HHMI requires posting of both initial and revised preprints. It defines an initial preprint as “a preprint that is published as the first formal communication of novel research findings.” These initial preprints must be published prior to first submission to any journal. A revised preprint is defined as “an additional preprint version that is published when peer review feedback or new results or analysis warrant substantial revisions to the initial preprint.”  By requiring multiple versions of a preprint to be shared under an open license, HHMI ensures timely public access to its scientists’ work as it unfolds over time. 

Requiring a CC-BY license allows scientists to retain credit for their contributions, while easing the pathway to reuse for others. Richard Sever, Chief Science and Strategy Officer at openRxiv, writes that the policy “is thus not just a smart move that ensures immediate, free access to the research it funds but also a push towards a better scholarly communication ecosystem.” In support of community-led providers, HHMI designates bioRxiv, medRxiv, ChemRxiv, and arXiv as preferred designated servers, depending on the topic of the research.

Going forward, preprints will form the basis of HHMI’s assessments of its researchers’ work. Although HHMI researchers have already been able to choose to include preprints in their evaluation materials, the policy change means that all researchers will now be required to do so. The policy enables HHMI to strongly center preprints in its assessment processes. Such a shift further removes the pressure for HHMI researchers to focus their efforts on publishing in particular journals. Instead researchers can shift their behavior towards sharing quality research that is useful to their communities as soon as it is ready. Peer review can be used to improve the work over time rather than as a gatekeeping mechanism. 

The ASAPbio Preprint Policy Framework, developed in collaboration with Creative Commons, has been updated to reflect the change in HHMI policy. This framework allows for the easy comparison of policies between different funders for six key components. HHMI joins many other funders in requiring (Aligning Science Across Parkinson’s, the European Molecular Biology Laboratory, the Gates Foundation, the Simons Foundation) or recommending (Michael J. Fox Foundation, Templeton World Charity Foundation, the Wellcome Trust) preprints for the research that they support.

Of note, HHMI’s “Immediate Access to Research” policy aligns closely with the response provided recently by ASAPbio to an NIH request for information, in which we recommended requiring preprinting to maximize the reuse potential and impact of NIH funded research. We encourage research funders to learn more about requiring preprints and other preprint policies at the Preprint Policy Framework.

One approach to measuring the rate of preprinting is to look at the percentage of journal articles that have an associated, or matched, preprint. In the diagram below, this value is represented by the light pink area divided by the light grey circle. This approach normalizes the quantity of preprinting relative to the quantity of article publishing in journals. It’s also possible to look at the percentage of preprints published in journals relative to all preprints (light pink area divided by the red circle), but here we focus on the first quantity.

Several platforms provide data on preprint:journal matches, but it turns out that these different data sources provide diverging estimates of rates of preprinting. The question then arises as to which platform gives the most accurate estimates. If the algorithm that the platform uses is too liberal, false positive matches will cause the estimated rate of preprinting to be higher than it should be. On the other hand, if the algorithm is too conservative, matches will be missed, causing the estimated rate to be too low.

Comparing Different Sources of Preprint Match Data

Here, we compare the estimated rate of preprinting (i.e., the percentage of journal articles that have an associated preprint) based on matches derived from four open sources: Crossref, Europe PMC, Open Science Indicators (OSI) from PLOS, and Rzayeva, Pinfield, and Waltman’s (2025) open data. We then compare the accuracy of matches in these sources.

Crossref, a non-profit membership organization that stewards the scholarly metadata record, has provided a detailed explanation of the strategy it has developed to make preprint:journal matches. In addition to matches declared by preprint servers and journals, their algorithm uses titles and author lists to make matches. Matches identified by the algorithm are provided in periodic data dumps, but Crossref has expressed an intention to eventually include these matches in the full database. The most recent data dump was published in April 2025, but our values here stem from an earlier deposit (November 2023), because that was what Rzayeva et al. (2025) used.

Europe PMC, an open bibliographic database containing preprints from over 30 different life science preprint servers, uses Crossref-provided preprint:journal matches when they are available in the Crossref API. It also augments the Crossref data with its own matches based on “matching titles and first author surnames” (Levchenko et al., 2024). 

