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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2023

The Preprint Club - A cross-institutional, community-based approach to peer reviewing

The academic community has been increasingly using preprints to disseminate their latest research findings quickly and openly. This early and open access of non-peer reviewed research warrants new means from the scientific community to efficiently assess and provide feedback to preprints. Yet, most peer review of scientific studies performed today are still managed by journals, each having their own peer review policy and transparency. However, approaches to uncouple the peer review process from journal publication are emerging. Additionally, formal education of early career researchers (ECRs) in peer reviewing is rarely available, hampering the quality of peer review feedback. Here, we introduce the Preprint Club, a cross-institutional, community-based approach to peer reviewing, founded by ECRs from the University of Oxford, Karolinska Institutet and Icahn School of Medicine at Mount Sinai. Over the past two years and using the collaborative setting of the Preprint Club, we have been discussing, assessing, and providing feedback on recent preprints in the field of immunology. In this article, we provide a blueprint of the Preprint Club basic structure, demonstrate its effectiveness, and detail the lessons we learned on its impact on peer review training and preprint authors perception.

scientific communication and education↗

bioRxiv2020

Quantifying and contextualizing the impact of bioRxiv preprints through social media audience segmentation

Engagement with scientific manuscripts is frequently facilitated by Twitter and other social media platforms. As such, the demographics of a papers social media audience provide a wealth of information about how scholarly research is transmitted, consumed, and interpreted by online communities. By paying attention to public perceptions of their publications, scientists can learn whether their research is stimulating positive scholarly and public thought. They can also become aware of potentially negative patterns of interest from groups that misinterpret their work in harmful ways, either willfully or unintentionally, and devise strategies for altering their messaging to mitigate these impacts. In this study, we collected 331,696 Twitter posts referencing 1,800 highly tweeted bioRxiv preprints and leveraged topic modeling to infer the characteristics of various communities engaging with each preprint on Twitter. We agnostically learned the characteristics of these audience sectors from keywords each users followers provide in their Twitter biographies. We estimate that 96% of the preprints analyzed are dominated by academic audiences on Twitter, suggesting that social media attention does not always correspond to greater public exposure. We further demonstrate how our audience segmentation method can quantify the level of interest from non-specialist audience sectors such as mental health advocates, dog lovers, video game developers, vegans, bitcoin investors, conspiracy theorists, journalists, religious groups, and political constituencies. Surprisingly, we also found that 10% of the highly tweeted preprints analyzed have sizable (>5%) audience sectors that are associated with right-wing white nationalist communities. Although none of these preprints intentionally espouse any right-wing extremist messages, cases exist where extremist appropriation comprises more than 50% of the tweets referencing a given preprint. These results present unique opportunities for improving and contextualizing research evaluation as well as shedding light on the unavoidable challenges of scientific discourse afforded by social media.

scientific communication and education↗

bioRxiv2020

From amazing work to I beg to differ - analysis of bioRxiv preprints that received one public comment till September 2019

While early commenting on studies is seen as one of the advantages of preprints, the nature of such comments, and the people who post them, have not been systematically explored. We analysed comments posted between 21 May 2015 and 9 September 2019 for 1,983 bioRxiv preprints that received only one comment. Sixty-nine percent of comments were posted by non-authors (n=1,366), and 31% by preprint authors (n=617). Twelve percent of non-author comments (n=168) were full review reports traditionally found during journal review, while the rest most commonly contained praises (n=577, 42%), suggestions (n=399, 29%), or criticisms (n=226, 17%). Authors comments most commonly contained publication status updates (n=354, 57%), additional study information (n=158, 26%), or solicited feedback for the preprints (n=65, 11%). Our study points to the value of preprint commenting, but further studies are needed to determine the role that comments play in shaping preprint versions and eventual journal publications.

scientific communication and education↗

bioRxiv2024

The Impact of Preprints on COVID-19 Research Dissemination: A Quantitative Analysis of Journal Publications

