CASRAI Dictionary

Author: MCP Service

  • bioRxiv Alerts: Email, RSS or API Options

    bioRxiv alerts let researchers and developers track newly posted preprints in a chosen subject area without manually rechecking the site — the three core options are subject-category email alerts, per-category RSS/Atom feeds, and the public bioRxiv API, each suited to a different workflow. bioRxiv is the preprint server for biology operated by openRxiv, a nonprofit dedicated to advancing scientific communication, and it exposes the same underlying content through all three channels plus social feeds on Bluesky, Mastodon and X.

    This guide compares the four practical ways to follow new bioRxiv postings — email alerts, RSS/Atom feeds, the REST API, and social feeds — so you can pick the right combination for a literature-monitoring workflow, a lab dashboard, or an automated pipeline.

    What are bioRxiv’s alert options?

    bioRxiv is a preprint server for the biological sciences; a preprint is a complete scientific manuscript posted online before, or without, formal peer review. Because thousands of preprints are posted every week across dozens of subject categories, bioRxiv publishes the same feed of new content through four distinct channels rather than a single notification system.

    Each channel trades off timeliness, filtering precision and technical effort differently. Email alerts and RSS feeds are built for passive monitoring by individual researchers; the API is built for developers who need structured metadata inside another tool; social feeds suit anyone already working inside those platforms.

    How do bioRxiv email alerts work?

    Email alerts are the lowest-effort option for an individual researcher who wants a periodic digest. You sign up on the bioRxiv Alerts page, select one or more of bioRxiv’s roughly 30 subject categories — from Bioinformatics to Zoology — and bioRxiv emails you when matching preprints are posted.

    • Alerts can be scoped to a subject category, a keyword search, or a specific author.
    • You can add or remove subject-area alerts at any time from the same sign-up page, without deleting your account.
    • No bioRxiv account or login is required simply to receive category alerts — the sign-up form only asks for an email address.

    This makes email alerts the right default for anyone who wants new preprints in their inbox without building or maintaining anything.

    How do bioRxiv RSS feeds work?

    bioRxiv’s Alerts/RSS page publishes an Atom 1.0 feed for each subject category, plus a combined feed across all categories. Each feed returns only the most recent 30 posts for that category — a hard limit set by bioRxiv, not a filter you can extend — so an RSS reader that checks infrequently can silently miss older items once more than 30 new preprints accumulate.

    Feeds can be combined by chaining subject categories with a plus sign in the URL, and multi-word category names use an underscore in place of a space. For example, a feed combining Genomics and Bioinformatics takes the form:

    • http://connect.biorxiv.org/biorxiv_xml.php?subject=genomics+bioinformatics

    This lets a single feed reader subscription cover several adjacent subject areas — useful for interdisciplinary groups — without needing separate subscriptions per category.

    What can the bioRxiv API do that alerts and RSS can’t?

    The bioRxiv API is a pull-based REST interface returning structured JSON metadata — DOI, title, authors, category, posting date and abstract — for preprints on bioRxiv and medRxiv. Unlike email alerts or RSS, it has no built-in subject-category filter parameter and no push/webhook mechanism: a developer must query by date interval or DOI and filter the returned category field client-side.

    That distinction matters for anyone building automated tooling:

    • The API suits scheduled polling jobs, institutional repository harvesters, and research-tool dashboards that need structured metadata, not just a headline and link.
    • RSS and email alerts remain the simpler choice for a single researcher who only wants to read new titles as they appear.
    • Because the API is pull-based, any “alert” built on top of it requires you to run your own polling schedule and de-duplication logic.

    Detailed field definitions and endpoint syntax are published in bioRxiv’s own API documentation, which developers should consult directly before building a production integration.

    Should you follow bioRxiv on Bluesky, Mastodon or X?

    bioRxiv also mirrors new postings to social platforms, and this is where the biggest recent change sits — one that generic alert guides tend to miss. Beyond the long-standing X/Twitter account (@biorxivpreprint, over 140,000 followers, plus a dedicated account per subject category), bioRxiv now runs an equivalent set of per-category streams on Bluesky (e.g. biorxiv-bioinfo.bsky.social) and Mastodon (e.g. biorxiv_bioinfo on biologists.social).

    This matters because X restricted free API access in 2023, which reduced the reliability of X-based bots and dashboards that many labs had built to watch subject feeds. Bluesky and Mastodon’s open, API-friendly protocols make them a more dependable base for anyone building a custom preprint-monitoring bot today, rather than a nice-to-have alternative.

    Which option should you choose?

    The right channel depends on how much filtering precision you need and how much technical effort you are willing to invest.

    Channel Best for Filtering Setup effort Key limitation
    Email alerts Individual researchers wanting a digest Subject, keyword, author None (email only) No login needed, but digest cadence isn’t real time
    RSS/Atom feed Feed-reader users, interdisciplinary groups Subject category, combinable Low (add feed URL) Capped at the most recent 30 posts per category
    REST API Developers, institutional tools, dashboards None built-in; filter client-side High (build a polling job) Pull-based only, no webhook/push
    Bluesky/Mastodon/X Social monitoring, bot-building Per subject-category account Low–Medium X reach reduced since 2023 API restrictions

    For most individual researchers, subject-category email alerts remain the simplest reliable option. Developers building institutional or lab-wide monitoring tools should combine the API for structured metadata with RSS as a lightweight fallback.

    Common questions about bioRxiv alerts

    Why are my bioRxiv email alerts not working?

    Missed bioRxiv alerts are usually caused by an out-of-date subject-category selection, an alert email landing in a spam or promotions folder, or an expired confirmation link. Re-visiting the bioRxiv Alerts page and re-confirming your chosen categories resolves most cases.

    Do I need a bioRxiv account or login to set up alerts?

    No account or login is required for basic email alerts — only an email address. A bioRxiv account is only needed for actions like submitting a manuscript, posting a comment, or managing an author profile, not for receiving subject-area notifications.

    Does bioRxiv have a public API for developers?

    Yes. bioRxiv publishes a public REST API returning JSON metadata — including DOI, title, category and abstract — for content on bioRxiv and medRxiv. It is pull-based, so developers must schedule their own queries rather than receive push notifications.

    Should I track bioRxiv or arXiv for my subject area?

    Choose based on discipline, not preference: bioRxiv covers biology-specific subject categories, while arXiv covers physics, mathematics, computer science and quantitative biology. Researchers working across both fields — for example in computational biology — often need alerts from both servers rather than treating them as interchangeable.

    What this means for research-monitoring workflows

    Preprint volume keeps growing across biology subject categories, and no single channel covers every use case. A researcher who only needs a daily digest is well served by email alerts; a developer building a literature-surveillance tool for an institution needs the API’s structured metadata and should plan for its pull-based, polling architecture from the outset. Teams that previously relied solely on X-based bots should treat the 2023 API restrictions as a prompt to add Bluesky or Mastodon, or the official RSS feed, as a more durable foundation.

    Research administrators supporting open-scholarship workflows can pair these tracking methods with broader terminology in the CASRAI Dictionary when documenting how preprints fit into an institution’s research-administration processes.