For the last few years, the non-profit publisher PLOS has maintained a longitudinal dataset of Open Science Indicators (OSI). The dataset, developed in collaboration with DataSeer, provides a quarterly snapshot from 2018 to 2024 of the rate of uptake of several open science practices – including preprinting – in both PLOS and comparator journals.  

The figure and the table below compare the estimates provided by these three sources alongside data from Rzayeva et al. (2025), who combined matches from OpenAlex, Dimensions, and Crossref to yield a comprehensive set of preprint matches. 

One complication of comparing these different data sources is that their coverage of journals differs, making it hard to compare preprinting rates obtained from the different sources. To address this issue, we focus here on articles published in two journals (PLOS One and PLOS Biology) that are present in all of the sources. This strategy makes the total number of articles the same for all sources. The only difference is whether a given source catalogs a given matched preprint. 

Europe PMC indexes 90,061 PLOS One and PLOS Biology articles spread across 2018-2023 that also appear in the OSI corpus. The figure and table below show the percent of these articles that have a matched preprint according to the different sources. 

Estimates of the rate of preprinting vary widely across the different sources, even when restricting our focus to a common set of articles. For instance, Europe PMC estimates the rate of preprinting in 2022 for PLOS Biology and PLOS One to be 9.8%, whereas Crossref estimates it to be 13.9%, Rzayeva et al. estimate it to be 14.5%, and PLOS’s own OSI data estimates it to be 18.4%. 

Assessing the Accuracy of Matches from Different Sources

One way to unpack the discrepancies reported above is to look at “disputed matches,” that is, papers that are alleged to match according to one data source, but not another. Those matches can then be checked manually to see whether they are errant or not. If false positive matches are identified, this finding implies that the estimated rate of preprinting is too high. If false negative matches are found, the estimated rate of preprinting is too low. 

We examined a randomly selected sample of 20 disputed matches to compare Rzayeva et al.’s data to the OSI data. Of these matches, 17 were false positives (85%), suggesting that OSI’s matching algorithm is too liberal. Of the remaining three matches, two were correctly linked to a preprint, meaning they were missed by Rzayeva et al. The final article was matched to a conference presentation (though the match looked correct). 

We also examined a random sample of 25 disputed matches detected by Rzayeva et al., but not present in Europe PMC. We found a high rate of misses, with 21 of 25 matches being correctly identified in Rzayeva et al. but missed by Europe PMC (84%), suggesting that Europe PMC’s algorithm is too conservative. The remaining 4 of 25 matches in Rzayeva et al. were false positives (16%).

Limitations and Caveats

We chose to focus here on PLOS One and PLOS Biology to more easily compare our data sources, but it is unlikely our results are restricted to these journals. We suspect that Europe PMC’s algorithm is too conservative in most contexts and likewise that the OSI algorithm is too liberal.

It’s worth noting that each data source brings some unique matches to the collection. Of the total 90,061 articles considered here, 85.3% have no indicated matches in Europe PMC, OSI, or Rzayeva et al. (which subsumes Crossref). 8.3% have a match in all three of these sources. The remaining 6.3% are unique to either one or two of the sources. Of course, all purported matches can be either false or true positives. It seems likely that matches that reflect agreement across sources are more likely to be true positives than false positives, but we did not evaluate this claim.

The small samples here mean that the margin of error of these estimates is quite high, but nonetheless, the apparently high rates of false positives (for OSI) and misses (for Europe PMC) are both cause for follow-up. ASAPbio has been in conversation with Crossref, Europe PMC, and PLOS to encourage improvements to matching algorithms. Each of these organizations has been very receptive to the outreach, and likewise, they plan to adjust their approach in the coming months to try to provide more accurate matches. Already, PLOS is adjusting their approach with their upcoming version (V10) of the OSI data, which is expected to be released soon.

Reflections on How to Best Assess the Rate of Preprinting

Advocates and the researcher community alike need accurate information about matches between papers published in journals and preprints. For advocates like ASAPbio, having accurate data helps us understand whether our advocacy efforts are improving uptake. For researchers, being able to review different versions of a paper has benefits for understanding the story behind a piece of research. 

