CASRAI Dictionary

Author: MCP Service

  • 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.

  • 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.

  • scGPT bioRxiv: AI Biology Models Bypass Review

    scGPT bioRxiv preprints, alongside ESM3, AlphaFold-Multimer, Geneformer, EvolvePro and Chai-2, illustrate a 2026 pattern: AI foundation models for biology now reach bioRxiv months or years before — and sometimes instead of — formal peer review, shifting scrutiny onto the research community itself.

    A foundation model in biology is a large neural network pretrained on a broad corpus of sequence, structure or single-cell data, then fine-tuned for specific downstream tasks such as cell-type annotation, protein design or complex-structure prediction. bioRxiv is the open-access preprint server, now operated by the nonprofit openRxiv, where most of these models first appear.

    What is the bioRxiv wave of AI biology preprints?

    Since 2021, a cluster of high-profile AI foundation models for biology has appeared first as bioRxiv preprints rather than journal articles. scGPT, ESM3, AlphaFold-Multimer, Geneformer, EvolvePro and Chai-2 each disclosed model weights, training corpora and benchmark results on bioRxiv before, or without, completing formal peer review.

    This is not unique to biology, but the scale is notable. bioRxiv’s bioinformatics collection alone now holds over 42,000 preprints, and many of the field’s most-cited foundation-model papers spent a year or more circulating in preprint form before any journal version existed.

    Which models are driving this trend?

    Each model targets a different layer of biology — from single cells to protein complexes — but all six followed the same preprint-first disclosure pattern, with varying paths to formal review.

    Model Domain bioRxiv preprint date Peer-review status Headline result
    scGPT Single-cell multi-omics 1 May 2023 Nature Methods, 2024 Pretrained on over 10 million cells; preprint drew 1,490+ citations before formal publication
    ESM3 Protein sequence/structure/function 2 July 2024 Science, January 2025 Generated esmGFP, a novel fluorescent protein only 58% identical to its nearest known relative
    AlphaFold-Multimer Protein complex structure 4 October 2021 Still bioRxiv-only 67% success rate on heteromeric interfaces despite ubiquitous structural-biology use
    Geneformer Single-cell network biology No precursor preprint; v2 update posted August 2024 Nature, 31 May 2023 Pretrained on Genecorpus-30M, 29.9 million single-cell transcriptomes
    EvolvePro Protein engineering 17 July 2024 Still bioRxiv-only 2- to 515-fold activity gains across five therapeutic proteins
    Chai-2 Antibody and miniprotein design 6 July 2025 Still bioRxiv-only 16% hit rate in de novo antibody design, over 100x prior computational methods

    Two patterns stand out. First, Geneformer’s core 2023 paper went directly to Nature without a bioRxiv precursor, showing the pattern is not universal. Second, AlphaFold-Multimer, EvolvePro and Chai-2 remain, as of mid-2026, without any confirmed journal record despite being cited and deployed across thousands of downstream studies.

    Why publish before peer review?

    Competitive priority and speed dominate. Posting to bioRxiv creates a timestamped, public record of a result the moment it exists, which matters in a field where multiple labs often chase the same architecture within weeks of each other.

    • Immediate community stress-testing of code, weights and benchmark claims, often faster than a journal’s reviewer pool can respond.
    • Priority establishment ahead of competing labs working on the same problem class.
    • Faster onward use: downstream researchers can build on and cite a preprint immediately rather than waiting through a multi-month review cycle.

    Journals have adapted to this reality. Many now formally accept bioRxiv-posted work, and scGPT’s own trajectory — a 2023 preprint that drew over 1,490 citations before its 2024 Nature Methods publication — shows how much scientific traffic a foundation model can carry while still formally unreviewed.

    What are the research-integrity and attribution risks?

    The lack of independent review before wide reuse is the core risk. A 2026 bioRxiv preprint on researcher perceptions found that scientists rely heavily on author reputation, rather than review status, as their main heuristic for judging a preprint’s credibility — a fragile substitute for structured peer review, particularly for tools other labs adopt wholesale.

    Attribution is a related, distinct problem. When a foundation model like Chai-2 or ESM3 generates a candidate sequence that a human team then validates experimentally, contributor-credit questions arise: who conceived the method, who ran validation, and who is accountable for the claim. Both the International Committee of Medical Journal Editors and the Committee on Publication Ethics have stated that AI tools cannot be listed as authors, because they cannot take responsibility for the work’s accuracy or integrity.

    Structured contributor-role frameworks help resolve this. CASRAI originated the CRediT contributor role taxonomy in 2014, and the standard is now stewarded by NISO as ANSI/NISO Z39.104-2022. Applying CRediT roles to preprint co-authorship — distinguishing methodology, software, validation and formal analysis — gives institutions a documented way to assign human accountability even when an AI foundation model contributed materially to the output. See the broader CRediT framework overview and CASRAI’s authorship resources for related guidance.

    Answer-first Q&A

    Has the scGPT bioRxiv preprint been peer reviewed?

    Yes. The original scGPT preprint was posted to bioRxiv on 1 May 2023 and later passed formal peer review, publishing in Nature Methods in 2024. The preprint itself had already drawn more than 1,490 citations while still formally unreviewed.

    Why do AI foundation models for biology publish on bioRxiv before peer review?

    Competitive pressure and pace drive it. Posting to bioRxiv establishes priority and lets the wider research community stress-test claims, code and weights immediately, rather than waiting the months or years a formal peer-review cycle can take in a fast-moving field.