  • 101 Innovations in Scholarly Communication: 2026

    101 Innovations in Scholarly Communication is a 2015–2016 survey and open dataset, built by Bianca Kramer and Jeroen Bosman of Utrecht University Library, that mapped how more than 20,000 researchers, librarians, publishers and funders were adopting digital tools across six phases of the research workflow. Revisited a decade on, the underlying dataset and taxonomy still frame how institutions read today’s tool landscape — and they show preprints moving from a peripheral publication tactic to a structural stage in the scholarly communication cycle.

    101 Innovations in Scholarly Communication is best understood as both a crowdsourced database of research tools and a workflow taxonomy: it organises tool adoption into six stages — discovery, analysis, writing, publication, outreach and assessment — and remains the most cited empirical baseline for how digital tools reshaped academic practice before the current wave of open-science mandates.

    What is the 101 Innovations in Scholarly Communication project?

    The project began in spring 2015 when Kramer and Bosman launched a survey asking researchers and research-support staff which tools and services they actually used, rather than which they were told to use. The survey ran from May 2015 to February 2016 and drew responses from over 20,000 participants worldwide, making it one of the largest empirical pictures of research-tool adoption ever assembled.

    Crucially, the project was never a simple popularity poll. Kramer and Bosman built a crowdsourced resource database of research tools alongside the survey, and published the anonymised dataset openly — a practice that itself demonstrated the open-science values the project was measuring. The output most people recognise is the poster mapping roughly 101 tools by year of launch and workflow stage, first presented at Force2015 and reproduced across library guides and blogs ever since.

    What did the six-phase workflow reveal about tool adoption?

    The survey’s most durable contribution is its six-phase model of the research workflow: discovery, analysis, writing, publication, outreach and assessment. Each phase captured a different cluster of emerging tools, from literature-alert services in discovery to altmetrics providers in assessment, and the analysis found a median of around 22 different tools in active use per respondent.

    That figure mattered because it quantified a problem institutions were only beginning to name: workflow fragmentation. Researchers were not choosing a single platform; they were stitching together a personal stack, often spanning free, subscription and institutionally licensed tools. The published analysis also flagged a specific risk — that publishers such as Elsevier and Springer Nature were acquiring tools across multiple phases, raising the prospect of vendor lock-in across an entire research workflow rather than a single product.

    Workflow phase 2015 survey emphasis 2026 landscape signal
    Discovery Alerts, Google Scholar, library databases AI-assisted literature search layered onto existing indexes
    Analysis Excel, SPSS, early notebooks Open notebooks and reproducible-analysis pipelines
    Writing Word processors, early collaborative editors Cloud-native collaborative authoring as default
    Publication Preprints as an emerging, minority practice Preprints as a funder-recognised compliance route
    Outreach Dropbox used more than GitHub for sharing protocols Persistent-identifier-linked outputs (DOIs, ORCID) as default
    Assessment Early altmetrics alongside citation counts Contributor-role taxonomies alongside altmetrics

    Where do preprints sit in the research cycle now?

    In the 2015 dataset, preprint servers appeared in the publication phase as one option among many, used by a minority of respondents concentrated in physics, mathematics and, increasingly, biology. A decade later, scientific preprints have moved from a niche discovery-to-publication bridge to a structural checkpoint that funders and journals actively reference.

    This shift is visible in funder policy rather than survey sentiment alone. cOAlition S’s Plan S rights-retention approach explicitly permits preprint deposit combined with a rights-retention licence as a route to immediate open-access compliance, and journals across the life sciences now routinely accept manuscripts that have already circulated on bioRxiv or medRxiv. The practical effect is that preprints no longer sit only in the “outreach” gap the original survey identified between writing and formal publication — they now function as a recognised, citable stage in their own right within the scholarly communication cycle.

    What the 2015 baseline still gets right is the underlying diagnosis: tool adoption in scholarly communication rarely moves as a single wave. Preprints diffused unevenly by discipline then, and adoption of preprint-linked policies remains uneven by discipline and funder now — the survey’s disaggregated view of workflow stages is why that unevenness is still visible rather than averaged away.

    How has the standards and identifier layer changed since 2015?

    The 2015 survey’s vendor lock-in warning has a direct institutional answer that has matured substantially since the data was collected: the persistent-identifier and standards layer. ORCID identifiers for researchers, DataCite DOIs for datasets, and the Research Organization Registry (ROR) for institutional affiliation now interoperate across discovery, publication and assessment tools in a way that was still emergent in 2015.

    Contributor attribution has followed the same trajectory. CASRAI originated the CRediT contributor role taxonomy in 2014, the same year the 101 Innovations survey was being designed; the standard is now stewarded by NISO as ANSI/NISO Z39.104-2022, giving the “assessment” phase of the original workflow model a formal, interoperable vocabulary for who-did-what that the survey’s respondents were, at the time, largely improvising without.

    • ORCID: persistent identifiers for individual researchers, reducing name-disambiguation friction across discovery and assessment tools.
    • DataCite: DOI registration for datasets and other non-article outputs, extending citability beyond the journal article.
    • ROR: standardised institutional identifiers, used increasingly by funders and publishers for affiliation matching.
    • ANSI/NISO Z39.104-2022 (CRediT): a controlled taxonomy of contributor roles, now stewarded by NISO.

    Answer-first questions on the survey and its legacy

    What is the 101 Innovations in Scholarly Communication survey?

    It is a 2015–2016 survey and open dataset created by Bianca Kramer and Jeroen Bosman of Utrecht University Library, which asked over 20,000 researchers and research-support staff which digital tools they used across six phases of the research workflow, then published the anonymised results openly.

    What are the six phases of the scholarly communication cycle it identified?

    The survey defined the cycle as discovery, analysis, writing, publication, outreach and assessment. Each phase groups a distinct set of tools, from literature-alert services and reference managers through to altmetrics and peer-review platforms, giving institutions a structured way to audit workflow tool adoption.

    Why did the survey warn about vendor lock-in?

    The analysis found large commercial publishers acquiring tools spanning multiple workflow phases, meaning a researcher could end up dependent on a single company’s suite from discovery through assessment. That concentration risk is the reason interoperable, standards-based alternatives such as ORCID, DataCite and ROR have gained institutional priority since.

    Are preprints still a minority practice in scholarly communication?

    No. Preprints have shifted from a discipline-specific minority practice in 2015 to a funder-recognised compliance route under policies such as cOAlition S’s rights-retention strategy, with routine preprint-to-journal pipelines now standard in fields including biomedicine and physics.

    What this means for institutions, publishers and developers

    For research administrators and institutional leaders, the practical lesson from re-reading the 101 Innovations dataset in 2026 is that workflow fragmentation has not disappeared — it has been partially re-solved through standards rather than consolidation. Where the 2015 survey found researchers assembling a median of 22 tools with little interoperability, the current landscape increasingly links those tools through shared persistent identifiers and controlled vocabularies rather than through a single vendor suite.

    For publishers and developers building on the scholarly communication cycle, the implication is that preprint infrastructure, contributor-role metadata, and organisational identifiers are no longer optional add-ons; they are the connective tissue the original survey’s respondents were missing. The next iteration of tool-landscape research will need to measure not just which tools researchers pick, but how well those tools speak to each other across the discovery-to-assessment pipeline — a question the original taxonomy was designed to surface, and one that remains unresolved a decade on.

