CASRAI Dictionary

Tag: elife biorxiv

  • PNAS bioRxiv Direct Submission: How B2J Works

    The PNAS bioRxiv submission pathway runs through bioRxiv’s own bioRxiv-to-journal (B2J) transfer tool, which sends manuscript files, figures and author metadata straight from a preprint’s “Author Area” into a partner journal’s editorial system. PNAS Nexus, the open-access companion journal published with Oxford University Press, is a listed B2J partner; the flagship PNAS journal instead accepts bioRxiv preprints under its standard “posting is permitted” policy, handled through ordinary manual submission. Nature and eLife each use a third and fourth mechanism again — this guide maps all of them.

    Direct submission, in the strict bioRxiv sense, means B2J: an automated transfer of files and metadata that removes the need to re-upload a manuscript at the receiving journal. That is a narrower, more specific claim than “the journal accepts preprints,” and conflating the two is the most common error in advice about preprint-to-journal workflows.

    Does PNAS accept direct submission from bioRxiv?

    Yes, but the route depends on which PNAS title is involved. PNAS’s Standard License Terms state that authors retain “the right to post the manuscript on preprint servers such as arXiv or bioRxiv,” and its editorial policies confirm that posting on preprint servers “is permitted and will not affect editorial consideration.” That is a preprint-tolerance policy, not a file-transfer mechanism.

    For an actual B2J connection — where bioRxiv pushes the manuscript and metadata into the journal’s submission system — the relevant partner on bioRxiv’s own list is PNAS Nexus, the fully open-access companion journal the National Academy of Sciences launched with Oxford University Press in 2022. Authors submitting to the flagship PNAS still upload independently and disclose the bioRxiv DOI in their cover letter or submission form.

    How does bioRxiv’s B2J transfer system actually work?

    bioRxiv describes B2J as a service that “can save authors time in submitting papers to journals or peer review services by transmitting their manuscript files and metadata directly from bioRxiv.” Authors do not re-enter author lists, funding statements or figure files; the receiving journal’s system pulls them from the preprint record.

    bioRxiv’s live Submission Guide lists 192 partner journals and peer-review services participating in B2J at the time of this analysis (mid-2026), spanning the PLOS family, EMBO’s three journals, Cell Press titles such as Cell Reports and Cell Genomics, the Royal Society’s journals, AAAS’s Science-family titles (Science Advances, Science Immunology, Science Signaling, Science Translational Medicine), Genetics Society journals, and independent review services including Review Commons.

    • Confirm the preprint version you want to transfer — revisions keep the same DOI, so specify the version-specific URL if it matters.
    • Select a reuse licence on bioRxiv (CC BY, CC BY-NC, CC BY-ND, CC BY-NC-ND or CC0) before transfer, since this travels with the metadata.
    • Check the receiving journal’s own preprint-disclosure requirement — B2J moves files, but editorial policy compliance remains the author’s responsibility.
    • Verify funder mandate compatibility (for example NIH Public Access or cOAlition S requirements) before relying on the preprint version alone for compliance.

    bioRxiv itself is operated by openRxiv, described on its own Submission Guide as “a non-profit organization dedicated to advancing science communication” — a distinct entity from any single receiving journal, which is why B2J participation is a per-journal opt-in list rather than a universal feature.

    How does Nature handle bioRxiv preprints?

    Nature and most Nature-branded journals treat a bioRxiv posting as compatible with submission, not as prior publication, so authors can submit a manuscript that already exists as a bioRxiv preprint. Unlike PNAS Nexus, however, neither the flagship Nature journal nor its major sister titles appear on bioRxiv’s public B2J partner list, so there is no automated file transfer from bioRxiv into Nature’s own submission system as of this analysis.

    The practical route is the standard one: submit through the journal’s own online system and disclose the preprint DOI in the cover letter. Springer Nature separately runs “In Review,” a partnership with Research Square that posts a preprint alongside transparent, published peer-review reports for participating journals — a related but functionally different bridge from bioRxiv’s B2J, since it originates on the journal side rather than the preprint-server side.