Returning to the question of how high the rate of life science preprinting is and whether it is growing over time, the answer depends on what question is asked. The statistics reported above show a higher rate of journal articles with matched preprints in 2022 than there was in 2018 and 2019, but 2023 has somewhat lower levels. For Crossref and Rzayeva et al., this apparent decrease might be due to limitations in the 2023 data (see discussion in Rzayeva et al.). Europe PMC and OSI disagree on whether or not a decrease is occurring, but given the potential for false positives and misses in those datasets, more investigation is needed to calculate more accurate estimates. 

Additionally, the rate of articles with associated preprints is somewhat separate from the question of the total number of preprints (red circle above), or from the ratio of preprints to articles. Preprints may not always be published as journal articles for many reasons, one of which is that preprints are dynamic and reflect the natural evolution of research projects over time. This is a desirable feature of preprints, rather than a downside. Considering different statistics (raw counts, percentage of journal articles, percentage of preprints) provides different views on the overarching question of how much life science research is preprinted. Taking all of these factors into account, our current best guess is that somewhere around 13-14% of life science journal articles in 2024 are preprinted – a number we’re working to increase substantially.  

Europe PMC also displays a data dashboard, updated monthly, depicting the overall volume of preprints on the servers they index. On the whole, preprint posting has continued to steadily increase, following a rapid jump during the early days of the COVID-19 pandemic. Monthly submissions exceed 10,000 and routinely approach (or even surpass) 15,000. 

Eagle-eyed readers will notice an apparent drop in submissions during the early months of 2025. Closer inspection reveals that the decrease is specific to the Research Square preprint server (which is owned by Springer Nature). Daily postings dropped from about 236 per day in the first quarter of 2024 (Q1) to fewer than 80 per day in 2025. On average, this represents a 66.6% decrease from Q1 2024 to Q1 2025. Over the same time period, bioRxiv submissions increased moderately, by an average of 9.8%.

A representative from Springer Nature confirms that “the recent decrease in preprints is due to a temporary reduction in our screening capacity.” They also report that “our team is working to increase capacity so we can resume previous posting volumes” and additionally confirm that “we did experience a backlog, but this is steadily improving.” Additional information about Research Square screening processes is available at https://www.researchsquare.com/legal/editorial. Screening verifies the presence of statements about ethics and conflicts of interest, along with the lack of patient identifiers and pseudoscientific claims.

Researchers should be aware that they may experience a delay in posting of their preprints at Research Square. ASAPbio will continue to monitor the posting volume and report back when there are further developments. Have a recent preprinting experience you think would be useful for the community to know about? 

How do preprints fit into the bigger picture of open science at EMBL?

Preprints are relevant for all research articles at EMBL. Preprinting became a requirement in EMBL’s Open Science Policy on December 21, 2021. For EMBL, preprints can enable our researchers to maximize the impact of their research. 

As a signatory of DORA, EMBL also aims to improve transparency and fairness in research assessment. Thus, the research assessment section of our policy also states that research outputs such as preprints, peer review contributions, data and software should be considered alongside publication. Preprints are one of our priorities in our open science roadmap in both how we disseminate research and how we diversify the types of research outputs in research assessment. 

What’s necessary to create the change you envision?

We needed to communicate the preprint requirement and Open Science Policy change through various channels. In addition to EMBL-wide communication, we identified opportunities to integrate open science training and introductions to concepts like preprinting. Some examples where we have integrated open science training include Ph.D. and postdoc fellow courses, faculty retreats, software workshops, newcomer introductions etc. In addition, we include a check for preprints in our open-access publishing workflows for EMBL lead author articles. Lastly, inspired by a strategy from ASAPbio, we found our local preprint advocates like ASAPbio Board Member/EMBL Group Leader Gautam Dey and EMBO Director Fiona Watt, to share their perspectives on the importance of preprinting.

What barriers are in the way of that change?

Since the introduction of the preprint requirement, 76% of all primary research articles (EMBL lead author articles ~15% of all articles) processed in our open access workflow were posted as a preprint. In many cases where the researcher did not publish the preprint, it was due to insufficient time and resources. Preprints integrated as a part of the publication process can lighten the workload for researchers. 