  • Scholarly Communication Librarian: Remit & KPIs

    A scholarly communication librarian is the institutional specialist who manages an organisation’s research-dissemination lifecycle — open access compliance, institutional repository content, author rights and copyright advice, and research-impact metrics — usually from within, or alongside, the university library. For research administrators scoping this function for the first time, the practical questions are rarely about the job title itself but about remit, reporting line, and how success is measured.

    Scholarly communication is defined by the Association of College & Research Libraries (ACRL) as “the system through which research and other scholarly writings are created, evaluated for quality, disseminated to the scholarly community, and preserved for future use” — a definition first published in ACRL’s 2003 white paper Principles and Strategies for the Reform of Scholarly Communication and still the field’s standard reference point.

    What does a scholarly communication librarian actually do?

    A scholarly communication librarian coordinates four practical work streams: institutional repository management, publishing services, copyright and author-rights advice, and research-impact assessment. The NASIG Core Competencies for Scholarly Communication Librarians, adopted in 2017 and revised in 2020, describes the role’s duties as “broad and amorphous” by design — a single post-holder rarely owns every strand, and responsibility is often diffused across a wider library team.

    In day-to-day terms, that means: encouraging and processing repository deposits, checking publisher self-archiving and embargo terms, advising authors on publication agreements and Creative Commons licensing, running open access and OER outreach (often timed around International Open Access Week), and helping researchers interpret citation and altmetrics data for tenure, promotion, or funder reporting.

    What is the remit of an institutional office of scholarly communication?

    An office of scholarly communication is the organisational unit — typically nested inside the university library — that holds institution-wide responsibility for these duties rather than leaving them to individual subject librarians. Its remit generally spans five areas: institutional repository management, publishing services, copyright services, research data management, and assessment/impact metrics, as set out in the joint COAR/OCLC Librarians’ Competencies Profile for Scholarly Communication and Open Access (Calarco et al., 2016).

    Institutions vary in how much of this remit sits in one office versus being distributed. The University of Edinburgh’s Scholarly Communications Team is a working example of a centralised model: it “supports University staff and students before, during and after publication of their research,” managing policy compliance, the institutional repository (ERA), and the research information system (PURE) as a single service point.

    Who does a scholarly communication librarian report to?

    There is no single reporting model across the sector. Four structures recur most often in job postings and organisational charts, and the choice usually reflects whether an institution treats scholarly communication as a collections function, a research-support function, or a technology function.

    Reporting model Typical manager Institutional emphasis
    Collections-integrated Associate University Librarian for Collections & Scholarly Communication Ties open access and repository work to acquisitions and collection strategy
    Research-services-integrated Associate University Librarian for Research Services / Academic Success Positions the role alongside research support, data management, grants
    Digital-scholarship unit Head of Digital Scholarship Groups scholarly communication with data curation and digital publishing
    Distributed/diffuse No single line manager; shared across subject librarians Spreads responsibility rather than centralising it in one post

    For research administrators building a business case, the reporting line matters because it determines which budget line funds the post, which committee sets its priorities, and whether the role has authority to negotiate publisher agreements directly or must route decisions through acquisitions or general counsel.

    What competencies and skills does the role require?

    NASIG’s framework groups core competencies into four cross-cutting themes — background knowledge, technical skills, outreach and instruction, and team building — layered under whichever of the five areas of emphasis a given post prioritises. Practical requirements include:

    • Working knowledge of copyright law, fair use/fair dealing, and publisher self-archiving policies
    • Familiarity with repository platforms (e.g. DSpace, Digital Commons, Fedora) and identifier systems such as CrossRef and DataCite DOIs and ORCID
    • Ability to interpret bibliometrics and altmetrics without overstating what a single indicator (such as the Journal Impact Factor) can support
    • Project management skills to run cross-departmental initiatives with subject librarians, university counsel, and IT
    • Comfort advising on funder open access mandates and institutional policy drafting

    Author-identifier and contribution-tracking literacy increasingly falls within this remit too. CASRAI originated the CRediT contributor role taxonomy in 2014; the standard is now stewarded by NISO as ANSI/NISO Z39.104-2022, and scholarly communication librarians are frequently the staff who explain CRediT tagging to authors submitting to journals that require it.

    What KPIs do institutions use to measure the role?

    Because the remit spans compliance, service, and advocacy work, institutions typically track a mixed basket of KPIs rather than a single output metric:

    • Compliance KPIs: proportion of eligible outputs deposited in the repository within funder-mandated windows (for UK institutions, this maps to REF open access requirements and UKRI’s policy, in force for journal articles and conference proceedings since 1 April 2022 and extended to monographs, book chapters and edited collections from 1 January 2024)
    • Service KPIs: turnaround time on copyright and publishing-agreement queries; number of consultations delivered
    • Adoption KPIs: repository deposit volume and growth; OER adoption rate and associated student cost savings
    • Outreach KPIs: workshop and training attendance; policy and guidance page usage
    • Impact-reporting KPIs: volume of impact-metrics consultations supporting tenure, promotion, or funder reporting cycles

    Compliance and adoption KPIs are the ones most directly reportable to institutional leadership and funders, since they map to external mandates rather than internal service-level judgement calls.

    Answer-first Q&A

    What does a scholarly communication librarian do?

    A scholarly communication librarian manages an institution’s research dissemination lifecycle: encouraging and processing institutional repository deposits, advising authors on copyright and publisher agreements, supporting open access compliance, and helping researchers interpret citation and altmetrics data for promotion or funder reporting purposes.

    Who does a scholarly communication librarian report to?

    Reporting lines vary by institution. Most commonly the role sits under an Associate University Librarian for Collections, Research Services, or Digital Scholarship, though some institutions run a distributed model where duties are shared across subject librarians rather than assigned to one dedicated post.

    Not exactly. Copyright services are one of five recognised areas of emphasis within scholarly communication work, alongside repository management, publishing services, data management, and impact assessment — a copyright librarian is typically a specialist within, not synonymous with, the broader role.

    What skills does a scholarly communication librarian need?

    Core requirements include copyright and licensing knowledge, familiarity with repository platforms and identifier systems (DOIs, ORCID), bibliometrics literacy, project management ability, and comfort translating funder open access mandates into institutional policy and researcher-facing guidance.

    Implications for research administrators building the team

    Institutions standing up this function from scratch should decide the reporting line before writing the job description, since the five areas of emphasis rarely fit into one full-time post. A common pattern is to hire a generalist scholarly communication librarian first, then add copyright or data-management specialists as the repository, compliance, and outreach workload grows. Aligning KPIs to funder mandates — UKRI open access policy, REF-linked deposit windows — gives the post measurable, leadership-visible outcomes from year one rather than only qualitative service-desk activity.

    As funder identifier requirements expand and CRediT-style contribution tagging becomes more common in submission systems, institutions that fold author-identifier and contribution-metadata literacy into this role early will spend less time retrofitting compliance processes later. Research administrators building or reviewing this function should treat it as a standing institutional capability, not a project team, and revisit its remit and KPIs whenever a major funder policy changes.