    Is AlphaFold-Multimer peer reviewed?

    No confirmed journal record exists for AlphaFold-Multimer itself; DeepMind’s preprint has remained on bioRxiv since 4 October 2021. It is nonetheless used routinely across structural biology — a stark example of a foundational tool that never completed formal peer review.

    Who owns bioRxiv?

    bioRxiv is operated by openRxiv, an independent nonprofit that assumed ownership from Cold Spring Harbor Laboratory in March 2025. The transfer aimed to secure the preprint server’s long-term governance as its role in disseminating AI foundation model research has grown.

    Implications for institutions and publishers

    Research offices and publishers now need explicit policy on how preprinted AI foundation models are cited, credited and re-used before formal review completes. Institutional research-integrity offices should treat a bioRxiv-only model — such as AlphaFold-Multimer, EvolvePro or Chai-2 — as provisionally validated, not settled science, when it underpins funded work or clinical-adjacent claims.

    Research administrators managing grant compliance and output tracking should build preprint-status checks into their reporting workflows; CASRAI’s research administration resources outline how contributor-role and output-tracking practices adapt to fast-moving, preprint-first fields. As more foundation models follow this path, the distinction between “published” and “peer reviewed” will matter more, not less, for research integrity.

  • Is medRxiv Reputable? Screening vs bioRxiv Explained

    medRxiv is a reputable, non-profit preprint server for medicine and the health sciences, co-founded in 2019 by Cold Spring Harbor Laboratory, Yale University and BMJ, and since March 2025 operated by the independent non-profit openRxiv. It is reputable as a rapid-dissemination archive, not as a substitute for peer review: every preprint carries an explicit warning that it has not been certified by peer review and must not be used to guide clinical practice.

    medRxiv is defined by its own operators as an online repository for preprints — complete but unpublished manuscripts — in medicine, clinical research and related health sciences, distributed free of charge before formal peer review.

    What screening does medRxiv apply before posting a preprint?

    medRxiv operates a screening process, not a peer-review process. Submissions are checked by in-house staff and an affiliate network of scientists and clinicians for plagiarism, non-scientific content, and material that could plausibly cause harm if acted on before formal review. Manuscripts that pass screening are posted unedited and unproofed, exactly as submitted, with an author-supplied DOI-bearing record that remains permanently linked to any later journal publication.

    This is a materially lighter bar than peer review. medRxiv’s own FAQ states plainly that submissions “are not certified by scientific peer review, edited, or typeset before being posted online,” and that they “may contain errors and/or omissions.” The screening exists to filter out fraud and clearly dangerous content — not to validate methodology, statistics or conclusions.

    How does medRxiv’s screening differ from bioRxiv’s?

    medRxiv and bioRxiv share governance, infrastructure and an operator (openRxiv) but apply different levels of scrutiny because their content carries different real-world risk. bioRxiv covers basic and translational biology — work several steps removed from direct patient action. medRxiv covers clinical trials, epidemiological studies, case reports and public-health research that a patient, clinician or journalist could misread as actionable guidance the same day it is posted.

    As a result, medRxiv layers an additional clinical-risk screen onto the standard plagiarism and legitimacy checks, and it carries a more prominent, standardised disclaimer banner than bioRxiv’s — one that explicitly tells readers not to use the content “to guide clinical practice or health-related behaviour” and not to report it “in news media as established information.” That distinction matters for how research offices and communications teams should treat the two archives when advising authors or fielding press enquiries.

    Feature medRxiv bioRxiv
    Subject scope Clinical, epidemiological and health-sciences research Basic and translational biology
    Additional clinical-risk screen Yes — checks for content that could pose a direct health risk Not applied in the same form
    Clinical-guidance disclaimer Prominent, standardised warning banner on every preprint Standard preprint notice, less clinically specific
    Operator (since March 2025) openRxiv (non-profit) openRxiv (non-profit)

    Is medRxiv peer reviewed, and is it indexed in PubMed?

    No. medRxiv preprints are not peer reviewed at the point of posting. medRxiv is, however, indexed by Crossref, Google Scholar, Semantic Scholar, Europe PubMed Central, and Web of Science’s Preprint Citation Index. Preprints reporting research funded by the U.S. National Institutes of Health are separately indexed in PubMed under NIH public-access requirements — but general medRxiv posting alone does not confer PubMed indexing, and medRxiv is not itself a journal with an impact factor.

    Citation practice already reflects this ambiguity in the literature. A 2022 peer-reviewed study published via PubMed Central found that, among 205 COVID-19 research articles published in four major medical journals in 2020, 60 articles — 29.3% — cited at least one medRxiv preprint, and a meaningful share of those citations pointed to a version that had since been superseded by a peer-reviewed publication elsewhere. That gap between what was cited and what was current is precisely the reputational risk research offices need to manage.

    What misinformation risks come from premature clinical findings?

    The pandemic demonstrated the two-edged nature of clinical preprints. medRxiv and bioRxiv were, in the words of researchers tracking the period, major sources for the rapid dissemination of COVID-19 research — a genuine public-health benefit when speed mattered. But the same speed let unreviewed clinical claims reach journalists, policymakers and the public before methodological flaws could be caught, corrected or retracted.

    • Findings can change materially between preprint and peer-reviewed publication — in titles, data or conclusions.
    • Small, uncontrolled or statistically underpowered clinical studies can circulate as if settled, particularly when picked up by non-specialist media.
    • Preprints are citable and DOI-bearing, which can lend an unwarranted appearance of permanence to findings that were never independently verified.