    How does eLife’s preprint-review model differ?

    eLife’s relationship with bioRxiv is the tightest of the three, but it is not a simple file-transfer either. eLife announced its bioRxiv-integrated transfer option in 2017, letting authors “upload a preprint to bioRxiv first and then transfer their files for consideration by eLife.” In December 2020, eLife announced it would require all new submissions to be posted as preprints on bioRxiv, medRxiv or an equivalent server before review — a policy shift reported by Science/AAAS at the time.

    Since its 2023 “Publish, Review, Curate” model, eLife no longer issues accept/reject decisions after review. Every manuscript it reviews is published as a Reviewed Preprint — the bioRxiv (or medRxiv) posting itself, plus public peer reviews and an eLife Assessment summarising significance and evidence strength. The preprint version and the eLife editorial layer stay linked rather than being replaced by a separate “Version of Record.”

    Journal / publisher Preprint policy Mechanism from bioRxiv Notable detail
    PNAS (flagship) Posting permitted; not prior publication Manual submission; author discloses DOI Reviewers may see the preprint version directly
    PNAS Nexus Same NAS preprint stance Listed bioRxiv B2J partner Open-access companion journal, launched with OUP in 2022
    Nature (and most sister titles) Preprints not treated as prior publication Standard submission; not on bioRxiv’s B2J list Separate “In Review” service via Research Square for some titles
    eLife Preprint posting required since Dec 2020 Author-initiated transfer from bioRxiv Author Area (since 2017) Since 2023, all reviewed papers are published as bioRxiv-linked Reviewed Preprints

    Common questions on bioRxiv journal submission

    Does PNAS allow bioRxiv?

    Yes. PNAS’s Standard License Terms and editorial policies explicitly state that posting on preprint servers such as arXiv or bioRxiv is permitted and does not count as prior publication. Authors must disclose the preprint and its DOI during submission, and the flagship title is submitted manually rather than via bioRxiv’s automated B2J transfer.

    Who owns bioRxiv?

    bioRxiv is operated by openRxiv, which describes itself as “a non-profit organization dedicated to advancing science communication.” It is independent of any single publisher, which is why individual journals — including flagship PNAS and Nature — must separately opt in to its B2J transfer list rather than automatically inheriting it.

    Is eLife a preprint?

    Not exactly. eLife is a journal whose reviewed output is published as a Reviewed Preprint — the underlying bioRxiv or medRxiv posting plus eLife’s public peer reviews and an eLife Assessment. Since its 2023 model change, eLife does not issue a separate accept/reject “Version of Record”; the linked preprint remains the article of record.

    How long does a bioRxiv submission take?

    bioRxiv’s own FAQ states manuscripts are screened and typically post within hours of submission, with full-text HTML and XML conversion following one to two days later. This screening checks for offensive or non-scientific content and biosecurity risk, not scientific validity — bioRxiv preprints are explicitly not peer-reviewed before posting.

    What this means for authors and research offices

    For corresponding authors, the practical takeaway is definitional precision: check whether a target journal is a bioRxiv B2J partner (automated transfer) or merely preprint-tolerant (manual submission plus disclosure) before assuming a “direct” route exists. The two are not interchangeable, and the difference determines whether re-uploading files is necessary.

    For research administrators and institutional research offices tracking author compliance across preprint and published versions, the distinction also affects funder-mandate reporting: a bioRxiv posting satisfies green open-access requirements under policies such as those referenced by cOAlition S signatories, independent of whether the receiving journal later uses B2J or a manual route. Institutions monitoring this pipeline should treat “preprint accepted” and “direct B2J transfer available” as two separate checklist items, not one.

    Journal-side preprint bridges will likely keep diverging rather than converging: bioRxiv’s B2J list continues to add peer-review services (such as Review Commons) alongside traditional journals, while eLife’s Reviewed Preprint model and Springer Nature’s In Review service represent journal-initiated alternatives built for transparency rather than upload convenience. Authors and research offices should expect to track policy pages per title rather than assume a single universal standard.