Preprints have played an unprecedented role in disseminating COVID-19-related science results to the public. The study aims to elucidate the role of preprints during the COVID-19 public health emergency (2020-2023) through a quantitative analysis of journal papers. Among the 247,854 COVID-19-related papers published in PubMed, 12,152 were initially released as preprints and were eventually published in 1,380 journals. This number is more than five times the 246 journals to which submissions can be made directly from bioRxiv through the B2J program. Journals with higher impact factors and Normalized Eigenfactor scores tend to publish a larger number of preprint-derived articles. The proportion of preprints among PubMed papers was 0.049, but this varies significantly by journal. In the top 30 journals, most exceed this proportion, indicating that these journals are preferred by authors for submitting their work. These findings highlight the growing acceptance and impact of preprints in the scientific community, particularly in high-impact journals.

scientific communication and education↗

bioRxiv2019

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the readers ability to independently interpret data and reproduce findings. MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals. ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication. ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.

scientific communication and education↗

bioRxiv2019

Releasing a preprint is associated with more attention and citations

Preprints in biology are gaining popularity, but release of a preprint still precedes only a fraction of peer-reviewed publications. We examined whether having a preprint on bioRxiv was associated with metrics of the corresponding peer-reviewed article. We assembled a dataset of 74,239 articles, 5,405 of which had a preprint, published in 39 journals. Based on log-linear regression and random-effects meta-analysis, articles with a preprint had a 51% higher Altmetric Attention Score and 37% more citations compared to articles without one. These associations were independent of several other article- and author-level variables (e.g., scientific subfield and last author publication age) and unrelated to journal-level variables such as access model and Impact Factor. This observational study can help researchers and publishers make informed decisions about how to incorporate preprints into their work.

scientific communication and education↗

bioRxiv2026

Preprint solicitation as a natural experiment in scholarly publishing

Preprinting is a growing and increasingly recognized mechanism for scientific communication and productivity and a way to facilitate global access to science. The interplay of preprinting practices with formal peer-reviewed publication is an open question that is now tractable to targeted analysis. Here, we take advantage of nearly a decade of preprint solicitation at Proceedings B to address this question, which offers a quasi-experimental setting for comparing outcomes for solicited preprints and traditionally submitted manuscripts. We used submission records from 15,368 manuscripts from 2018-2024 to assess whether preprint solicitation affects acceptance rates, journal scope, author geographic diversity, and post-publication uptake. Solicited manuscripts were accepted at nearly twice the rate of traditional submissions and received more downloads and citations after publication. Submission topics were broadly similar between the two routes, though solicited manuscripts showed marginally greater subject diversity. Geographic disparities favoring the Global North persisted, but acceptance rates for solicited manuscripts converged across regions, narrowing the gap seen in traditional submissions. These findings extend earlier work on this initiative and indicate that editor-driven solicitation can identify high-quality preprints, broaden geographic representation, and increase research visibility, offering a replicable model for journals seeking to diversify authorship while maintaining editorial standards.

scientific communication and education↗

bioRxiv2017

Preprinting Microbiology

The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain the Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer-review. Although use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem.

microbiology↗

bioRxiv2020

International authorship and collaboration in bioRxiv preprints

As preprints become integrated into conventional avenues of scientific communication, its critical to understand who is included and who is not. However, little is known about which countries are participating or how they collaborate with each other. Here, we present an analysis of all 67,885 preprints posted on bioRxiv (through 2019) using the first comprehensive dataset of country-level preprint author affiliations. We find the plurality of preprints (39%) come from the United States, and that countries such as the U.S. and U.K. are overrepresented on bioRxiv relative to their overall scientific output, while countries including China, Russia, and Turkey show lower bioRxiv adoption. We describe a set of "contributor countries" including Uganda, Croatia and Thailand that appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the U.S.

scientific communication and education↗

bioRxiv2021

Preprints in motion: tracking changes between posting and journal publication

Amidst the COVID-19 pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press and policymakers for the first time. This phenomenon has sharpened longstanding questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record? We assessed preprints from bioRxiv and medRxiv that had been posted and subsequently published in a journal through 30th April 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version. We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 7.2% of non-COVID-19-related and 17.2% of COVID-19-related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not qualitatively change the conclusions of the paper.