    This is why medRxiv’s disclaimer is not boilerplate: it is the archive’s primary defence against exactly the misuse pattern institutions most need to guard against — a preliminary clinical finding treated as established fact.

    Frequently asked questions

    Is medRxiv trustworthy?

    medRxiv is trustworthy as an archive, run by credible non-profit institutions with documented screening for plagiarism, legitimacy and health-risk content. It is not trustworthy as a source of validated clinical conclusions, because no submission is peer reviewed before it is posted.

    Who owns medRxiv?

    medRxiv was founded in 2019 by Cold Spring Harbor Laboratory, Yale University and BMJ. Cold Spring Harbor Laboratory operated the site until 11 March 2025, when ownership transferred to openRxiv, a newly formed non-profit dedicated to running both medRxiv and bioRxiv independently.

    Is medRxiv peer-reviewed?

    No. medRxiv preprints are screened, not peer reviewed. Screening checks for plagiarism, non-scientific content and material that could pose a health risk; it does not evaluate methodology, statistical validity or the soundness of a paper’s conclusions the way journal peer review does.

    Is a preprint a reliable source?

    A preprint can be a useful early indicator but is not a finished, validated source. Readers should treat preprint findings as provisional, check whether a peer-reviewed version now exists, and avoid citing preprints as if their conclusions were already established.

    What this means for research offices

    Research offices, communications teams and institutional leaders engaging with medRxiv content should build the following into standard practice:

    • Check publication status before external use. Search for a peer-reviewed version before citing, quoting or promoting a medRxiv finding externally.
    • Retain the disclaimer in any repost. If a preprint is shared via institutional channels, carry medRxiv’s own caution alongside it, not a paraphrased or softened version.
    • Brief media-facing staff explicitly. Journalists and public-affairs teams should be told, in advance, that a medRxiv posting is not equivalent to journal publication.
    • Track the DOI, not just the PDF. medRxiv assigns a persistent DOI to each version, which allows an institution to monitor whether a later, revised or peer-reviewed version supersedes the one initially shared.

    Conclusion: a legitimate archive, not a clinical authority

    medRxiv is reputable in the narrow, correct sense of that word: it is a legitimate, non-profit, well-governed repository operated by credible academic and publishing institutions, with a documented screening process and broad indexing across scholarly databases. It is not, and does not claim to be, a peer-reviewed journal, and its content should never be treated as clinical guidance. The distinction between “reputable archive” and “validated clinical evidence” is the single fact every research office, journalist and clinician needs to carry away from any encounter with a medRxiv preprint.

    For related terminology and role definitions used across the scholarly-communication ecosystem, see the CASRAI Dictionary.

  • 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.

  • BioRxiv Submission Guidelines: A 5-Step Process for First-Time Authors

    BioRxiv submission guidelines require a single PDF (or Word file plus separate figure files), a free author-area registration, an article-category selection, and a two-step in-house-plus-Affiliate screening that typically clears in 24-48 hours. There is no submission fee, no mandatory template, and no peer review before posting. This guide walks first-time authors through each stage, the templates available, and the reasons manuscripts most often get sent back.

    bioRxiv is the life-sciences preprint server operated by the non-profit openRxiv; a preprint is a complete, citable manuscript posted before or during formal peer review, and bioRxiv assigns it a Crossref DOI (prefix 10.1101) as soon as screening is passed. Clinical trial reports and most epidemiology studies must instead go to bioRxiv’s sister server, medRxiv — submitting one of these to bioRxiv is itself a common rejection reason, covered in section four below.

    1. What are bioRxiv’s submission requirements?

    bioRxiv does not enforce a house style, but it does enforce a fixed submission format and a content-eligibility test. The manuscript must be unpublished at the time of deposit, all co-authors must have consented to posting, and the work must fall within a relevant life-sciences subject category.

    Submission route What you upload Conversion
    Single PDF Full text, figures and tables combined None needed — this is the simplest route
    Word + separate figures Word file for text/tables; figures as JPEG, TIFF, EPS or PowerPoint bioRxiv’s automated engine builds the PDF
    LaTeX Manuscript converted to PDF before upload (LaTeX source may accompany it as Supplemental Material) Author-side conversion required

    Large primary datasets belong in a community database such as GenBank or the Protein Data Bank rather than as Supplemental Material, in line with the Fort Lauderdale data-sharing guidelines that bioRxiv references directly in its submission guide.

    2. Setting up your bioRxiv author area

    Every submission starts with a free account on the bioRxiv Manuscript Processing System at submit.biorxiv.org. The bioRxiv author area is where you register, start a new submission, continue a saved draft, proof a converted manuscript, and later submit revisions.

    1. Register with an institutional or personal email address — no institutional affiliation is required to create an account.
    2. Enter the author area and select “Submit a New Manuscript.”
    3. Upload files, enter co-author details for every listed author, and add funder names and grant numbers.
    4. Select an article category: New Results, Confirmatory Results, or Contradictory Results.
    5. Choose a distribution licence — CC BY, CC BY-NC, CC BY-ND, CC BY-NC-ND, CC0, or no reuse.

    Copyright remains with the author throughout. Once a version is posted, it cannot be deleted, but authors can submit a revision at any time before journal acceptance via the same author-area screen.

    3. Choosing a manuscript template

    A bioRxiv template is optional, not mandatory — the platform explicitly states it does not require a particular article format or style, and many authors simply reuse the formatting of their target journal. Two community-maintained options cover most first-time authors.