  • bioRxiv or medRxiv? Choosing the Right Server for Clinical vs Basic Research

    bioRxiv or medRxiv? Choose bioRxiv for basic, non-clinical life-sciences research such as genetics, microbiology or neuroscience, and medRxiv for clinical, epidemiological or public-health research that could influence patient care. The two preprint servers do not overlap: posting the same manuscript to both is prohibited and can result in withdrawal.

    A preprint server is an open-access repository where researchers post a scientific manuscript publicly before it has completed formal peer review. bioRxiv and medRxiv are the two sibling servers operated by openRxiv for the life and health sciences respectively, and the correct choice between them depends on subject scope, not on which sounds more prestigious.

    On this page:

    What is the difference between bioRxiv and medRxiv?

    bioRxiv launched in 2013 at Cold Spring Harbor Laboratory (CSHL) as a preprint server for basic biology; medRxiv followed in 2019 as a dedicated server for clinical and health-sciences manuscripts. In March 2025, CSHL transferred governance of both platforms to openRxiv, a newly formed independent nonprofit, marking the most significant structural change since bioRxiv’s founding.

    Neither server is a journal. medRxiv is not a journal — it is a repository, and nothing posted there has been peer reviewed or certified. Both platforms carry explicit caution notices stating that preprints should not guide clinical practice, inform health-related behaviour, or be reported as established findings.

    The practical distinction authors need is scope, not scale: bioRxiv covers fundamental biological research with new data, while medRxiv is reserved for work that could plausibly influence a clinical decision, a public-health response, or patient behaviour.

    Where should clinical trials and health research go?

    Any manuscript reporting a clinical trial, an epidemiological study, or research with direct implications for diagnosis, treatment or public-health policy belongs on medRxiv. bioRxiv’s own submission guidance is explicit that new clinical trial reports and most epidemiology submissions must now go to medRxiv rather than bioRxiv.

    medRxiv applies stricter screening than bioRxiv precisely because misinterpreted clinical claims carry public-harm risk. One detail authors frequently miss: medRxiv does not accept case reports or case series, so single-patient or small-series clinical write-ups need a different outlet even when the subject matter is unambiguously medical.

    • Randomised controlled trials and other interventional studies
    • Epidemiological and public-health surveillance research
    • Studies involving patient-level clinical or health-behaviour data
    • Infectious disease, oncology, cardiovascular medicine and psychiatry manuscripts

    Where should microbiology, neuroscience and basic biology go?

    bioRxiv is the correct venue when the research advances fundamental biological understanding without a direct clinical application. Its subject categories include microbiology, neuroscience, genetics, immunology, cell biology and bioinformatics, among others, and submissions are screened by volunteer bioRxiv Affiliates chiefly for scope, plagiarism and public-harm potential.

    A microbiology paper characterising a novel bacteriophage, or a neuroscience paper mapping neural circuitry in a model organism, sits comfortably on bioRxiv provided it does not extend into patient data or treatment recommendations. The moment a microbiology study becomes an infectious-disease outbreak analysis, or a neuroscience study becomes a neurology or psychiatry treatment study, the correct server changes to medRxiv.

    How do you decide when a study sits on the border?

    Most submission confusion happens in a handful of predictable grey zones where a basic-science category on bioRxiv has a clinical counterpart on medRxiv. openRxiv’s own subject-category lists make the pairing explicit, and mapping them side by side is the fastest way to resolve a borderline decision.

    bioRxiv category (basic science) medRxiv category (clinical counterpart) Decision rule
    Genetics / Genomics Genetic and Genomic Medicine Patient-directed diagnosis or therapy → medRxiv
    Neuroscience Neurology / Psychiatry and Clinical Psychology Patient treatment or behaviour outcomes → medRxiv
    Microbiology Infectious Diseases Outbreak, surveillance or patient-cohort data → medRxiv
    Pharmacology and Toxicology Pharmacology and Therapeutics Human dosing, trial or therapeutic outcome data → medRxiv

    As a working test: if the manuscript’s conclusion could reasonably change what a clinician does at the bedside, or what a public-health body recommends, it belongs on medRxiv regardless of how “basic” the underlying technique feels. If it reports mechanism, model-organism data or method development with no direct patient or population-health claim, bioRxiv is the right home.

    Under the International Committee of Medical Journal Editors’ recommendations, posting to a recognised preprint server does not count as prior or duplicate publication and does not preclude subsequent journal submission — but authors should still confirm the target journal’s own preprint policy before posting either version.

    Questions authors ask

    Is bioRxiv reputable?

    Yes. bioRxiv is a well-established, widely used life-sciences preprint server operated by openRxiv, screened by volunteer affiliates for plagiarism, scope and biosafety concerns. It is not peer reviewed, but it is recognised across academic biology as a legitimate venue for early-stage research dissemination.

    Is medRxiv trustworthy?

    medRxiv applies a stricter, additional screening layer beyond bioRxiv’s because of the public-harm risk in clinical and health content. Every posted manuscript carries a prominent caution notice stating it has not been certified by peer review and should not guide clinical practice, making its scope and limitations transparent to readers.

    What is the difference between bioRxiv and medRxiv?

    bioRxiv covers basic, non-clinical life sciences; medRxiv is reserved for clinical, epidemiological and health-sciences research with potential patient or public-health impact. Screening intensity, disclaimer wording and accepted article types differ accordingly, and a single manuscript cannot be posted to both servers simultaneously.

    What are the alternatives to bioRxiv?

    Depending on field, authors also use arXiv for quantitative and computational biology work, Research Square or journal-integrated “In Review” services, and discipline-specific repositories such as ChemRxiv. None of these substitute for medRxiv when a manuscript is clinically actionable.

    What this means for authors and institutions

    For individual authors, the server choice is a compliance decision, not a branding one: submitting a clinical manuscript to the wrong server risks a request to withdraw and resubmit, delaying the timestamp priority a preprint is meant to secure. Research administrators tracking institutional preprint activity — an increasingly routine part of research administration workflows — should build the bioRxiv/medRxiv scope test into pre-submission checklists rather than leaving it to individual author judgement.

    For institutions and publishers, the March 2025 move to independent openRxiv governance is worth tracking: it signals that preprint infrastructure for biology and medicine is now managed as permanent scholarly-communication infrastructure rather than a single laboratory’s side project, with implications for long-term archival stability and policy planning. Definitions of related terms, including preprint, postprint and version of record, are maintained in the CASRAI Research Administration Dictionary.

    The practical rule holds regardless of field: match the manuscript’s real-world consequence, not its disciplinary label, to the server’s scope, and treat the bioRxiv/medRxiv boundary as a public-harm question rather than a prestige one.

  • Preprint Servers List by Discipline: 2026 Guide

    The right preprint server depends entirely on discipline: bioRxiv and medRxiv serve biomedicine, arXiv still dominates physics, mathematics and computer science, TechRxiv and engrXiv cover engineering, PsyArXiv leads psychology, and Preprints.org is one of the few platforms that formally accepts review articles alongside original research. This preprint servers list compares scope, governance, screening rules and 2026 policy changes across each field, so researchers and research offices can match a manuscript to the right platform rather than defaulting to the best-known name.

    A preprint server is an online repository where researchers deposit a complete but not-yet-peer-reviewed manuscript so it becomes citable and publicly readable before formal journal publication. Coverage, screening rigour and accepted article types vary sharply by field, which is why a single “best preprint server” answer is misleading.