In our central open-access publication workflow, EMBL authors contact the Open Science team upon the acceptance of their article. We support the authors in checking licensing, payment of the Article Processing Fee, and deposition of their article as full-text in our institutional repository EuropePMC. In the workflow, we incorporate a check of compliance with our Open Science policy, where we remind authors to post a preprint. At this stage, the article has already been peer-reviewed and accepted, therefore some of the benefits of early dissemination from earlier preprinting are diminished. In some cases, authors thought that since the article would be published open-access, then posting a preprint is not necessary. Thus, we have more work to do to convey the advantages of preprinting and help researchers find their own motivation to post preprints. 

What approach have you been using to identify the preprints created by EMBL researchers?

We have an ongoing project to track EMBL preprints, as a part of a larger effort to monitor open science at EMBL. We are interested in tracking our progress in implementing the Open Science Policy and recognizing preprints as an important research output at EMBL.

Our starting point is peer-reviewed publications. We track our publications using preprint linking on Europe PMC. We query EMBL’s publications, and whether there is a preprint link. An alternative strategy is to first assign our institutional IDs ROR ID to our known publications on Europe PMC (these links are not publicly displayed, but help us to track publications using the Europe PMC database). This allows EMBL publications to be searchable with the ROR IDs. With a ROR ID query, we would be able to show how many publications have been posted as a preprint, how many have data published etc. 

Another possibility is to identify EMBL preprints using researcher identifiers ORCIDs. We run an annual ORCID campaign across the organization, inviting all researchers to create ORCIDs, and also keep their profiles up to date, by claiming their preprints using the EuropePMC ORCID claiming tool. Our campaigns included messages from EMBL’s leadership and webinars, followed by targeted emails, which allowed us to achieve near 100% ORCID adoption at EMBL. With high levels of ORCID adoption, we can obtain a more complete and comprehensive source of information on preprints and research outputs from EMBL authors.

What challenges do you face in identifying preprints?

Looking for preprints from publications is a limiting factor. This means that we are only able to find preprints at a much later stage. We found that ~50% of our known EMBL preprints are not linked to the published journal article. In some cases, the preprint exists independently of any journal publications. Lastly, the variety of preprint servers used also can pose a challenge, due to a lack of indexing and linking. 

Moving forward, having a strong adoption of ORCID at EMBL will help us discover our preprints. I’m very curious how other research organizations and universities are currently tracking their preprints, and hope those who are interested reach out to me! Please reach out by email at victoria.yan@embl.de.

What strategies have been effective in changing attitudes, policies, and practices?

I think what works well is that researchers can see that EMBL has made open science and open scholarship a part of the core mission. The Open Science Policy made preprinting relevant for all EMBL researchers. 

High-level engagement and support from EMBL’s leadership made the Open Science Policy possible. A broad and non-exclusive group led the development of the Policy. The group first surveyed current open science related practices, which also advertised the idea that the Open Science Policy was in development. The survey results showed that there were many good practices in place, however, a policy would formalize these practices across the entire research organization. The working group developed a separate implementation guideline to contain the practical aspects of how to adopt the Open Science policy. The group that developed the implementation guidelines is continually working to improve user-friendliness and keep the guidelines up-to-date. 
Adoption of the policy wouldn’t be possible without training our community of researchers. Therefore, we began to coordinate open science training across EMBL. You can see a catalogue of our publicly available training resources here. At the moment, we have mandatory open science training for all PhD students, 75% of our post-docs, and all of our principal investigators. To make clear that openness is a norm at EMBL, we continue to recognize and highlight open research projects and leaders.

Awareness of preprints in Africa

The adoption of preprints across the globe has not been equitable, with most preprints being posted by the USA, UK, Western Europe and China. Regions such as Africa have a low level of preprinting. Unfortunately, data around the usage, awareness and perceptions of preprints in Africa is lacking. Therefore a group of Fellows undertook a survey to investigate the awareness and perceptions of preprints amongst Africa based researchers. The survey received over 180 responses and will culminate in a preprint posted to AfricaArXiv. 

Preprints and graduation requirements

Across the world graduation requirements for PhD programs vary from no requirements to having published in multiple journals. Additionally, within the same institutions, programs can be just as variable. A further compounding issue is that requirements for graduation are not always formal requirements, often existing as expectations from departments or supervisors. Moreover, where requirements exist, they are often not transparent. 