    • Word template: a community-built .docx template on GitHub styled after published bioRxiv papers, useful if you want a clean starting structure without building one from scratch.
    • bioRxiv LaTeX template: several Overleaf templates are built specifically for bioRxiv preprints and can often be re-purposed for the eventual journal submission, saving reformatting time later in the pipeline.

    Whichever route you choose, convert LaTeX output to PDF before upload — bioRxiv’s system does not compile .tex source directly.

    4. What happens after you submit (timeline and screening)

    Submitted manuscripts go through two screening stages before posting. In-house staff first check completeness and confirm the article type is eligible; volunteer Principal Investigators known as bioRxiv Affiliates then assess whether the work constitutes genuine biological research and whether it poses any public-harm or biosecurity risk.

    This combined process is the answer to a frequent search — bioRxiv submission time — and typically completes within 24-48 hours of upload. Once approved, the PDF posts immediately; conversion to full-text HTML and XML can take a further 1-2 days, so the machine-readable version usually lags the PDF by up to 48 hours.

    Stage Typical duration
    Registration and upload Immediate
    In-house completeness/eligibility check Same day to 24 hours
    Affiliate biosecurity/scope review Within 24-48 hours total
    PDF posting after approval Immediate
    Full-text HTML/XML conversion Up to 48 additional hours

    5. Common rejection reasons and how to avoid them

    bioRxiv’s own screening documentation and content-scope rules point to a consistent set of avoidable rejections for first-time authors.

    • Wrong content type: case reports, narrative reviews, editorials, letters, opinion pieces, hypotheses without new data, and laboratory protocols without accompanying results are all excluded from bioRxiv’s scope.
    • Wrong server: clinical trial results and most epidemiology studies must go to medRxiv, not bioRxiv — this single misrouting error is one of the most common first-submission mistakes.
    • Already published: a manuscript that has already been accepted by a journal cannot be deposited as a new bioRxiv submission.
    • Missing author consent: every listed co-author must have agreed to posting before submission; disputes here stall or block screening.
    • Biosecurity or dual-use concerns: Affiliates specifically screen for material that could pose a health or biosecurity risk, which can delay or prevent posting even for otherwise sound science.
    • Non-scientific or promotional content: bioRxiv is explicitly not a channel for news, product advertisements, or policy statements.

    6. Frequently asked questions

    Can anyone submit to bioRxiv?

    Yes — any author whose manuscript concerns a relevant scientific field, is unpublished, and has the consent of all co-authors can deposit it after free registration. No institutional affiliation is required, and there is no submission fee.

    When should you submit to bioRxiv?

    A manuscript can be submitted at any point before journal publication. Once a journal has formally published the paper, it can no longer be newly deposited as a bioRxiv preprint, though the platform still allows revisions of an existing preprint right up to journal acceptance.

    How long does a bioRxiv submission take?

    Screening typically completes within 24-48 hours of upload, after which the PDF posts immediately. The full-text HTML and XML version follows separately and can take up to 48 further hours to appear.

    How much does it cost to submit to bioRxiv?

    There is no charge for registration or for depositing an article. bioRxiv funds screening and hosting as a non-profit service operated by openRxiv rather than through author-facing fees.

    7. Implications for research offices and institutions

    Research-administration teams increasingly track preprints as part of grant-compliance and output reporting, not just publication records. The U.S. National Institutes of Health has, since Notice NOT-OD-17-050, explicitly permitted investigators to cite preprints — including bioRxiv postings — in grant applications and progress reports, and cOAlition S’s Plan S framework recognises preprints as a valid interim compliance route ahead of a peer-reviewed version.

    Because a bioRxiv DOI is assigned at posting and persists across revisions, institutions can use it as a stable identifier to link the preprint, the eventual journal version, and contributor metadata. Where a project already uses the CRediT contributor role taxonomy to record who did what — CASRAI originated CRediT in 2014, and the taxonomy is now stewarded by NISO as ANSI/NISO Z39.104-2022 — carrying those role assignments into the preprint stage keeps authorship records consistent from first deposit through final publication.

    bioRxiv’s direct-transfer (B2J) programme, which now spans more than 190 partner journals and peer-review services, also removes a second manual re-entry step for research-office staff supporting authors through submission — files and metadata move directly from the bioRxiv author area to the receiving journal without being re-uploaded.

    Building preprinting into standard practice

    For first-time authors, the practical barrier to bioRxiv is low: no fee, no mandatory template, and a screening turnaround measured in hours rather than weeks. The remaining friction is almost entirely about content fit — choosing the right server, the right article category, and confirming every co-author has consented before upload.

    Institutions that build preprint deposit into standard research-administration workflows — alongside DOI tracking, contributor-role records, and funder-mandate checks — turn a one-off submission task into a repeatable, auditable step in the research lifecycle.

  • bioRxiv Impact Factor: Why It Doesn’t Exist

    bioRxiv does not have an impact factor, and it never will unless its governance model changes: impact factors are calculated only for peer-reviewed journals indexed in Clarivate’s Journal Citation Reports, and bioRxiv is a preprint repository, not a journal. The “biorxiv impact factor” search that ~50-70 people run every month reflects a structural misunderstanding, not a missing data point — no amount of waiting will produce one.

    bioRxiv is a free preprint server for the life sciences, operated by the non-profit openRxiv and co-founded by John Inglis and Richard Sever in 2013; it distributes unpublished, non-peer-reviewed manuscripts under persistent DOIs, which is precisely the feature set that disqualifies it from journal-level citation metrics.