    What is a preprint server, and why does discipline matter?

    A preprint server is a repository that posts a complete scholarly manuscript before it has undergone formal peer review, giving it a timestamp, a DOI and open readability. Screening is typically limited to checking that a submission is genuinely scholarly, complete and does not pose a public-health or safety risk — it is not equivalent to peer review.

    Disciplines differ in what they will screen for and what article types they will accept. A biology preprint about a novel protein structure and a psychology preprint reporting a null replication result face entirely different moderation standards, which is why choosing the correct preprint server list entry for your field matters more than choosing the largest or most famous platform.

    Which preprint server should biomedical and clinical researchers use?

    Biomedicine is served by two related but distinct platforms, both operated by openRxiv, the nonprofit spun out of Cold Spring Harbor Laboratory. bioRxiv covers basic life-sciences research, while medRxiv — described on its own site as “the preprint server for Health Sciences” — is reserved for clinical, epidemiological and public-health manuscripts and applies stricter screening because its content can influence clinical practice.

    • A manuscript cannot be posted to both bioRxiv and medRxiv simultaneously.
    • medRxiv states plainly in its FAQ that “there is no fee to submit manuscripts.”
    • medRxiv screening includes clinicians who check for content that could mislead patients or clinical decision-making.

    Which preprint server leads for physics, mathematics and computer science?

    arXiv, founded in 1991 and hosting more than a million articles, remains the dominant server for physics, mathematics, computer science, quantitative biology, statistics and quantitative finance. Its moderation relies on volunteer subject-area moderators rather than paid editorial staff.

    Two 2026 developments matter for anyone comparing arXiv to newer platforms. First, arXiv formally declared operational independence from Cornell University in March 2026, a governance shift reported by Science that separates its stewardship from a single host institution. Second, arXiv tightened its new-author policy: as of January 2026, first-time submitters in all categories need either an institutional email address plus a prior publication record on arXiv, or a personal endorsement from an established arXiv author — and in computer science categories specifically, review articles and position papers must already be accepted by a recognised journal or conference before they can be posted.

    Which preprint servers cover engineering and psychology?

    Engineering does not have a single dominant server in the way physics or biology do. TechRxiv, backed by the Institute of Electrical and Electronics Engineers (IEEE), and engrXiv, supported by the Center for Open Science, both accept a broad range of engineering and technology manuscripts, alongside arXiv’s own electrical-engineering and systems-science categories.

    PsyArXiv, hosted on the Open Science Framework and managed by the Society for the Improvement of Psychological Science, is the closest thing psychology has to a discipline-wide default. It moderates submissions for scholarly relevance and, in 2026, moved to stricter verification of authors’ publication records for certain submission types, alongside its existing encouragement of preregistration and data-availability statements.

    Server Primary discipline Governing body Accepts review articles Notable 2026 development
    bioRxiv Biology / life sciences openRxiv (nonprofit) Not as a standalone article type —
    medRxiv Medicine / health sciences openRxiv (nonprofit) No No submission fee (confirmed in FAQ)
    arXiv Physics, maths, CS, stats Independent nonprofit (formerly Cornell-hosted) Restricted; CS reviews need prior journal/conference acceptance Declared independence from Cornell, March 2026
    TechRxiv Engineering & technology IEEE Yes —
    engrXiv Engineering sciences Center for Open Science Yes —
    PsyArXiv Psychology Society for the Improvement of Psychological Science / OSF Yes Stricter author-verification moderation, 2026
    Preprints.org Multidisciplinary MDPI Yes — explicit “Review” article type Passed 124,000+ hosted preprints

    Which preprint server accepts review articles — Preprints.org vs arXiv?

    This is where discipline-agnostic platforms diverge sharply from field-specific ones. Preprints.org, governed by MDPI and hosting over 124,000 preprints, explicitly lists “Review” as one of its recognised submission types alongside original articles, communications and data descriptors — making it one of the more accommodating multidisciplinary choices for authors of literature reviews and systematic reviews.

    arXiv, by contrast, treats review and position papers as a special case rather than a default article type: in its computer science categories, such papers must already have been accepted by a recognised journal or conference before arXiv will host them. bioRxiv similarly does not treat “review article” as a standard submission category — its FAQ describes comment-based peer discussion, not narrative reviews, as the mechanism for post-publication critique.

    For authors specifically searching for where to deposit a review manuscript, this is a genuine and under-reported distinction: Preprints.org and general-purpose repositories such as SSRN or Research Square are structurally more open to review articles than the flagship subject-specific servers.

    Frequently asked questions

    What is a preprint server?

    A preprint server is an online repository where researchers deposit a complete, unpublished manuscript before peer review, so it receives a timestamp, a citable DOI and open access. It performs basic scholarly and safety screening but does not certify the findings the way peer review does.

    Is medRxiv free to use?

    Yes. medRxiv’s own FAQ states there is no fee to submit manuscripts. Authors do not pay to post, and readers access preprints without a paywall, consistent with its role as an open, nonprofit health-sciences repository operated by openRxiv.

    Does bioRxiv accept review papers?

    Not as a standard submission type. bioRxiv is built around original research reports, and its FAQ describes structured comments — not narrative or systematic review articles — as its mechanism for post-posting critique. Authors of review manuscripts typically use Preprints.org or a discipline-general server instead.

    What are the disadvantages of preprints?

    Preprints have not been peer-reviewed, so findings can be incomplete, later revised, or misreported by media before formal validation. Negative public comments on a preprint may also influence subsequent peer review, and some journals still restrict submissions that overlap heavily with an already-public preprint.

    Implications for research administrators and institutions

    Research offices advising authors on open-access compliance need a discipline-aware view, not a single institutional default. A biomedical clinical trial preprint belongs on medRxiv given its clinician screening; a systematic review destined for a multidisciplinary audience is far more likely to be accepted on Preprints.org than on arXiv or bioRxiv. Institutions building preprint guidance pages should map manuscript type and discipline to platform before recommending “post it on arXiv” as a blanket instruction.

    Funders and publishers referencing preprint policy should also note governance changes such as arXiv’s 2026 separation from Cornell, since institutional affiliation and stewardship arrangements can affect long-term archiving guarantees that research administrators rely on when advising on data-management and preservation plans.

    Conclusion: choosing by discipline, not by brand

    There is no universal “best” preprint server. bioRxiv and medRxiv fit biomedicine, arXiv still defines physics, mathematics and computer science despite tightened 2026 submission rules, TechRxiv and engrXiv split the engineering space, PsyArXiv anchors psychology, and Preprints.org stands out as the multidisciplinary option most open to review articles. Authors and research offices get the best outcome by treating this preprint servers list as a field-by-field decision, not a single default choice.

  • Scientific Preprints: What the 2026 Survey Shows

    Scientific preprints are now a routine part of research life, but new 2026 survey evidence shows researchers remain deeply divided on whether posting one helps or hurts a career. A scientific preprint is a complete draft of a research manuscript shared publicly before formal peer review, most commonly via a discipline-specific server such as bioRxiv, medRxiv, arXiv or Preprints.org. Across three separate studies published in 2025-2026, most researchers say preprints speed up dissemination and widen visibility, yet a majority still believe evaluators reward peer-reviewed journal articles over preprints when it comes to hiring, promotion and funding decisions.

