely what several funders have moved to close: the Howard Hughes Medical Institute’s preprint requirement, effective 1 January 2026, and the Bill & Melinda Gates Foundation’s preprint mandate, in force since 1 January 2025, both require grantee preprints to carry CC BY. The licence-update feature exists to let authors already out of step with those mandates fix a specific preprint without a full resubmission.

    For institutions and research-integrity offices, the practical implication is that a preprint’s licence — not merely its posting on an open server — is the operative variable for downstream reuse and AI-training permissions. Auditing grantee preprints for licence compliance, not just for the fact of preprint deposit, is now a distinct compliance step.

    Answer-first Q&A

    How do I update a bioRxiv?

    Authors can request a licence update from the Author Area of the bioRxiv submission system, using the “Request License Update” box, without submitting a full revision. The change applies only to preprints posted in the past two years and only to the most recent version, moving to a less restrictive licence.

    What are the licence options for bioRxiv?

    bioRxiv authors can choose CC BY, CC BY-ND, CC BY-NC, CC BY-NC-ND, or leave the preprint with no licence (all rights reserved). A CC0 public-domain option is also available specifically for US federal employees, such as NIH intramural researchers.

    Does bioRxiv count as published?

    No. A bioRxiv preprint is not peer reviewed and does not constitute formal journal publication; it is a publicly posted manuscript with its own DOI. Authors remain free to submit the same work to a journal afterward, and the preprint record persists independently of that later publication.

    Who maintains bioRxiv?

    bioRxiv is operated by openRxiv, a non-profit organisation dedicated to advancing science communication, which also runs the companion health-sciences server medRxiv. openRxiv is supported by institutions including Cold Spring Harbor Laboratory, the Chan Zuckerberg Initiative, and the Sergey Brin Family Foundation.

    Implications for institutions, funders, and authors

    Research-administration offices tracking open-access compliance should treat the licence update as a remediation tool, not a substitute for correct licence selection at submission. It closes a specific gap — preprints posted before an author understood their funder’s CC BY requirement — but it does not apply to preprints older than two years, to superseded versions, or where a revision is already mid-process.

    For anyone advising authors on authorship rights and responsibilities, the clearest guidance is to check funder licensing terms before first posting, since fixing a mismatched licence later depends on the preprint still being within the two-year eligibility window. Related open-research terminology, including licensing and reuse definitions, is tracked in the CASRAI open-research dictionary.

    Expect other preprint servers to face similar pressure as CC BY mandates spread across research funders. The direction of travel — author-initiated, platform-mediated licence correction rather than manuscript resubmission — is a practical template other repositories are likely to adopt as funder compliance checks tighten.

  • 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 PubMed Indexing: How the NIH Pilot Works

    BioRxiv PubMed indexing is not automatic. Preprints reach PubMed through a single federal mechanism — the NIH Preprint Pilot, run by the U.S. National Library of Medicine (NLM) — which pulls in preprints that acknowledge direct NIH funding or carry an NIH-affiliated author, provided they were posted from 1 January 2023 onward under the pilot’s current phase.

    The NIH Preprint Pilot is an NLM programme that makes NIH-funded preprints from eligible servers — bioRxiv, medRxiv, arXiv, and Research Square — discoverable through PubMed Central (PMC) and PubMed ahead of formal peer review, with a corresponding citation added on a weekly cycle.

    What is the NIH Preprint Pilot?

    The NIH Preprint Pilot began in June 2020 as a narrow, COVID-19-only initiative. NLM made more than 3,300 preprints reporting NIH-supported SARS-CoV-2 research discoverable in PMC and PubMed between June 2020 and June 2022, testing whether preprint records could accelerate discovery during a public-health emergency.

    Phase 2 launched on 30 January 2023 and dropped the COVID-only restriction. It now covers any preprint that acknowledges direct NIH support and/or lists an NIH-affiliated author, posted to an eligible server on or after 1 January 2023. Eligible preprints are added to PMC on a weekly basis and receive a corresponding PubMed citation automatically — authors do not submit anything separately.

    How a preprint moves from bioRxiv to PubMed

    The pipeline is largely invisible to authors and runs on a fixed weekly cadence. NLM does not wait for a submission; it identifies eligible content and pulls it in automatically, then layers PubMed on top of the PMC record.