    What bioRxiv Is, and Why It Has No Impact Factor

    bioRxiv is a repository, not a periodical: it posts complete but unpublished manuscripts in the biological sciences without editorial peer review, typically within 72 hours of submission. Its own FAQ states this without qualification: “bioRxiv is not a journal so it has no Impact Factor.”

    The confusion is understandable. bioRxiv issues DOIs, assigns subject categories, displays usage metrics, and looks — to a casual visitor — like a journal homepage. But the Journal Impact Factor (JIF) is a specific, licensed Clarivate product calculated from citation counts to items indexed as “articles” in the Web of Science Core Collection over a two-year window. That calculation requires a defined editorial process and a stable, recurring publication vehicle. A repository that posts author-submitted manuscripts with no acceptance/rejection decision does not meet the definition of a “source publication,” so no JIF can be computed for it, at any citation volume.

    Why Preprint Servers Are Structurally Ineligible for JCR and Scimago

    Both major citation-metric systems apply the same underlying logic, even though they run on different databases. Clarivate’s Journal Citation Reports draws only from titles accepted into the Web of Science Core Collection’s journal indexes, and that acceptance process screens for editorial peer review, a named editorial board, regular publication periodicity, and bibliographic standardisation — criteria a preprint repository cannot satisfy by design. Scimago Journal Rank works from Scopus’s source list, which applies an analogous journal/serial-title gate.

    • No editorial acceptance decision — bioRxiv screens submissions for plagiarism, scope, and safety, but does not accept or reject manuscripts on scientific merit, so there is no equivalent of a journal’s editorial board.
    • No fixed publication periodicity — preprints post continuously, not in issues or volumes, which breaks the citation-window model both JCR and Scimago use.
    • Preprints remain mutable — authors can revise a preprint indefinitely until journal publication, unlike a journal’s version of record.

    This is why “biorxiv scimago” searches also return nothing: bioRxiv is absent from Scimago’s journal rankings for the identical structural reason it is absent from JCR, not because of a data-processing gap. medRxiv, bioRxiv’s sister server for health sciences launched in 2019, is ineligible under the same rule set — hence “medrxiv impact factor” is equally unanswerable in the affirmative.

    bioRxiv’s ISSN, DOIs, and the Preprint Citation Index — What the Identifiers Actually Mean

    bioRxiv does hold an ISSN — 2692-8205 — issued because ISSNs are assigned to any continuing serial resource for cataloguing purposes, including repositories, and are unrelated to JIF eligibility. This is a distinction most explainers on this topic skip: an ISSN registers bioRxiv as a citable, ongoing publication series in library catalogues; it does not signal peer review, and it carries no weight in Clarivate’s or Scopus’s source-selection criteria.

    A second, frequently overlooked identifier detail: individual bioRxiv preprints are indexed in Clarivate’s Preprint Citation Index, a distinct Web of Science product launched to track preprint citations separately from the peer-reviewed Core Collection. Being present in the Preprint Citation Index is not the same as JCR eligibility — it is a citation-tracking layer, not a metric-generating one. bioRxiv preprints are also indexed by Crossref, Google Scholar, Semantic Scholar, and Europe PMC, and PubMed indexes preprints of NIH-funded research specifically.

    Attribute Peer-reviewed journal bioRxiv / medRxiv
    Peer review before posting Yes, editorial + referee decision No — screening only, for scope and safety
    JCR / Journal Impact Factor eligible Yes, if indexed in WoS Core Collection No — structurally excluded
    Scimago / SJR eligible Yes, if indexed in Scopus source list No — same structural exclusion
    ISSN Yes, per title Yes — bioRxiv: 2692-8205 (cataloguing only)
    DOI Yes, per article Yes, per preprint version
    Indexed in Web of Science Preprint Citation Index N/A Yes

    What Metrics Actually Apply to bioRxiv and medRxiv Preprints

    bioRxiv publishes per-preprint usage data on each article’s Metrics tab: abstract views and PDF downloads, updated daily, plus altmetric attention scores that aggregate mentions in news, blogs, and social platforms. These sit within the broader altmetrics framework that NISO formalised through its Alternative Assessment Metrics project (NISO RP-25-2020), which set recommended practices for defining and reporting non-citation research metrics.

    There is also downstream evidence linking preprint attention to eventual journal outcomes. A 2019 analysis of all bioRxiv preprints (Abdill & Blekhman, published in eLife and indexed at PMC6510536) found a measurable correlation between a preprint’s bioRxiv download count and the Journal Impact Factor of the journal in which it was later published — useful context, but a correlation about the destination journal, not a metric of the preprint itself.

    • Abstract and PDF views — updated daily on the preprint’s own page.
    • Altmetric attention score — tracks news, policy, and social-media mentions.
    • Citation counts via Crossref/Google Scholar/Semantic Scholar — real citations to the DOI, independent of any journal metric.
    • Eventual journal IF, once published — applies only after the manuscript is accepted by a peer-reviewed title, and belongs to that journal, not to the preprint record.

    Answer-First Q&A

    Does bioRxiv count as published?

    No. Posting on bioRxiv is not formal publication; it is a preliminary, non-peer-reviewed manuscript. Most journals do not treat a preprint as prior publication, so authors can still submit the same work to a peer-reviewed journal afterwards without disqualification.