    What do the 2026 preprint surveys actually show?

    The most detailed new evidence comes from a survey of nearly 1,800 biomedical researchers in the United States and Canada, fielded in early 2025 and posted to bioRxiv in March 2026 under the title “Faster science, penalties in evaluation, and concerns on quality and impact: Researchers’ use and perceptions of preprints”. Its findings, also reported by Science/AAAS, describe engagement driven mainly by speed rather than any deeper commitment to open science.

    Two smaller but complementary studies add discipline and geography to the picture: a 2026 cross-sectional survey of 103 medical faculty at Marmara University in Türkiye, published in JMIRx Med, and a 2025 nationwide survey of 170 early-career researchers in India, run by the Indian National Young Academy of Science with the International Science Council and reported by Research Matters. Together they show that global attitudes to preprints are not converging; they are fragmenting by discipline, career stage and national research-assessment culture.

    How many researchers read, cite and post preprints?

    In the US/Canada biomedical survey, two-thirds of respondents had read at least one preprint in the previous two years, roughly half had submitted one themselves, and only about one-third had cited one in their own published work. Nearly half of respondents said they worried preprints could spread shoddy research or misinformation before it has been checked.

    Survey Population and date Sample size Headline finding
    Researchers’ Use and Perceptions of Preprints (bioRxiv, 2026) US and Canadian biomedical researchers, fielded early 2025 ~1,800 Two-thirds had read a preprint in two years; most did not believe posting one improved career prospects
    Awareness, Experiences and Attitudes Toward Preprints Among Medical Academics (JMIRx Med, 2026) Medical faculty, Marmara University, Türkiye 103 Awareness was inconsistent and clinical adoption remained cautious
    INYAS/International Science Council nationwide survey (2025) Early-career researchers, India 170 52.3% cited fear of being “scooped” as the top barrier to posting a preprint

    The gap between reading, citing and posting matters. Researchers evidently trust preprints enough to consult them for current findings, but a much smaller group is willing to stake a citation, and fewer still are willing to post their own unreviewed work under their name.

    Do preprints help or hurt career advancement?

    The bioRxiv survey is unambiguous on this point: researchers on average do not believe publishing preprints enhances their career advancement. More than 60% of respondents who sit on funding, hiring or tenure committees said they give more credit to peer-reviewed papers than to preprints, and fewer than 12% said they credit both equally. Only around 16% strongly agreed that preprints reduce the weight evaluators place on articles in subscription, peer-reviewed journals.

    Yet the same respondents were not dismissive of preprints as a practice. Two-thirds of hiring-committee members said they viewed preprints favourably as evidence of productivity and momentum, even while acknowledging that a preprint carries less formal weight than a peer-reviewed publication. Researchers also credited preprints with two concrete, non-evaluative benefits: they spread findings faster than peer-reviewed journals do, and they help authors find collaborators. Credibility judgements, meanwhile, still lean heavily on author reputation rather than any formal quality signal attached to the preprint itself.

    • Career-advancement belief: low, on average, across all three 2025-2026 surveys.
    • Speed-to-dissemination benefit: consistently rated the strongest advantage.
    • Credibility heuristic: author and institutional reputation, not peer review status.
    • Formal recognition in tenure and promotion frameworks: still rare or absent.

    Why does adoption vary so much by country and discipline?

    Adoption is shaped less by technology access than by how national research-assessment systems treat unreviewed work. In India, the top-cited barrier to posting a preprint was fear of being “scooped” (52.3% of respondents in the INYAS/International Science Council survey), closely followed by a lack of institutional recognition. A genuine, if narrow, policy shift is under way there: India’s University Grants Commission guidelines now permit preprints to be considered as part of doctoral-degree assessment, a concrete recognition step most other jurisdictions have not yet matched.

    In Türkiye, the JMIRx Med survey of clinical academics found inconsistent awareness of what a preprint even is, alongside caution rooted in traditional publishing norms in medicine. That pattern echoes wider findings from Digital Science’s 2025 State of Open Data report, the longest-running annual survey of open-research behaviour, which found that two-thirds of over 43,000 researcher respondents still feel they receive insufficient credit for open practices generally — a “credit gap” that maps directly onto preprint hesitancy.

    Answer-first: common preprint questions

    What is a scientific preprint?

    A scientific preprint is a complete manuscript version shared publicly, typically via a dedicated server, before it has completed formal peer review or journal publication. It lets researchers establish priority and gather early feedback while the manuscript is still moving through review at a journal.

    Are preprints credible?

    Preprints carry no guarantee of quality because they bypass formal peer review, but many undergo basic screening by the hosting server. Survey evidence shows readers judge credibility mainly by author reputation and institutional affiliation rather than any formal quality mark on the preprint itself.

    Can preprints be cited in academic work?

    Yes. Major style guides, including APA, provide explicit reference formats for preprints, and ICMJE recommendations permit citing them provided the version is clearly identified as unreviewed. Reviewers should still prefer the peer-reviewed version once one exists.

    Do preprints help or hurt a researcher’s career?

    2026 survey data show a split effect: preprints speed up dissemination and help researchers find collaborators, but most respondents do not believe posting one improves career advancement, and over 60% of evaluators still credit peer-reviewed papers more heavily in hiring and tenure decisions.

    What this means for institutions and publishers

    The consistent finding across all three 2025-2026 surveys is a mismatch between researcher behaviour and institutional recognition. Researchers are reading, and increasingly posting, preprints for pragmatic reasons — speed, visibility, collaboration — while formal evaluation frameworks lag behind. India’s UGC decision to count preprints toward doctoral assessment is a rare example of policy catching up with practice; most institutions have not made an equivalent move.

    For research administrators and publishers, the practical implication is that preprint policy cannot be treated as a peer-review question alone. It touches authorship and contribution standards, since credit for early-shared work still needs to be attributed accurately, and it belongs firmly within research administration policy on how non-traditional outputs are counted in assessment. Clear institutional guidance — not just server-level screening — is what closes the credit gap these surveys describe.

    Where preprint culture goes next

    None of the 2025-2026 evidence suggests preprint use will slow. Reading and posting rates are already high across biomedical fields, and funders are steadily normalising rapid, open sharing of results. What has not caught up is formal recognition: until hiring, promotion and funding committees credit preprints on comparable terms to peer-reviewed work, the gap between researcher enthusiasm and institutional reward will persist. The 2026 surveys make that gap measurable for the first time at this scale — the next test is whether assessment frameworks respond.

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

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

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

    What is the PreprintToPaper dataset?

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

    The dataset sorts every preprint into one of three categories:

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

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

    How does bioRxiv link a preprint to its published paper?

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

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

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

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

    What publication delays does the dataset reveal?

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

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

    How much do titles and abstracts change before publication?

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

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

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

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

    Does bioRxiv count as published?

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

    Can I cite a preprint in my paper?

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

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

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

    What are the implications for institutions and publishers?