  • eLife BioRxiv Model: Review After Posting Changes Peer Review

    eLife biorxiv review works in reverse order to a conventional journal: the paper is posted publicly on bioRxiv first, and eLife’s editors and reviewers evaluate it only after it is already visible to the world, publishing the result as a “Reviewed Preprint” rather than issuing an accept-or-reject verdict.

    A Reviewed Preprint is a bioRxiv or medRxiv manuscript that has been through eLife’s editorial and peer-review process and is published, alongside public reviews and an eLife Assessment, without a binary publication decision attached to it.

    What Is eLife’s Preprint-Only Review Model?

    eLife requires every submission to already exist as a preprint, typically on bioRxiv or medRxiv, before its editors will consider it. Editors — themselves active researchers — screen incoming preprints and select a subset for full review. In 2023, eLife formalised this into its Publish, Review, Curate model, removing the accept/reject gate entirely: any preprint that goes through full review is published as a Reviewed Preprint, regardless of how favourable the assessment turns out to be.

    This inverts the journal’s traditional role. Instead of deciding whether a paper reaches readers, eLife’s reviewers now decide how a paper readers can already see should be interpreted, through a public review and a standardised eLife Assessment describing the significance of the findings and the strength of the evidence.

    How Does eLife Review a Preprint Already on bioRxiv?

    The workflow eLife uses is consultative rather than adversarial, and it produces a single, consolidated verdict rather than several disconnected reviewer reports. In practice it runs through six stages:

    1. The author posts the manuscript to bioRxiv or medRxiv as a preprint.
    2. The author submits the same preprint to eLife for consideration.
    3. A reviewing editor screens the preprint and decides whether to send it for full review; many submissions are declined at this stage.
    4. Two or three external reviewers and the editor hold a consultative discussion to produce one consolidated set of comments rather than separate, sometimes-conflicting reports, with authorship and contribution details carried over from the original preprint.
    5. eLife publishes the preprint together with the public reviews and an eLife Assessment as a Reviewed Preprint.
    6. The author chooses whether, and when, to revise the work, resubmit it for further review, or declare it a Version of Record.

    This builds on a service eLife had already run since May 2020, when it launched “Preprint Review” to bring peer review to manuscripts already on bioRxiv, and on a submission pathway available since 2017 that let authors upload to bioRxiv while submitting to eLife in parallel.

    How Does This Differ From Traditional Pre-Publication Peer Review?

    The core difference is sequencing: in a conventional journal, review happens before the public ever sees the manuscript, and the outcome of that review is a gatekeeping decision. In eLife’s model, the manuscript is already public, and review adds an evaluative layer on top of it rather than deciding whether it exists at all.

    Feature eLife’s model Traditional pre-publication review
    Timing Publish first, review second Review first, publish only if accepted
    Outcome No accept/reject; all reviewed work is published as a Reviewed Preprint Binary accept/reject decision
    Transparency Reviews and eLife Assessment published openly Reviewer identities and comments usually confidential
    Author control Author decides when to revise or declare a Version of Record Author must satisfy editor/reviewers to be published at all
    Unit of evaluation Article-level assessment Journal-level acceptance, often read as a proxy for quality

    The trade-off is real, not just structural. Because Clarivate’s Journal Impact Factor methodology requires an indexed journal to publish only papers that editors have formally validated as acceptable, eLife’s decision to publish every reviewed preprint — regardless of the assessment’s verdict — led Clarivate to discontinue eLife’s Journal Impact Factor from its 2025 Journal Citation Reports release, ending a metric that had stood at 6.4.

    Where Does bioRxiv Fit Among Preprint Servers?

    bioRxiv (pronounced “bio-archive”) is a free preprint server for the life sciences, operated by openRxiv, a nonprofit dedicated to advancing scientific communication. It sits within a wider ecosystem of subject-specific preprint servers, several of which are frequently confused with one another or with journal-run review platforms such as Research Square’s In Review.