To begin to tackle this issue, a group of 2023 Fellows undertook a global survey to gather information on the graduation requirements of master-level and PhD programs. This group gathered over 80 responses across 18 countries and produced a detailed blog post including recommendations on graduation requirements. 

Awareness of preprints in India

Similarly to Africa, the adoption of preprints across India has lagged behind the USA, UK, Western Europe and China. In 2022 ASAPbio ran a workshop on research assessment and preprints in India. Building from this, in 2023 the ASAPbio Fellows, in collaboration with India BioScience held 3 workshops to gather a deeper understanding of the attitude and perspectives of preprints in India. The outcome of these workshops is partially communicated in a blog post (link to follow) and will inform some of our activities in 2024. 

Preprints in progress

One of the major benefits of preprints over the traditional publishing model is that preprints allow authors to share work at earlier stages, including as iterative updates. To date, there are no studies assessing the number or use of iterative preprints, although there are a small number of known examples. A group of 2023 Fellows produced a preprint investigating potential iterative preprints. A second group of Fellows produced an infographic outlining the alternative uses of preprints, beyond the traditional journal article styled output.  

Crowd preprint review

In 2021, ASAPbio started activities to facilitate public reviews on preprints inspired by the crowd review model pioneered by the journal Synlett. In the first year, 14 public reviews of cell biology preprints were posted. In 2022, crowd review activities expanded to include cell biology, biochemistry and infectious diseases preprints (in Portuguese from SciELO Preprints). This resulted in 27 public reviews for bioRxiv preprints and 13 reviews for SciELO Preprints. In 2023, there were 4 crowds led by ASAPbio Fellows covering neuroscience, cancer biology, metabolism and meta-research; together, these crowds posted 35 public reviews of preprints. These reviews are available from sciety and PREreview:

• ASAPbio Cancer Biology Crowd
• ASAPbio Metabolism Crowd
• ASAPbio Meta-Research Crowd
• ASAPbio Neurobiology Crowd

Crowd preprint review will return next year in an expanded format. Additionally, in 2024 ASAPbio will provide support for current departmental journal clubs to convert into preprint review clubs in a further effort to expand preprint peer review and help train the next generation of scientists. 

2023 Fellows

I want to thank all of the 2023 ASAPbio Fellows for their contributions over the year. They have provided valuable insights into preprints across different geographical locations and communities, produced preliminary data on graduation requirements and further expanded the crowd review. They have been a source of inspiration to bring positive change in scholarly communication. I look forward to continuing to interact with the Fellows across other ASAPbio initiatives and within the community.

Looking to 2024

We’re undertaking plans to revitalize the Fellows program for 2024 and look forward to opening applications soon. If you’d like to be the first to know when the applications open, sign up to our newsletter and follow us on social media. If you have any questions please email jonny.coates@asapbio.org. 

Since the launch of bioRxiv in 2013, preprints have seen an explosion in use and adoption across the life sciences. Preprints now represent ~10% of the biomedical literature and are seeing increasing recognition across funding bodies, policy makers, academics and universities in promotion and hiring decisions. However, this adoption and recognition is not globally universal with large disparities existing not only between countries but sometimes even within the same institution. 

Many institutions across the globe require the submission or publication of one or more journal articles before a PhD student can graduate. This contributes to an increasing amount of lower quality publications and other issues in the wider literature. It is also a practice that is often preyed upon by predatory publishers and special issue journals. For the individual students however, this requirement can have more personal impacts including increasing stress and uncertainty as graduation is delayed until manuscripts have completed the peer review process – which can take 6+ months. The use of publications as a requirement for graduation can also feed into the issues of journal impact factors or names being used as proxies for quality and may encourage some examiners to not scrutinise a thesis appropriately. 

Institutional recognition of preprints has progressed more outside of graduation requirements. For example, many institutions in the US and EU accept preprints for fellowship applications and in job applications. However, this is still relatively rare outside of these geographical regions and even within these areas the adoption of preprints in this manner remains highly variable. To better understand the use of preprints and published articles as a requirement for graduation, we conducted a global survey of researchers. Although we received limited responses, the data provides an interesting insight into the current landscape and perceptions of publication requirements. 