    • Identification: NLM text-mines new bioRxiv and medRxiv postings for NIH-support acknowledgements and cross-checks the NIH Office of Portfolio Analysis tool for NIH-affiliated authors.
    • PMC ingestion: Citation and abstract metadata are pulled from the preprint server’s machine-readable feed to build an “article header” record, and a PMCID is assigned immediately to enable rapid discovery.
    • PubMed record creation: Once the PMC record exists, NLM generates the corresponding PubMed citation the same week, tagged with publication type “Preprint.”
    • Full-text conversion: Preprints posted under a Creative Commons licence enter a separate workflow to produce archival full-text XML, a process NLM says takes a few days and enables full-text search within PMC.

    Every record carries a prominent yellow information panel confirming the work has not been peer-reviewed, and NLM runs weekly checks — against the bioRxiv API, the Crossref API, and the Europe PMC API — to link a preprint to its eventual journal version, updating the PubMed status to “Updated” once that link is confirmed.

    Which preprint servers qualify

    Only four servers currently feed the pilot. NLM evaluates candidate servers against a published checklist — clear non-peer-review labelling, transparent versioning, open licensing information, machine-readable metadata, and a public archiving policy — modelled on NIH’s 2017 interim-research-products guidance (NOT-OD-17-050) and COPE’s preprint discussion document.

    Server Subject scope Operator DOI registration
    bioRxiv Life sciences openRxiv (independent nonprofit, formerly a Cold Spring Harbor Laboratory service) Crossref
    medRxiv Health and clinical sciences openRxiv, with Yale University and BMJ as founding partners Crossref
    arXiv Physics, mathematics, computer science, quantitative biology Cornell University Crossref
    Research Square Multidisciplinary Research Square Company Crossref

    bioRxiv and medRxiv are the two servers most relevant to biomedical research administrators, since both fall under openRxiv, the independent nonprofit that took over operation of both platforms from Cold Spring Harbor Laboratory. openRxiv’s separation from a single host institution was framed explicitly around long-term sustainability for the two servers NIH now indexes directly — a governance detail that matters for anyone assessing the pilot’s durability, since NLM’s own eligibility criteria require a “publicly stated archiving strategy to ensure long-term access.”

    What this means for discoverability, DOIs, and citation

    PubMed indexing changes where a preprint can be found, not whether it can be cited. Every bioRxiv preprint already receives a DOI registered through Crossref at posting, which is what makes it part of the citable scientific record regardless of NIH eligibility.

    According to bioRxiv’s own FAQ, preprints are indexed by “Google, all other search engines, Google Scholar, Crossref, Semantic Scholar, Europe PubMed Central, and Preprint Citation Index (connected to the Web of Science)” independent of the NIH pilot — PubMed indexing is an additional, funder-gated channel layered on top of that baseline discoverability.

    One clarification worth making explicitly: bioRxiv and medRxiv do not carry a Scimago Journal Rank or an impact factor. Both metrics are journal-level indicators computed from peer-reviewed citation data; a preprint server is a distribution platform, not a journal, so no SJR score exists for bioRxiv as a whole, and any figure circulating under “bioRxiv impact factor” searches is not an NLM, Crossref, or Scimago-sourced metric.

    Indexing also does not substitute for compliance. NLM is explicit that even when a preprint sits in PMC under the pilot, the NIH Public Access Policy still requires the peer-reviewed, accepted author manuscript to be separately deposited via NIHMS, with its own PMCID reported as proof of compliance.

    Answer-first questions about bioRxiv and PubMed

    Does bioRxiv show up in PubMed?

    Yes, but only conditionally. A bioRxiv preprint appears in PubMed only if it acknowledges direct NIH funding or lists an NIH-affiliated author and was posted under Phase 2 of the NIH Preprint Pilot (from 1 January 2023). Non-NIH preprints stay discoverable via Google Scholar, Crossref, and Europe PMC instead.

    What is a preprint in PubMed?

    In PubMed, a preprint is a record carrying the publication type “Preprint,” which separates it from peer-reviewed literature in search filters. It displays a yellow information panel stating the work has not undergone peer review, and PubMed links it automatically to the journal version once one is published.

    Does bioRxiv count as published?