    Is bioRxiv a credible source?

    bioRxiv preprints undergo screening for plagiarism, scope, and safety risks, but not scientific peer review, so credibility must be assessed manuscript-by-manuscript rather than assumed from the platform. Readers should treat findings as provisional until formal peer review or replication confirms them.

    Is it okay to cite bioRxiv preprints?

    Yes. bioRxiv preprints receive a DOI and are part of the citable scientific record, indexed by Crossref, Google Scholar, and Europe PMC. NIH explicitly encourages citing preprints as interim research products in grant applications.

    Is bioRxiv considered a journal?

    No. bioRxiv is a preprint repository operated by the non-profit openRxiv, distinct from a journal because it lacks an editorial acceptance decision, a fixed issue/volume structure, and formal peer review — the three conditions JCR and Scimago require for metric eligibility.

    Implications for Research Administrators

    For institutional research offices, funders, and evaluators, the practical takeaway is definitional discipline: preprint usage and altmetrics belong in a different evidence category from journal-level citation metrics, and conflating them in tenure, grant, or REF-adjacent narrative CVs misrepresents what each number measures. A downloads count on bioRxiv answers “how much attention has this manuscript attracted,” not “how citable is this journal” — the two questions require different data sources and different caveats when reported to a research-administration committee.

    As preprint servers proliferate across disciplines, the underlying eligibility logic will not change: JCR and Scimago metrics remain reserved for peer-reviewed, editorially governed serial publications. What is likely to evolve is the sophistication of preprint-specific metrics — the Web of Science Preprint Citation Index and NISO’s altmetrics recommended practices are both signs that the field is building dedicated infrastructure rather than forcing preprints into journal-shaped metrics they were never built to receive.

  • 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.

  • Is bioRxiv Peer-Reviewed? What Screening Checks

    bioRxiv preprints are not peer-reviewed. Every submission passes a basic screening process — checked for plagiarism, offensive or non-scientific content, and research-integrity or biosecurity concerns — before posting, usually within 24-48 hours. That screening confirms a manuscript is a genuine, appropriately scoped scientific report; it does not evaluate whether the methods are sound, the data support the conclusions, or the findings are correct. Formal peer review only happens later, if and when the manuscript is submitted to a journal or an independent review service.

    bioRxiv is a free preprint server for the life sciences, operated by the non-profit openRxiv and founded by Cold Spring Harbor Laboratory in 2013, that lets researchers post manuscripts publicly before or during journal submission.

    What bioRxiv’s screening process actually checks

    bioRxiv runs a documented two-step screen on every submission. The first pass is done by in-house staff with scientific and editorial backgrounds, who confirm the manuscript is complete, correctly formatted, and within the server’s life-sciences scope. This stage automatically checks for plagiarism and rules out content that is not a research article — news items, advertisements, policy statements, narrative reviews, and protocols without new data are all excluded.

    The second pass is carried out by bioRxiv Affiliates, a network of volunteer principal investigators, who confirm the work is genuine biological research and flag anything that could pose a public-health or biosecurity risk, including what the US National Institutes of Health defines as dual-use research of concern. Overtly identifying patient information is also removed at this stage.

    • Plagiarism detection against published and preprint literature
    • Confirmation the submission is a scientific research article, not opinion, protocol, or promotional content
    • Dual-use and public-health risk screening by volunteer affiliates
    • Removal of overt patient- or participant-identifying material
    • Scope check — routing clinical-research submissions to medRxiv where appropriate

    bioRxiv’s own documentation states that roughly 5% of submissions do not clear this screen and are not posted. Screening typically completes within 24-48 hours — a fraction of the weeks or months a journal’s peer review takes, which is the entire point of a preprint server.

    Screening vs peer review: what’s the difference

    Screening is a gatekeeping check on form and conduct. Peer review is an expert evaluation of scientific substance — whether the experimental design supports the stated conclusions, whether statistics are applied correctly, and whether the work advances the field. bioRxiv is explicit that no endorsement of an article’s methods, assumptions, conclusions, or scientific quality is implied by its appearance on the server.

    Dimension bioRxiv screening Formal peer review
    Who performs it In-house staff + volunteer affiliates Independent subject-matter expert reviewers
    What it checks Plagiarism, scope, ethics, biosecurity, format Methodology, data integrity, validity of conclusions
    Typical duration 24-48 hours Weeks to several months
    Outcome Posted or rejected (~5% rejected) Accept, revise, or reject a specific journal submission
    Result on the record A citable preprint with a DOI A certified, published journal article

    Some preprints do receive structured external review while still hosted as preprints — eLife launched its Preprint Review service on bioRxiv in May 2020, and services such as Review Commons operate similarly. These are useful signals, but they are separate, named services layered on top of bioRxiv, not a function of bioRxiv’s own screening.

    Independent research (Abdill & Blekhman, cited widely including on Wikipedia) has found that roughly two-thirds of bioRxiv preprints are eventually published in a peer-reviewed journal, and bioRxiv automatically links to the published version once a match is found. That figure is a useful proxy for eventual quality, but it says nothing about the third that are never formally reviewed, and it cannot be applied to any single preprint you are reading today.

    Is medRxiv peer-reviewed too?

    No. medRxiv, bioRxiv’s sister server for clinical and health-related research, follows the same principle: manuscripts are screened, not peer-reviewed. Because medRxiv covers clinical and public-health topics, its screening is deliberately stricter — submissions undergo additional review for content that could directly influence patient behaviour or clinical practice, and certain categories (such as case reports without a clear scientific contribution) are restricted or excluded outright.