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

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

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

  • Chai-2 bioRxiv: Comparing AI Biology Preprints Ahead of Peer Review

    The Chai-2 bioRxiv preprint, posted by Chai Discovery on 5 July 2025, reports a 16% hit rate in fully de novo antibody design — more than 100-fold above prior computational methods — but like the ESM3 and Geneformer foundation models it sits alongside, the claim has not yet cleared peer review. All three are part of a wider pattern: AI biology foundation models are increasingly disseminated as bioRxiv preprints first, journal articles later (if at all), which changes how institutions, publishers, and funders must scrutinise their claims.

    A bioRxiv preprint is a manuscript posted to the Cold Spring Harbor Laboratory’s biology preprint server before, or instead of, formal peer review. This article compares how Chai-2, ESM3, Geneformer, EvolvePro, and AlphaFold-Multimer have each used that route, and what the differences mean for reproducibility.

    What is Chai-2, and why was it posted as a bioRxiv preprint?

    Chai-2 is a multimodal generative model from Chai Discovery that designs antibodies and nanobodies from scratch, taking a target structure and epitope as input and returning a complete antibody design. The original preprint, “Zero-shot antibody design in a 24-well plate”, reported a 16% success rate in de novo design against 52 diverse targets, completed from AI design to wet-lab validation in under two weeks.

    Chai Discovery followed with an updated bioRxiv preprint on 29 November 2025, “Drug-like antibody design against challenging targets”, reporting that more than 86% of designed full-length monoclonal antibodies showed developability profiles comparable to approved therapeutics. Neither preprint has yet been published in a peer-reviewed journal. The company has since raised a $130 million Series B round, taking total funding above $225 million at a $1.3 billion valuation, according to Genetic Engineering & Biotechnology News.

    How do ESM3 and Geneformer differ from Chai-2 in preprint dissemination?

    ESM3 and Geneformer address different biological scales entirely, and their publication paths diverge from Chai-2’s in an instructive way. ESM3, from EvolutionaryScale, is a general-purpose protein language model trained on roughly 2.78 billion protein sequences with a 98-billion-parameter flagship configuration. It was posted as a preprint before its 2025 publication in Science — meaning it eventually completed the peer-review cycle that Chai-2’s antibody preprints have not yet reached.

    Geneformer operates at the cellular level rather than the molecular level. Built on a transformer-encoder architecture pretrained across tens of millions of single-cell RNA-sequencing profiles, it classifies cell types and predicts disease-relevant genes. Its foundational description, credited to Christina Theodoris and colleagues, circulated as a preprint before formal publication in Nature in 2023.

    EvolvePro and AlphaFold-Multimer extend the comparison further. EvolvePro is a few-shot protein-engineering framework that uses language-model embeddings to guide directed evolution from very few labelled variants, disseminated via bioRxiv. AlphaFold-Multimer, Google DeepMind’s extension of AlphaFold2 for multi-chain complex prediction, is the starkest case: its 2021 bioRxiv preprint (Evans et al.) has been cited thousands of times and underpins structural biology workflows worldwide, yet it has never been published in a peer-reviewed journal.

    Model Domain bioRxiv posting Weight access Peer-review status
    Chai-2 De novo antibody design v1 Jul 2025; updated Nov 2025 Platform/API access, not fully open weights Preprint only
    ESM3 General protein sequence/structure/function Preprint, then Science (2025) Smaller checkpoints open; 98B flagship gated via Forge API Peer-reviewed
    Geneformer Single-cell transcriptomics Preprint, then Nature (2023) Fully open-weight release Peer-reviewed
    EvolvePro Few-shot directed protein evolution bioRxiv preprint Open code/model release Preprint at time of posting
    AlphaFold-Multimer Multi-chain complex structure prediction bioRxiv preprint (2021) Code and weights open-sourced Never published in a peer-reviewed journal

    Why does preprint-first publication intensify reproducibility scrutiny?

    Preprint-first publication compresses the interval between a headline result and its public citation, which is valuable for fast-moving fields but removes a layer of independent verification before claims circulate. AlphaFold-Multimer shows this can persist indefinitely: a preprint can become de facto infrastructure without ever completing formal review.

    • Model weight access varies sharply: Geneformer and AlphaFold-Multimer are fully open, while Chai-2 and ESM3’s largest configuration require platform or API access, limiting independent replication of the exact reported result.
    • Benchmark scale differs: Chai-2’s 16% hit rate is drawn from a company-run benchmark across 52 targets, not an externally adjudicated challenge such as CASP or CAPRI.
    • Versioning matters: Chai-2’s updated November 2025 preprint extends claims to full-length monoclonal antibodies, meaning readers must track which version underlies any given statistic.

    For research administrators and institutional evaluators, the practical implication is that a citation to “Chai-2” or “ESM3” is not self-evidently a citation to peer-reviewed work — the preprint status, version, and weight-access terms all need checking before the claim is treated as settled.

    Common questions about AI biology preprints on bioRxiv

    Is the Chai-2 bioRxiv preprint peer-reviewed?

    No. As of publication, both Chai-2 preprints — the July 2025 original and the November 2025 update — remain bioRxiv preprints. Neither has completed formal peer review, so the reported 16% hit rate and 86% developability figures should be read as company-reported, not journal-vetted, results.

    Has ESM3 been published in a peer-reviewed journal?

    Yes. ESM3 was first circulated as a preprint before EvolutionaryScale’s results were published in Science in 2025, giving it a completed peer-review path that Chai-2’s antibody-design claims currently lack.

    What is Geneformer used for?

    Geneformer analyses single-cell RNA-sequencing data to classify cell types, model gene regulatory networks, and identify disease-relevant genes, using a transformer architecture trained on large single-cell transcriptome corpora rather than protein or antibody sequences.

    What is the difference between Chai-2 and AlphaFold-Multimer?

    AlphaFold-Multimer predicts the 3D structure of existing multi-chain protein complexes, while Chai-2 generates entirely new antibody sequences and structures for a chosen target — structure prediction versus de novo generative design.

    What are the implications for institutions, publishers, and funders?

    Research administrators citing Chai-2, ESM3, Geneformer, or comparable models in grant reports, technology assessments, or institutional communications should distinguish preprint claims from peer-reviewed findings explicitly, note the exact preprint version, and record whether model weights are open or platform-gated. Publishers and editors evaluating manuscripts that build on these models should likewise verify which version of the underlying preprint is cited, since headline metrics can shift between versions.

    The broader lesson is structural rather than model-specific: as AI biology moves faster than journal review cycles, the preprint-to-journal gap itself becomes a due-diligence checkpoint that institutions, funders, and publishers now need to track as routinely as they track the results themselves.

  • bioRxiv Template: LaTeX & Word Formatting Guide

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

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

    Does bioRxiv Require a Specific Manuscript Template?

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

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

    Which LaTeX Template Should You Use for bioRxiv?

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

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

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

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

    Formatting a bioRxiv Manuscript in Word

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

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

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

    What File Formats and Figure Rules Does bioRxiv Require?

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

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

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

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

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

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

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

    Frequently Asked Questions About bioRxiv Submission

    Can anyone submit to bioRxiv?

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

    How much does it cost to submit to bioRxiv?

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

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

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

    When should you submit to bioRxiv?