    No. bioRxiv distributes complete but unpublished manuscripts, so posting there is not equivalent to journal publication. A preprint carries a DOI and is part of the citable record, but it lacks the peer-review certification that ICMJE and COPE norms attach to a published article.

    Is it okay to cite bioRxiv?

    Yes. bioRxiv preprints receive a DOI through Crossref, making them formally citable, and are indexed by Google Scholar, Crossref, Semantic Scholar, and Europe PMC. Authors citing them should flag that the underlying findings have not yet completed peer review.

    Why other funders are watching the pilot

    NIH’s approach is unusual because it is infrastructural rather than a mandate: it does not require authors to preprint, it simply makes eligible preprints easier to find once posted. That distinction is why other funders are studying it rather than replicating it wholesale.

    cOAlition S, the funder coalition behind Plan S, already treats preprints as an acceptable route to satisfying immediate open-access requirements, but no cOAlition S member currently operates an equivalent centralised indexing pipeline into a national biomedical database. UKRI’s open access policy similarly recognises preprints as compliant interim outputs without building comparable PMC-style ingestion.

    For research administrators, the practical takeaway is that discoverability infrastructure and funder mandates remain two separate policy levers. NIH has built the first at meaningful scale; whether other national funders follow with their own PMC-equivalent indexing pipeline — rather than policy language alone — is the open question institutions tracking preprint compliance should watch through 2026 and beyond.

  • bioRxiv API: A Developer’s Guide to Metadata

    The bioRxiv API is a free, unauthenticated REST interface at api.biorxiv.org that returns structured JSON or XML metadata — DOI, version number, posting date, subject category, licence, and author list — for any bioRxiv or medRxiv preprint, queryable by date range or by DOI, with no API key required. This guide sets out the endpoints, pagination rules, and field-level detail a developer needs to wire preprint metadata into a CRIS, discovery layer, or citation tool.

    A preprint DOI in this ecosystem is a Digital Object Identifier issued under the 10.1101 prefix, registered with Crossref by Cold Spring Harbor Laboratory Press, and it resolves to a specific, versioned manuscript record — the same identifier the bioRxiv API uses as its primary lookup key.

    Contents

    What is the bioRxiv API?

    The bioRxiv API is a read-only HTTP interface, hosted at api.biorxiv.org, that exposes preprint metadata as JSON, XML (OAI-PMH), or HTML. It was built to support text and data mining, discovery-tool indexing, and institutional repository harvesting without scraping the public website. It requires no registration, no API key, and no OAuth flow — a plain HTTPS GET request is sufficient.

    Because bioRxiv and medRxiv share the same underlying submission platform, the same API structure serves both servers; you select the server with a path segment (biorxiv or medrxiv) rather than a different base domain. This matters for CRIS and discovery-tool developers who need one integration pattern to cover both the life-sciences and health-sciences preprint corpora.

    Which endpoints return DOIs, versions, and subject categories?

    Metadata retrieval is split across five endpoint families. Each returns a defined JSON schema with a messages block (cursor position, total count) and a collection array of preprint records.

    Endpoint Purpose Example
    /details/[server]/[DOI]/na/[format] Full metadata for one preprint by DOI, including every posted version api.biorxiv.org/details/biorxiv/10.1101/339747
    /details/[server]/[start]/[end]/[cursor] Metadata for all preprints posted in a date range, paginated 30 per call api.biorxiv.org/details/biorxiv/2025-03-21/2025-03-28/0
    /details/…?category= Filters the date-range endpoint by subject category (e.g. cell_biology) ?category=cell_biology
    /pubs/[server]/[DOI]/na/[format] Links a preprint DOI to its eventual published-journal DOI, once available api.biorxiv.org/pubs/medrxiv/10.1101/2021.04.29.21256344
    /funder/[server]/[interval]/[ROR ID]/[cursor] Filters preprint metadata by funder, using a ROR identifier ?ROR=00k4n6c32 (European Commission)

    Each preprint record returned by the /details endpoint carries the following core fields:

    • doi — the versionless preprint DOI (prefix 10.1101)
    • version — an integer indicating which revision of the manuscript this record represents
    • date — the posting date of that specific version
    • category — the subject category assigned at submission (e.g. Bioinformatics, Genomics, Epidemiology)
    • title, authors, author_corresponding, abstract, license — standard bibliographic and rights fields

    Because each version of a preprint is returned as a separate array entry under the same DOI, a CRIS integration must group records by doi and sort by version to reconstruct a manuscript’s full revision history — the API does not collapse versions for you.

