New publishing models will only work if authors embrace them

Complaints about the broken academic publishing system have been around for years and are getting louder. A common theme is that with the rise of open access publishing, commercial publishers have grasped the opportunity to grow their profits from article-processing-charges (APCs). Whereas in the past, journals competed to be the most highly respected outlet, now they compete to publish on the grounds of speed and quantity of publications (see e.g. Timmis et al, 2025).

In response, various new initiatives have arisen. My focus here is on the F1000 publishing model, which was adopted by the Wellcome Trust in 2016 for their journal Wellcome Open Research. In this model, the author deposits an article on the platform (in effect as a preprint), which then is updated to a published version if two positive peer reviews are obtained. The only editorial input is from office staff who check that the submission meets basic criteria and that the selected peer reviewers are appropriate. This system could quickly get overwhelmed with low quality submissions, but aims to avoid that by restricting submissions to authors funded by the Wellcome Trust, which agrees to pay their APCs. I've always been a fan of open access, and have published several papers in Wellcome Open Research, encouraged by the prospect of straightforward and free open access publication.

A check on the Dimensions platform shows that Wellcome Open Research has grown in popularity over the years, and now dominates outputs from Wellcome-funded researchers.

Figure 1. Plot of the top 5 journals, publications funded by Wellcome Trust between 2016-2025.

My funding by Wellcome Trust came to an end and in 2016 I took up an ERC Advanced Grant. Towards the end of that grant, in March 2021, the European Commission (EC) announced that they were setting up a new journal, Open Research Europe that adopted the same F1000 model and offered free open access publication for EC-funded researchers. In contrast to Wellcome Open Research, Open Research Europe has not been enthusiastically embraced. A search on Dimensions showed that a large proportion of EC-funded research is published open access with for-profit publishers (see Figure 2). Open Research Europe is not shown because the number of publications is relatively small: 213, 251, 290, 374 for the years 2021 to 2024 respectively. It rates 25th among journals used by EC researchers, whose favourite publisher appears to be MDPI.

Figure 2. Plot of the top 5 journals, publications funded by EC between 2021-2025.

This raises two questions: who is paying the APCs, and why don't researchers publish on their funder's platform, which offers them free open access?

Of course, Open Research Europe is relatively young, and its uptake may have been influenced by its launch coinciding with emergence from lockdown. It's possible that communications from the EC encouraging grantholders to publish there haven't been sufficient to raise awareness of this option. I'd be curious if any readers who have EC funding could comment on barriers to uptake. Meanwhile, between 2021-2025 around US$973 million* in APCs has gone into the coffers of publishers - money that could have been used to fund researchers in other ways. On a rough estimate, around US$197 million of this has been paid to the most popular publisher, MDPI.

*To obtain this estimate, I searched Dimensions.ai using search terms Funder = European Commission (EC), Publication Type = Article, and year range from 2021-2025, and then used Analytical views to generate a table of source titles. For the first 30 titles, I manually checked the APC and used a currency converter to convert to $US. For the remaining titles, I estimated the APC as equivalent to the average for the first 30 titles. I coded MDPI as publisher for titles I recognised, but I did not carefully check each one. A csv file with the relevant data can be found here: https://osf.io/rcxd3.

Reference

Timmis, K., et al. (2025). Journals operating predatory practices are systematically eroding the science ethos: A gate and code strategy to minimise their operating space and restore research best practice. Microbial Biotechnology, 18(6), e70180. https://doi.org/10.1111/1751-7915.70180 

 

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Trouble at t' (review) mill: How MDPI lets down authors

 I guess many readers will have had peer reviews where the reviewer doesn't appear to have understood, or even properly read, the paper they are criticising. But I doubt that you'll have experienced anything like Pérez et al (2023). Their growing exasperation with increasingly irrelevant comments can be sensed in their response to reviewer 2, who asked them to revise statements that were unproblematic, to add information already in the article, to correct information that was not in the article, and to add two references that bore no relationship whatever to the topic of the article.

So, how can this happen? Well, all becomes plain when you read this article by Maria Ángeles Oviedo-García (2024), who has documented what she terms "review mills": groups of reviewers who generate boilerplate peer reviews that do not evaluate the content of the article, and so can be applied to almost any field. Their main function appears to be to act as citation vehicles for members of the review mill, who encourage authors to "improve" their article with "latest literature", with references to papers by themselves or confederates.

When you see numerous reviews by the same set of people side by side, the boilerplate nature of the reviews becomes obvious, with the same phrases repeated across completely different contexts, e.g.: 

1. The title of the manuscript is not impressive so rewrite the title. 
2. In the abstract, the author should add more scientific findings. 
3. Keywords: There are so many keywords in this manuscript and reduce it. So, modify the keywords. 
4. In the introduction part, the introduction part is not well organized and cited references should cite recently published articles such as 10.3390/toxics10110657, 10.1016/j.rinp.2022.105817

Oviedo-García meticulously documented the evidence for review mill activity on PubPeer, and on 13 February 2024, MDPI's communications department wrote a report outlining how they planned to deal with the situation, noting "MDPI is committed to transparency and integrity in scholarly publishing. We will provide updates as the investigation progresses and appreciate your understanding and cooperation in addressing this matter." 

Neither Oviedo-García nor I have heard of any update to the report, and so in an idle moment I thought it would be interesting to revisit the list of 84 papers to see if anything had been done in the 17 months since that statement. A manual check on 18-20th July 2025, revealed that 46 articles had no action, 13 had a “Journal notice”, stating that they were being looked at, two had the “Review Reports” tab deleted on the website, and the remaining 23 had a Correction. I have added information about Notices and Corrections to PubPeer.

The cases of Correction reveal a lack of consistency in how matters have been handled. The most popular option has been to just delete the peer review from the review mill from the website. The Correction is at explicit that this has been done, but it can be confusing because it often leads to some renumbering of reviews, making it hard to track earlier PubPeer comments against what is online. The other thing that is usually done with the Correction is to remove the coerced references from the article.

Serious problems arise, however, if there were only two original reviews, because MDPI's procedures specify that two reviews are needed; hence, if one has been deleted as improper, they have to seek another review. No doubt the editor fervently hopes that the replacement review will not raise new issues, and sometimes that was the case, but there are instances where the new reviewer wanted substantial changes to the article.

This then creates a most unfortunate circumstance for all concerned. Authors, who thought their article was accepted two or three years previously, are now told that the review process was corrupted, and are expected to revise the article in light of a new review. As far as I can tell from what is publicly on the record, a few authors agreed to do that, but others did not. If it happened to me, I'd be incandescent.

I've only looked at 84 articles from one review mill, but Oviedo-García has documented many more examples, nearly all from MDPI journals, and she suggests urgent actions that publishers should take: be vigilant for fraudulent and plagiarised peer review, blacklist review millers, and develop guidelines for publishers to follow in this situation. Until this is done, authors should be aware that their published article could be slapped with a "Journal notice" expressing concern about the review process, and they could be asked for revisions, even when they are entirely innocent of any wrongdoing.

Reference

Oviedo-García, M. Á. (2024). The review mills, not just (self-)plagiarism in review reports, but a step further. Scientometrics. https://doi.org/10.1007/s11192-024-05125-w 

Pérez, I.; Heitkamp, T.; Börsch, M. (2023) Mechanism of ADP-inhibited ATP hydrolysis in

single proton-pumping FoF1-ATP synthase trapped in solution. Int. J. Mol. Sci. 24, 8442. 

https://doi.org/10.3390/ijms24098442