    Server Field Screening model
    bioRxiv Life sciences Basic screening only; operated by nonprofit openRxiv
    medRxiv Health sciences / clinical Additional screening for clinical risk; also run by openRxiv
    arXiv Physics, maths, computer science Moderated but not peer-reviewed; run by Cornell University
    Research Square Multidisciplinary Preprint posting plus optional “In Review” integrated peer review, tied to Springer Nature journals
    SSRN Social sciences, economics, law Basic screening; owned by Elsevier
    ChemRxiv Chemistry Basic screening; run by chemical societies

    The distinction that matters for the “biorxiv or arxiv” question is disciplinary scope, not rigour: arXiv predates bioRxiv by more than two decades and serves physical sciences, while bioRxiv (launched 2013) was purpose-built for biology. Neither performs peer review itself — that is precisely the gap eLife’s model was designed to fill for bioRxiv content.

    What Does This Mean for Research Administrators and Institutions?

    For research administration offices, the practical question is no longer whether a preprint has been reviewed, but whether assessment, promotion, and funding-reporting processes recognise a Reviewed Preprint as equivalent to a conventional accepted article. That question is not yet uniformly answered.

    • The US National Institutes of Health has permitted preprints to be cited in grant applications and biosketches since 2017, establishing precedent that funders can recognise unpublished-but-posted work.
    • eLife reports that a growing number of funders now explicitly recognise Reviewed Preprints, rather than only the eventual Version of Record, in research assessment.
    • Institutions signed to the San Francisco Declaration on Research Assessment (DORA) already commit to evaluating research on its own merits rather than journal-level metrics — directly compatible with article-level eLife Assessments, since Clarivate no longer supplies a journal Impact Factor to fall back on.
    • Research administrators handling REF-style exercises, tenure dossiers, or grant reports need local guidance on whether the Reviewed Preprint, the eLife Assessment, or the Version of Record is the citable unit — under the 2023 model, all three can exist for one piece of work, each with its own DOI in a single version log.

    A data point often missing from commentary on the model: a 2019 eLife study by Abdill and Blekhman tracking bioRxiv preprint outcomes found eLife published almost as many bioRxiv preprints (394) in 2018 as any other single journal — over a third of its 1,172 articles that year — years before the 2023 model made this the default route.

    Common Questions About eLife and bioRxiv

    Is eLife a preprint?

    No. eLife is a journal, not a preprint server. It reviews manuscripts that authors have already posted as preprints on bioRxiv or medRxiv and publishes the result as a Reviewed Preprint — the preprint plus public reviews and an eLife Assessment, distinct from the original unreviewed posting.

    What is bioRxiv used for?

    bioRxiv is used to share life-sciences research immediately, before or independent of journal peer review. Researchers post manuscripts to establish priority, gather early feedback, and make findings available while formal review — at eLife or elsewhere — is still under way, sometimes for months.

    Why did eLife lose its impact factor?

    Clarivate discontinued eLife’s Journal Impact Factor because eLife now publishes every peer-reviewed submission as a Reviewed Preprint regardless of the review outcome, rather than issuing conventional accept/reject decisions. Clarivate’s indexing rules require journals to publish only editorially validated papers, so eLife’s model fell outside that requirement from the 2025 Journal Citation Reports release.

    Is eLife a high-impact journal?

    eLife’s citation performance was historically strong — its last Journal Impact Factor was 6.4 — but it no longer carries a Clarivate-assigned Impact Factor. Its standing is now judged through article-level eLife Assessments and public reviews rather than a single journal-wide citation metric.

    As more funders and institutions formalise how they treat Reviewed Preprints, Public Reviews, and eLife Assessments in research assessment, eLife’s model looks less like an isolated experiment and more like an early test case for peer review as a layer added on top of open preprints, rather than a gate placed in front of them. Research offices that decide this now — before it becomes a routine dossier question — will have a real advantage over those that wait for a funder mandate to force the issue.