Survey demographics

The survey was translated to several languages to achieve a wider reach. We received a total of 81 responses from across the world. Over half (51.8%) of the survey respondents came from Spain, 8.6% from Chile, 7.4% from the United States, and 6.1% from Germany. The rest of the respondents represented less than 5% each from the countries listed in Fig 1A. Although this was a relatively limited response, it did cover a relatively wide geography. 

Survey respondents represented individuals from diverse career stages (Fig 1B). The majority were principal investigators/group leaders (42.5%), followed by PhD students (23.7%) and postdocs (8.7%). Master level students represented 6.2% of the total respondents. Individuals were not necessarily working in academia, with some survey respondents working in industry; for example, as science writers (1.25%). As respondents were answering about their current institution requirements, PhD students, masters students and group leaders would be reasonably expected to have the most accurate awareness of the graduation requirements.

Survey respondents were primarily representing Biology (50.4%) and Medical and health sciences (33.9%) fields, although Chemistry was also relatively well represented (6.9%) (Fig 1C). Other fields included less than 3 respondents each. This is a positive response for our survey focus on life sciences but does limit the findings to these fields. 

Results

All respondents were asked about their current interaction with preprints to gauge their understanding and use of preprints more generally. The majority actively read preprints with large numbers also posting and citing preprints. Fewer respondents posted reviews for preprints, representing an area that can be improved upon. Interestingly, more did engage in preprint discussions and journal clubs, suggesting that this may be a prime target for increasing preprint reviewing. A relatively large portion of respondents did not interact, or were not familiar with preprints (Fig 2).   

We first asked about any requirements for graduation from masters programs (Fig 3). The overwhelming majority did not have any formal graduation requirements although a number did require manuscripts to be ready, submitted, accepted or published in a journal. Very few respondents stated that preprints were accepted to graduate. A larger number of respondents either didn’t have a masters program or didn’t know the graduation requirements. Perhaps the most surprising aspect to these results are the number of institutions that require master level students to have submitted or published a journal article, especially given the generally short timeframes for such programs.  

In contrast, PhD graduation requirements had considerably more responses to requiring a journal article being published (Fig 4). The majority of respondents indicated that they needed to have a manuscript accepted in a journal to be able to graduate with a high number requiring the article to have actually been published. Preprints were accepted in similar numbers to manuscripts being ready to submit or those that have been submitted. Again, a large number of respondents indicated that there were no formal requirements for publication at their institution.

Finally, we asked respondents if they would be in favor of institutions including preprints for fulfilling graduation requirements (Fig 5). The responses were relatively evenly split between favoring preprints (41%) and not favoring preprints (43%). This is perhaps due to confusion in the wording of the question as the long form responses indicated that many would prefer no formal publishing requirements. The question had been intended to ask if, where requirements exist, would it be preferred to change these to preprints or keep them as publications.

One important aspect that this survey did not capture is the difference between formal requirements and expectations. Anecdotally, it was highlighted that even in institutions with no formal requirements, individual group leaders or institutions do still enforce unofficial publication requirements. This is not communicated transparently and represents an important area for future investigation.

We also collected long form responses for the question “What concerns would you have about your program making preprints a graduation requirement?” (Table 1). These responses highlighted 1) a desire to remove entirely or replace publication requirements with preprints 2) That publication requirements exert additional and unnecessary pressure on students and can be damaging to the literature and 3) that there are large concerns over the quality and reliability of preprints compared to peer reviewed publications.

Recommendations

Based on the data from our survey, the long form responses and conversations with others based on this work, we make three primary recommendations:

1. Make any graduation requirements (formal or expectations) clear and transparent
2. Remove requirements to have a manuscript accepted or published; if full removal is not possible then replace publication requirements with preprints
3. Provide better education to all staff and students on the role and effectiveness of peer review

These recommendations would boost preprint adoption and use in addition to relieving some undue stress and pressure on students. Additionally, the third recommendation would benefit a large number of scientists who place false reliance on peer review, an experiment that has, based on all available evidence, failed. Preprints place the emphasis back onto the science and content of individual articles. 

Supplemental tables

Tables detailing the responses to Fig 1. 

Career stage 

Geographical location

Discipline