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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I don't care about journal impact factors but I do care about visibility

There's been a fair bit of discussion about Clarivate's decision to pause inclusion of eLife publications on the Science Citation Index (e.g. on Research Professional).  What I find exasperating is that most of the discussion focuses on a single consequence - loss of eLife's impact factor.  For authors, there are graver consequences.   

I've reviewed for eLife but never published there; however, I have published a lot in Wellcome Open Research, which is another journal that aimed to disrupt the traditional publishing model, and has some similarities with eLife.  Wellcome Open Research has never been included in Science Citation Index, despite the fact that it uses peer review.  Wellcome Open Research has an unconventional model whereby submitted papers are immediately published, as a kind of pre-print prior to peer review, and then updated after peer review.  It is true that some papers don't get sufficient approval to proceed to the peer-reviewed stage; the distinction between those that do and do not pass peer review is clearly flagged on the article.  In addition to peer review, Wellcome Open Research maintains some quality control by limiting eligibility to researchers funded by Wellcome.  

 

When Wellcome Open Research started up, all Wellcome-funded researchers were encouraged to publish there.  As someone committed to Open Research, this seemed a great idea.  There were no publication charges, and everything was open: access to the publication, data, and peer review. Peer reviewers even get DOIs for their reviews, some of which are worth citing in their own right.  I was increasingly adopting open practices, and I think some of my best peer-reviewed work is published there. 

 

I was shocked when I discovered that the journal wasn't included in Web of Science. I remember preparing a progress report for Wellcome and using Web of Science to check I hadn't omitted any publications.  I was puzzled that I seemed to have published far less than I remembered. Then it became clear: everything in Wellcome Open Research was missing. 

 

I was on the Advisory Board for Wellcome Open Research at the time, and raised this with them. They were shocked that I was upset.  "We thought you of all people didn't care about impact factors", they said. This, of course, was true. But I did care a lot about my work being visible.  I was also aware that any WOS-based H-index would exclude all the papers listed below: not a big deal for me, but potentially harmful to junior authors.  

 

The reply I got was similar to the argument being made by eLife  - well, the articles are indexed in Google Scholar and PubMed.  That was really little consolation to me, given that I had relied heavily on Web of Science in my own literature searches, believing that it screened out dodgy journals. (This belief turns out to be false - there are many journals featured in WoS that are very low quality, which just rubs salt into the wound).  

 

I have some criticisms of eLife's publishing model, but I would like them to succeed. We urgently need alternatives to the traditional journal model operated by the big commercial publishers.  Their response to the open access movement has been to monetise it, with catastrophic consequences for science, as an unlimited supply of shoddy and fake work gets published - often in journals that are indexed in Web of Science.

 

I agree that we need an index of published academic work that has some quality control.  Whether alternatives like OpenAlex will do the job remains to be seen. 

 

Papers that aren't indexed on Web of Science

Bishop, D. V. M., & Bates, T. C. (2020). Heritability of language laterality assessed by functional transcranial Doppler ultrasound: A twin study. Wellcome Open Research, 4, 161. https://doi.org/10.12688/wellcomeopenres.15524.3

Bishop, D. V. M., Brookman-Byrne, A., Gratton, N., Gray, E., Holt, G., Morgan, L., Morris, S., Paine, E., Thornton, H., & Thompson, P. A. (2019). Language phenotypes in children with sex chromosome trisomies. Wellcome Open Research, 3, 143. https://doi.org/10.12688/wellcomeopenres.14904.2

Bishop, D. V. M., Grabitz, C. R., Harte, S. C., Watkins, K. E., Sasaki, M., Gutierrez-Sigut, E., MacSweeney, M., Woodhead, Z. V. J., & Payne, H. (2021). Cerebral lateralisation of first and second languages in bilinguals assessed using functional transcranial Doppler ultrasound. Wellcome Open Research, 1, 15. https://doi.org/10.12688/wellcomeopenres.9869.2

Frizelle, P., Thompson, P. A., Duta, M., & Bishop, D. V. M. (2019). The understanding of complex syntax in children with Down syndrome. Wellcome Open Research, 3, 140. https://doi.org/10.12688/wellcomeopenres.14861.2

Newbury, D. F., Simpson, N. H., Thompson, P. A., & Bishop, D. V. M. (2018). Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis. Wellcome Open Research, 3, 10. https://doi.org/10.12688/wellcomeopenres.13828.2

Newbury, D. F., Simpson, N. H., Thompson, P. A., & Bishop, D. V. M. (2021). Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis. Wellcome Open Research, 3, 85. 