    The same “originator, not owner” caution applies here as everywhere in preprint literature: a medRxiv posting is not evidence of clinical validation and should not be treated as equivalent to a peer-reviewed clinical trial report or a regulatory submission.

    What happens to a preprint after it’s screened and posted

    Once posted, a bioRxiv preprint is permanent and citable. It receives a DOI immediately, cannot be withdrawn once published, and authors can post revised versions that retain the same DOI. Authors typically submit the same manuscript to a journal in parallel or afterwards, where it then enters that journal’s own peer-review process.

    bioRxiv operates a “bioRxiv-to-journal” (B2J) transfer service with more than 300 partner journals — including Cell Reports, PLOS Biology, Genetics in Medicine, and Molecular Biology of the Cell — allowing authors to send a screened preprint directly into a journal’s submission and peer-review pipeline without re-uploading files. This accelerates the path from preprint to certified publication but does not shortcut peer review itself.

    • Readers can post public comments, moderated to professional standards
    • bioRxiv reserves the right to remove plagiarised material or work found to breach research-integrity standards after posting
    • A link to the eventual published version is added automatically, usually within a few weeks of journal publication

    Common questions about bioRxiv and peer review

    Is bioRxiv credible?

    bioRxiv is a credible, widely used distribution channel run by a respected non-profit, but credibility of the platform is separate from validity of any individual manuscript. Screening filters out plagiarism and ethical breaches; it does not certify scientific quality, so each preprint must be read critically on its own merits.

    Is it okay to cite bioRxiv?

    Yes — bioRxiv preprints receive a DOI and are formally citable as part of the scientific record. Most style guides and journals require the citation to note explicitly that the source is an unrefereed preprint, so readers understand it has not passed formal peer review.

    Is a preprint a reliable source?

    A preprint can be a reliable indicator of ongoing research but is not a validated source in the way a peer-reviewed article is. Reliability depends on the specific manuscript — its methods, transparency, and any subsequent independent review — not on the preprint server’s basic screening alone.

    Is bioRxiv considered published?

    bioRxiv preprints are publicly posted and citable, but they are not “published” in the traditional peer-reviewed sense used by journals, funders, and most academic assessment exercises. Many institutions and funders explicitly distinguish preprints from peer-reviewed publications in reporting requirements.

    Implications for authors, readers, and institutions

    For authors, bioRxiv’s fast, lightly gated screening is the trade-off that makes rapid dissemination possible — but it also means responsibility for accuracy sits with the authors, not the platform, until formal peer review occurs. For readers and journalists, the practical rule is definitive: treat unreviewed bioRxiv claims as provisional, check whether a published, peer-reviewed version exists via the automatic journal link, and note preprint status explicitly whenever citing or reporting on one. For institutions building research-integrity or preprint-citation policies, bioRxiv’s own screening criteria — plagiarism, scope, dual-use risk, and patient confidentiality — are a useful documented baseline to reference, precisely because they are narrow and clearly bounded rather than a substitute for peer review.

    As preprint volume continues to grow across the life sciences, the distinction between “screened” and “peer-reviewed” is likely to matter more, not less — particularly as overlay review services like eLife’s Preprint Review and Review Commons expand the space between the two.

  • openRxiv Explained: Why bioRxiv and medRxiv Went Independent

    openRxiv is the independent, researcher-led nonprofit that has run bioRxiv and medRxiv since March 2025, replacing Cold Spring Harbor Laboratory’s institutional stewardship with a six-member board, diversified funding, and a mandate to keep both preprint servers free to read and free to post. The spin-off was designed to insulate two of biomedicine’s most-used pieces of open-research infrastructure from dependence on any single institution or funder — a governance question every standards body and infrastructure provider eventually has to answer.

    openRxiv is the independent nonprofit, launched on 11 March 2025, that now stewards the bioRxiv and medRxiv preprint servers on behalf of the global research community, rather than as a programme of a single host institution.

    What is openRxiv, and what does it actually run?

    openRxiv is the organisational and legal home of two preprint servers: bioRxiv, covering life sciences, and medRxiv, covering health and clinical research. Neither server changed its submission process, screening policy, or URL when the transition happened — researchers post to biorxiv.org and medrxiv.org exactly as before.

    What changed is who is accountable for the platforms’ survival. bioRxiv was founded in 2013 at Cold Spring Harbor Laboratory (CSHL); medRxiv followed in 2019 as a joint initiative between CSHL, Yale University, and BMJ. Both grew into the dominant preprint venues for biomedicine, and by 2025 that success had outgrown the administrative capacity of a single laboratory to sustain indefinitely.

    Why did bioRxiv and medRxiv leave Cold Spring Harbor Laboratory?

    CSHL’s own account of the move calls it a “natural evolution,” not a rupture. Bruce Stillman, CSHL’s President and CEO, joined openRxiv’s board rather than severing ties, and co-founders John Inglis and Richard Sever moved with the platforms into the new entity.

    The stated rationale centres on three risks that concentrated stewardship inside one institution:

    • Sustainability risk — a single laboratory’s budget cycle is not designed to guarantee decades of continuity for global research infrastructure.
    • Governance risk — decisions about screening policy, features, and funding priorities benefited from a board drawn from outside CSHL alone.
    • Funder-concentration risk — the platforms needed a structure that could accept diversified funding without any one funder gaining outsized influence.

    openRxiv formally launched as an independent nonprofit on 11 March 2025, with the Chan Zuckerberg Initiative (CZI) providing three years of seed funding for the transition, according to openRxiv’s own governance Q&A published that May. In October 2025, arXiv — the physics, mathematics, and computer science preprint server run by Cornell University — joined openRxiv in submitting a joint response to a National Institutes of Health Request for Information on preprints, signalling a wider coalition forming around shared preprint-infrastructure interests, though arXiv itself remains a separate service.