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

    What This Means for Authors and Institutions

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

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

  • BioRxiv ISSN Explained: Why It’s Not a Journal

    BioRxiv holds ISSN 2692-8205, but an ISSN is a serial-registration number, not proof of peer review. BioRxiv is a preprint repository, not a peer-reviewed journal: it has no Scimago Journal Rank, no Scopus record and no impact factor, because those metrics apply only to indexed journals, and bioRxiv does not perform peer review.

    BioRxiv is an open-access preprint repository for the biological sciences, launched in November 2013 by John Inglis and Richard Sever and now operated by the nonprofit openRxiv. Confusion about its status is common because bioRxiv looks and behaves like a journal platform — it has a citable DOI, a formal ISSN and a Wikipedia entry — while lacking the editorial infrastructure that “indexing” actually measures.

    Does bioRxiv have an ISSN, and what does that prove?

    BioRxiv is registered with ISSN 2692-8205, listed in the ISSN Portal and cross-referenced in the NLM Catalog under record ID 101680187, where the U.S. National Library of Medicine lists its electronic ISSN and title abbreviation “bioRxiv: the preprint server for biology”. An ISSN is issued by the ISSN International Centre to any continuing resource — journals, newspapers, monograph series, and repositories that publish serially.

    Holding an ISSN confirms only that a publication is a recognised, ongoing serial with a stable identity. It carries no implication about peer review, editorial oversight, or scholarly indexing. Many predatory journals and informal newsletters also carry valid ISSNs, which is precisely why the number is frequently mistaken for a quality signal.

    Is bioRxiv indexed in Scimago or Scopus?

    No. Scimago Journal & Country Rank derives its rankings exclusively from the Scopus citation database, which indexes peer-reviewed journals, conference proceedings and book series — not preprint servers. Because bioRxiv preprints are not peer-reviewed at the point of posting, they fall outside Scopus’s inclusion criteria, and bioRxiv correspondingly has no Scimago Journal Rank (SJR) or quartile ranking.

    Search results that appear to show “bioRxiv” scientometric profiles, such as third-party aggregator pages listing publication and citation counts, are counting citations to the individual preprints hosted on the platform, not a journal-level metric assigned to bioRxiv itself. This distinction matters for anyone assessing where a piece of research sits in the scholarly record.

    ISSN record vs. Scimago-indexed journal
    Attribute bioRxiv (ISSN 2692-8205) Typical Scimago/Scopus-indexed journal
    Peer review before posting No — basic screening only Yes — mandatory
    ISSN Yes Yes
    Scopus/Scimago listing No Yes (if indexed)
    Impact factor / SJR None Assigned annually
    Editorial board with reject/accept decisions No Yes
    DOI registration Yes, via Crossref (prefix 10.1101) Yes, via Crossref or DataCite

    What does bioRxiv’s Wikipedia entry actually describe?

    The Wikipedia article for bioRxiv describes it plainly as “an open access preprint repository for the biological sciences”, founded by John Inglis and Richard Sever in November 2013 and inspired by arXiv, the physics and mathematics preprint server launched by Paul Ginsparg in 1991. The entry documents bioRxiv’s ownership history in detail: it was hosted by Cold Spring Harbor Laboratory (CSHL) until 11 March 2025, when ownership transferred to openRxiv, a newly formed nonprofit created to run bioRxiv and its clinical-sciences counterpart, medRxiv.

    Nowhere does the entry describe bioRxiv as a peer-reviewed journal. It explicitly notes that submissions “undergo a basic scrutinisation process, which includes safeguarding checks, an automated plagiarism screening and an assessment of appropriateness” — a moderation gate, not editorial peer review. The article also cites a 2019 eLife meta-research study (Abdill and Blekhman) finding that roughly two-thirds of bioRxiv preprints are subsequently published in peer-reviewed journals, underscoring that bioRxiv functions as a pre-publication staging ground rather than a publication venue in its own right.

    Is bioRxiv a journal, and what does “indexing” really mean?

    BioRxiv is not a journal. In scholarly-communication terms, “indexing” means a database such as Scopus, Web of Science, PubMed or the Directory of Open Access Journals has evaluated a title against inclusion criteria — regular publication schedule, peer review, editorial governance, ethical standards — and added its articles to a searchable, citation-tracked index. bioRxiv preprints are discoverable and citable via Google Scholar, PubMed Central (in some cases) and their own DOIs, but that is discovery, not journal indexing.

    • ISSN registration confirms serial identity only.
    • DOI registration (via Crossref) confirms a persistent, citable identifier for a specific preprint version.
    • Scopus/Web of Science indexing confirms a journal has passed a database’s editorial and peer-review vetting process.
    • Scimago/impact factor are journal-level citation metrics computed only for indexed journals — bioRxiv has neither.

    The bioRxiv-to-Journals (B2J) initiative, which by May 2020 allowed authors at 177 participating journals to submit a posted preprint directly into a journal’s manuscript system, illustrates the actual relationship: bioRxiv is a feeder and archive that sits upstream of formal, indexed publication, not a substitute for it. For definitions of related scholarly-communication terms, see the CASRAI Dictionary.

    Answer-first Q&A

    Does bioRxiv have an ISSN?

    Yes. BioRxiv holds ISSN 2692-8205, registered with the ISSN International Centre and cross-listed in the NLM Catalog (record 101680187). An ISSN is a serial-identification number confirming bioRxiv is a continuing publication series — it does not certify that content has passed peer review or editorial vetting.

    Is bioRxiv considered a journal?

    No. BioRxiv is a preprint repository, not a peer-reviewed journal. Submissions undergo only basic screening for plagiarism, safeguarding and appropriateness, not scientific peer review. A 2019 eLife study found roughly two-thirds of bioRxiv preprints are later published in peer-reviewed journals.

    Is bioRxiv a publisher?

    BioRxiv describes itself as an archive and distribution service, operated by the nonprofit openRxiv since March 2025 (previously hosted by Cold Spring Harbor Laboratory). It distributes manuscripts rather than publishing them editorially — authors remain free to submit the same work to a journal afterwards.

    How do you cite bioRxiv?

    Cite bioRxiv preprints using their DOI (prefix 10.1101, registered via Crossref), per bioRxiv’s own FAQ guidance. If multiple versions exist, cite the version-specific URL. ICMJE-aligned journals typically require the citation to flag the work explicitly as a preprint, unlike a peer-reviewed indexed article.

    What this means for authors and institutions

    For research administrators and institutional leaders verifying publication records, the practical takeaway is definitive: a bioRxiv deposit is not equivalent to a peer-reviewed, indexed publication for the purposes of research assessment exercises, promotion dossiers, or funder reporting, regardless of how citable or ISSN-bearing the platform is. Research administration teams verifying publication records for compliance purposes should treat a bioRxiv ISSN or DOI as evidence of deposit and discoverability, not as evidence of peer review or journal-level standing.

    Authors should continue citing bioRxiv preprints by DOI, clearly labelled as preprints, and should track whether a peer-reviewed version has since appeared in an indexed journal — since roughly two-thirds eventually do. Terminology precision matters here: conflating “has an ISSN” with “is indexed” or “is a journal” produces avoidable errors in CVs, grant reports and library catalogues. As preprint servers proliferate across disciplines, the ISSN-versus-indexing distinction bioRxiv illustrates will only become more relevant to how research administrators, publishers and funders classify the scholarly record.