https://doi.org/10.12688/wellcomeopenres.14677.4

Pritchard, V. E., Malone, S. A., Burgoyne, K., Heron-Delaney, M., Bishop, D. V. M., & Hulme, C. (2019). Stage 2 Registered Report: There is no appreciable relationship between strength of hand preference and language ability in 6- to 7-year-old children. Wellcome Open Research, 4, 81. https://doi.org/10.12688/wellcomeopenres.15254.1

Thompson, P. A., Bishop, D. V. M., Eising, E., Fisher, S. E., & Newbury, D. F. (2020). Generalized Structured Component Analysis in candidate gene association studies: Applications and limitations. Wellcome Open Research, 4, 142. https://doi.org/10.12688/wellcomeopenres.15396.2

Wilson, A. C., & Bishop, D. V. M. (2019). ‘If you catch my drift...’: Ability to infer implied meaning is distinct from vocabulary and grammar skills. Wellcome Open Research, 4, 68. https://doi.org/10.12688/wellcomeopenres.15210.3

Wilson, A. C., King, J., & Bishop, D. V. M. (2019). Autism and social anxiety in children with sex chromosome trisomies: An observational study. Wellcome Open Research, 4, 32. https://doi.org/10.12688/wellcomeopenres.15095.2

Woodhead, Z. V. J., Rutherford, H. A., & Bishop, D. V. M. (2020). Measurement of language laterality using functional transcranial Doppler ultrasound: A comparison of different tasks. Wellcome Open Research, 3, 104. https://doi.org/10.12688/wellcomeopenres.14720.3

 

 

 

Universities vs Elsevier: who has the upper hand?

 

The academic publisher Elsevier is currently negotiating a deal with UK universities. In Oxford, as in other universities, there have been extensive discussions about the proposed deal; the goals are to reduce costs to sustainable levels and to provide full and immediate open access to UK research. I have a nasty feeling that we could end up in the situation of those at the COP summit: with a deal that where the publishers feel they are giving away a huge amount, while the consumers are still unsatisfied. 

In the print era, publishers already had a large profit margin.  I was a journal editor when electronic publishing first came in, and I remember discussions with the publisher - who was clearly very nervous about how this might damage their bottom line. With some clever business practices, such as bundling, they managed to keep going, making more rather than less money.

Other new developments - the advance of metrics and requirements for open access publishing - also pose challenges to them, but their response, like any savvy business, is to take control of these new developments and find a way to profit from them as well.

So should we go along with this? The discussions have largely centred around money, and this is a real concern. Publishers charge massively inflated subscription charges, taking as profit money that our libraries could otherwise put to good use. But the problems go way beyond that, including blocking open access to authors' own work, and giving poor quality and even fraudulent material a veneer of respectability. The publisher currently has considerable power over what gets published but takes little responsibility when things go wrong.

But we also have power, and I think it's time we started to wield it. I have two proposals: one radical and the other less so, both of which go beyond what is currently being considered in the JISC discussions.

The radical option: move publishing in-house  

In an ideal world, we would not have any deals with for-profit publishers. Universities would take control of academic publishing. A model which I have found works well is the Wellcome Trust journal Wellcome Open Research (WOR). I served on its Editorial Advisory Board in the first years of its operation and I have published eight papers in WOR. 

Quality control is maintained by requiring that work published in WOR has been Wellcome-Trust funded. The platform is paid for by the Wellcome Trust, and all material is Open Access, with no charge to authors.

Universities could use this as a model for developing their own platforms for publishing work of their researchers. As with Wellcome Trust, researchers would be encouraged rather than required to publish there. Setting up and maintaining the platform would cost money, but this might be covered by savings from stepping back from deals with big publishers. This is not a perfect solution, of course; we would still want access to past material published by traditional publishers. But I feel this option should be given serious consideration.

The less radical option. An agreement with Elsevier that reflects what we want and need 

If we are to retain a working relationship with Elsevier, then we need to ensure that we are getting value for money, and that they are delivering what we want.

One way in which they fail to do this is through the copyright agreements that they require authors to sign. I agree with Sally Rumsey that any publisher that does not allow an author to retain rights to their own work is problematic. Furthermore, there is concern that even if Elsevier were to say they agreed to author rights retention, they would continue to adopt practices that would mislead authors into signing away their rights.

Another issue is how publishers deal with matters related to misbehaviour by editors and authors. We have a number of serious problems with the academic publishing system that have been developing for years, and have been thrown into stark relief by the pandemic. Publications in journals are a kind of academic currency, with potentially huge rewards in terms of promotion, pay and tenure of academic staff. Unfortunately, this means that some people will go to great lengths to procure publications, and this can include fraudulent means. A reputable publisher should recognise and indeed anticipate such problems and take steps to deal with them. Elsevier has been notably poor in doing so. I will give a handful of examples.