    Who governs openRxiv, and who pays for it?

    openRxiv is governed by a six-member board of directors: Scott Fraser (University of Southern California and the CZI Imaging Institute), Edith Heard (Francis Crick Institute), Jeff Huber (Triatomic Capital), Harlan Krumholz (Yale School of Medicine; medRxiv co-founder), Bruce Stillman (CSHL), and Shirley Tilghman (Princeton University). A separate Scientific and Medical Advisory Board, chaired by John Inglis with medRxiv co-founder Theo Bloom as deputy, advises on content policy.

    The funding question is where most scrutiny has landed, given CZI’s long involvement with both servers before the spin-off:

    Question openRxiv’s public answer (governance Q&A, May 2025)
    How long has CZI funded the servers? Eight years for bioRxiv, four years for medRxiv, plus three years of dedicated seed funding for the openRxiv transition itself.
    Does CZI have editorial or operational control? No. openRxiv states funding agreements carry no stipulations affecting editorial or operational independence.
    How much board influence does CZI hold? One of six directors (Scott Fraser) has a CZI affiliation; the board is not CZI-appointed as a bloc.
    Is openRxiv against traditional peer review? No — openRxiv reports roughly 75% of bioRxiv and medRxiv preprints go on to formal peer-reviewed publication, with direct-submission links to 350 journals.

    openRxiv itself frames the governance model as a direct answer to funder-concentration concerns: the organisation states its mission is to be “governed by and for the research community, not a single funder, founder, or any one stakeholder.” Whether a philanthropic vehicle tied to a single tech-sector family remains structurally sufficient as the largest funder of a nonprofit intended to resist single-funder capture is a debate that predates this specific spin-off and will likely recur as openRxiv pursues its stated goal of diversifying revenue further.

    What is openRxiv Labs, and what launched in June 2026?

    openRxiv Labs launched on 1 June 2026 as a structured experimentation programme sitting on top of the core bioRxiv and medRxiv infrastructure. Rather than running many small tests at once, openRxiv committed to a small number of larger, hypothesis-driven pilots with predefined success metrics and durations, publishing results — including failures — openly on a dedicated Labs blog.

    The first Labs pilot, built with the platform Curvenote, tests an interactive preprint-reading interface layered onto openRxiv’s existing corpus of preprints, figures, and metadata. openRxiv named a broad partner list for the programme, including CZI, CSHL, the Sergey Brin Family Foundation, Caltech, CNRS, Fred Hutchinson Cancer Center, Imperial College London, MIT, Stanford, the University of Washington, and Vrije Universiteit Amsterdam — underscoring that the funder-diversification effort begun at launch has continued into 2026 rather than stalling after the initial CZI seed grant.

    Answer-first questions people are asking about openRxiv

    Who is the CEO of openRxiv?

    Dr Tracy Teal is openRxiv’s first Chief Executive Officer, appointed on 18 August 2025 after serving as interim COO since the March 2025 launch. She previously led The Carpentries and Dryad, two established open-research infrastructure nonprofits, giving her direct prior experience running community-governed scientific platforms.

    Who owns medRxiv?

    No single institution “owns” medRxiv today. It was founded in 2019 by Cold Spring Harbor Laboratory, Yale University, and BMJ, but operational and governance responsibility now sits with openRxiv, the independent nonprofit created specifically to steward it and bioRxiv without institutional or single-funder control.

    Is medRxiv a credible source?

    medRxiv preprints are screened but not peer-reviewed, so they should be cited with that caveat clearly stated. openRxiv reports around 75% of postings eventually complete formal peer review; until then, findings represent unverified claims from qualified researchers, useful for rapid awareness but not equivalent to a published, peer-reviewed article.

    What is openRxiv, in one line?

    openRxiv is the independent 501(c) nonprofit, launched 11 March 2025, that operates bioRxiv and medRxiv under a six-member board and a diversified-funding mandate, replacing their prior status as programmes hosted by Cold Spring Harbor Laboratory.

    What the openRxiv spin-off means for research-infrastructure stewardship

    The openRxiv case is a useful reference point for any organisation weighing how to govern shared research infrastructure once it outgrows its founding institution. The pattern — an originating body incubates a tool, the tool becomes essential community infrastructure, and stewardship then transfers to an independent, multi-stakeholder body — is not unique to preprints.

    CASRAI originated the CRediT contributor role taxonomy in 2014. The standard is now stewarded by NISO as ANSI/NISO Z39.104-2022. That is the same “originator, not owner” pattern openRxiv is now navigating in public: CSHL originated bioRxiv and medRxiv, and stewardship has since passed to a body structured explicitly to prevent any one funder, founder, or institution from controlling research infrastructure the whole field depends on.

    For research administrators and institutional leaders, the practical takeaway is to watch governance structure, not just funding source, when assessing an infrastructure provider’s long-term reliability. A named, multi-institutional board; published funding-independence commitments; and open reporting of pilot outcomes (as with openRxiv Labs) are the concrete signals worth checking — independent of who wrote the first cheque.