    How does the medRxiv API differ for integrators?

    Structurally, the medRxiv API is not a separate product — it is the same api.biorxiv.org (or api.medrxiv.org, which mirrors the same routes) interface with medrxiv substituted as the server path segment. The field schema, pagination behaviour, and DOI prefix are identical.

    The practical differences developers should code for are:

    • Subject categories differ in vocabulary: bioRxiv uses life-science categories (Cell Biology, Genomics, Neuroscience); medRxiv uses clinical and public-health categories (Cardiovascular Medicine, Infectious Diseases, Epidemiology).
    • medRxiv, co-founded in 2019 by Cold Spring Harbor Laboratory, Yale University, and BMJ, carries additional clinical-trial registration and conflict-of-interest declaration fields relevant to health-research governance that bioRxiv records omit.
    • medRxiv content volumes and posting cadence are lower than bioRxiv’s, so date-range polling for medRxiv can safely use wider intervals without hitting the 30-record-per-page ceiling as often.

    What are the rate limits and pagination rules?

    bioRxiv does not publish a formal published rate limit for the metadata API, but pagination is fixed: the /details family returns 30 records per call and the /pubs, /pub, /publisher, and /funder families return 100 records per call, advanced via the cursor parameter until the messages block reports no records remaining.

    The community-maintained rbiorxiv R client — the top third-party wrapper indexed for this API — enforces a self-imposed one-second delay between paginated calls as good-citizen practice; developers building bulk harvesters for a CRIS or discovery index should adopt the same throttle even though it is not server-enforced.

    For full-text or PDF-scale mining rather than metadata alone, bioRxiv and medRxiv separately publish bulk corpora via Amazon Web Services’ Open Data programme — a route the metadata API is not designed to serve and that sits outside the scope of this guide.

    Answer-first Q&A

    What is the rate limit for the bioRxiv API?

    No official rate limit is published for api.biorxiv.org. In practice, pagination caps each call at 30 records for detail endpoints and 100 for publication and funder endpoints, and the community rbiorxiv client self-throttles to one request per second — a sensible default for any automated harvester.

    Is bioRxiv open access?

    Yes. bioRxiv provides free and unrestricted access to every posted article, for both human readers and machine analysis via the API. This applies equally to medRxiv, and neither server charges a fee to read, download, or programmatically query preprint metadata.

    Is it okay to cite bioRxiv?

    Yes. Every manuscript posted to bioRxiv or medRxiv receives a DOI under the 10.1101 Crossref prefix, making it a citable, versioned part of the scientific record. A correct biorxiv citation should reference the specific version number returned by the API, since the content of a DOI can change across revisions.

    Who operates bioRxiv and medRxiv?

    Since March 2025, both servers have been operated by openRxiv, an independent nonprofit spun out of Cold Spring Harbor Laboratory and backed by a $16 million grant from the Chan Zuckerberg Initiative. Its board includes CSHL President Bruce Stillman and medRxiv co-founder Harlan Krumholz — a governance change developers should note when citing the API’s institutional provenance.

    Implications for CRIS and discovery-tool integrators

    The March 2025 move to openRxiv governance is more than an institutional footnote for anyone building a research information system. openRxiv’s stated mandate is to expand — not just sustain — API access and machine-readable metadata as preprint volume grows, which means the endpoint contract described here should be treated as stable but not frozen; integrators should build a thin adapter layer rather than hard-coding field names.

    For CRIS platforms harvesting outputs for institutional repositories, the /funder endpoint’s ROR-based filtering is the highest-value addition since the API’s original release: it lets an institution pull every preprint that declares a specific funder without post-hoc text matching. Combined with the /pubs endpoint’s preprint-to-published-DOI linking, a discovery layer can track a manuscript from first preprint version through to its eventual journal-of-record entry using DOIs alone.

    Developers integrating author identity alongside this metadata should pair bioRxiv’s author_corresponding field with ORCID resolution rather than name-string matching, consistent with broader authorship attribution practice; teams building the CRIS side of this pipeline may also find it useful to cross-reference definitions in the research administration pillar and the CASRAI dictionary when mapping preprint metadata fields to internal schemas.

  • 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.