Clearly erroneous/fraudulent work remains in the literature In recent years, a massive problem has been discovered with so-called paper mills - a form of industrialised cheating that involves generation of literally thousands of fake papers.  This phenomenon was discussed at a meeting this summer, the Computational Research Integrity Conference (CRI-Conf), which brought together some of the scientists who uncovered paper mills and representatives of publishers (including Elsevier) and university integrity officers. A repeated complaint of the 'data sleuths' (scientists who uncovered the paper mills) was that when the problems were drawn to the attention of the editors or publishers, typically nothing was done.  Some of these papers are highly cited and have medical implications - see, for instance work by Jennifer Byrne and Cyril Labbé on cancer biology, or by Elisabeth Bik on image manipulations.

To its credit, Elsevier was recently cited as acting promptly when a cache of nonsense papers in special issues was uncovered, but one still has to ask how these papers, some of which were complete gibberish, originally got through the supposedly rigorous peer-review process. For another recent example, see here.

Part of the problem seems to be that there is very little oversight of editors.  I first became aware of Elsevier's lax attitude to research integrity when I discovered a ring of editors. There was overwhelming evidence that a set of editors were publishing one another's papers in their journals, with publication lags so brief as to indicate there had not been peer review. Emails to Elsevier received no reply, and so I started reporting the events on my blog. This created such publicity that Elsevier then posted a reply, but initially they denied that any papers had been published without peer review. Eventually, as the evidence mounted up, they were forced to acknowledge the problem, and claimed to be investigating it, but at no point did they communicate with me, and their investigation went on for years and has never led to any consequences. One of the offending editors, Johnny Matson, quietly disappeared without comment and is now editing another journal for another publisher. The unreviewed papers, many of which are concerned with intervention for children with developmental disorders, remain in the literature. 

More recently I did a bibliometric analysis of editors of psychology journals who publish prolifically in their own journals, and broke down the results by publisher. Elsevier had the highest number of editors-in-chief in this category,

A related case in another field is that of Didier Raoult, who was senior author on a paper advocating hydroxychloroquine as a treatment for Covid-19 that appeared in 2020 in an Elsevier journal for which he was Editor-in-Chief. It has subsequently been shown to be riddled with methodological errors, but, although Elsevier claimed to be investigating it in April 2020, it has not been retracted.

At the CRI-Conf publishers said that they were doing their best, but the problem of fake and fraudulent practices was so huge they could not be expected to tackle all of it. Yet we know publishers make enormous profits, so why aren't they putting more effort into checking the integrity of the work they publish - and dealing promptly with the problems that are drawn to their attention? Elsevier is not the only large publisher to be affected, but if it wants to be seen as a leader in the field, it should recognise that integrity of published material is of supreme importance - especially in clinical fields where people's health and wellbeing can be affected (as in the cases of Raoult and Matson noted above).

If UK Universities do strike a deal with Elsevier, then they should take the opportunity to include in any future contract conditions requirements that: 

(a) Elsevier allows authors the retention of the rights to their publications and  

(b) it provides annually an open report on the number of integrity issues that have been raised about its publications and how these have been dealt with. 

This would go some way toward ensuring that we get value for money, and are not simply adding to the profits of a company whose underlying ethos is not aligned with promoting scientific quality.

Universities have historically been extremely meek in accepting the terms and conditions imposed by big publishers, who have in turn treated academics as a cash cow. We on the one hand produce for free the product that they sell, and then pay to publish and read it. They cannot survive without the research created in Universities: we should start recognising that we need not bow down to their demands.

DISCLAIMER: I am writing in a personal capacity and not as a representative of the University of Oxford.

14/11/21

P.S. Some further examples of integrity problems with Elsevier have been pointed out to me on Twitter:

Geoff Frampton (@Geoff_Frampton) noted 'Elsevier had the largest market share among the publishers of retracted Covid-19 articles in our study' 

Patricia Murray (@PMurray_65) tweeted: Elsevier have failed to retract this 2008 Lancet paper that is known to be fraudulent and poses a risk to patients: https://thelancet.com/journals/lancet/article/PIIS0140-6736(08)61598-6/references… The paper stated the so-called 'bioengineered' airway had "a normal appearance and mechanical properties at 4 months." 

It is particularly shocking that the publisher is still making this article available (at a cost of $31) given that the author had a prison sentence for faked research, and conducted unethical experiments on seriously ill patients: see this report. 

PPS - it gets worse. There have been strenuous attempts to get the journal to retract the paper, to no avail. This has made the national news in the UK.

 

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