scientific communication and education↗

bioRxiv2022

Mapping the content of comments on bioRxiv and medRxiv preprints

IntroductionPreprints have been increasingly used in biomedical sciences, providing the opportunity for research to be publicly assessed before journal publication. With the increase in attention over preprints during the COVID-19 pandemic, we decided to assess the content of comments left on preprint platforms. MethodsPreprints posted on bioRxiv and medRxiv in 2020 were accessed through each platforms API, and a random sample of preprints that had received between 1 and 20 comments was analyzed. Comments were evaluated in triplicate by independent evaluators using an instrument that assessed their features and general content. Results7.3% of preprints received at least 1 comment during a mean follow-up of 7.5 months. Analyzed comments had a median size of 43 words. Criticisms, corrections or suggestions were the most prevalent type of content, followed by compliments or positive appraisals and questions. Most critical comments regarded interpretation, data collection and methodological design, while compliments were usually about relevance and implications. ConclusionsOnly a small percentage of preprints posted in 2020 in bioRxiv and medRxiv received comments in these platforms. When present, however, these comments address content that is similar to that analyzed by traditional peer review. A more precise taxonomy of peer review functions would be desirable to describe whether post-publication peer review fulfills these roles.

scientific communication and education↗

bioRxiv2019

bioRxiv: the preprint server for biology

The traditional publication process delays dissemination of new research, often by months, sometimes by years. Preprint servers decouple dissemination of research papers from their evaluation and certification by journals, allowing researchers to share work immediately, receive feedback from a much larger audience, and provide evidence of productivity long before formal publication. Launched in 2013 as a non-profit community service, the bioRxiv server brought preprinting to the life sciences and recently posted its 310,000th manuscript. The server now receives around ten million views per month and hosts papers spanning all areas of biology. Initially dominated by evolutionary biology, genetics/genomics and computational biology, bioRxiv has been increasingly populated by papers in neuroscience, cell and developmental biology, and many other fields. bioRxiv and its sister server, medRxiv, also played a critical role during the pandemic, rapidly disseminating new discoveries in immunology, virology and epidemiology related to the SARS-CoV-2 virus and its effects. Changes in journal and funder policies that encourage preprint posting helped drive adoption, as did the development of bioRxiv technologies that allow authors to transfer papers easily between bioRxiv and journals. A recent user survey found that 30% of authors post their preprints weeks to months before submitting to a journal whereas 55% post around the time of journal submission. Authors are motivated by a desire to share work early; they value the feedback they receive and very rarely experience any negative consequences of preprint posting. Rapid dissemination via bioRxiv is also encouraging new initiatives that experiment with the peer review process and the development of novel approaches to literature filtering and assessment.

scientific communication and education↗

bioRxiv2020

Study of the Influence of Preprint in bioRχiv for Peer Review and Acceptance Time of PLOS ONE

This study examines the relation between acceptance times in preprint publishing and journal publishing. Specifically, we investigated the association between a papers posting time to bioR{chi}iv, a preprints server, and journal articles peer-review and acceptance time for PLOS ONE. So far, of the total papers published in 1,626 academic journals, the average publication rate of those posted in bioR{chi}iv is 40.67%. Meanwhile, PLOS ONE was the journal that published more papers. Analysis of peer-review and acceptance time of papers published in journals via preprints showed the time these papers are posted in relation to these intervals. The median of the peer-review and acceptance time of the journal submission date that was later than the date of first posting to bioR{chi}iv was 110.00 days, and in the reverse case, it was 139.50 days. Posting to the preprint server before journal submission shows a better order than vice versa. This study provides us a good understanding of the peer-review process. It also gives us good insights into optimizing this process, which would then facilitate paper publication and knowledge dissemination.

scientific communication and education↗

bioRxiv2016

Has the time come for preprints in biology?

Preprints, non-peer reviewed drafts of manuscripts available on the internet, have been used in conjunction with peer review and publication in journals in the physical sciences for almost 25 years. Recently, more scientists have been discussing whether preprints can play a similar role in biological and biomedical research. Here, I discuss my excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences.

Scientific Communication and Education↗

bioRxiv2016

On the origin of nonequivalent states: how we can talk about preprints

Increasingly, preprints are at the center of conversations across the research ecosystem. But disagreements remain about the role they play. Do they \"count\" for research assessment? Is it ok to post preprints in more than one place? In this paper, we argue that these discussions often conflate two separate issues, the history of the manuscript and the status granted it by different communities. In this paper, we propose a new model that distinguishes the characteristics of the object, its \"state\", from the subjective \"standing\" granted to it by different communities. This provides a way to discuss the difference in practices between communities, which will deliver more productive conversations and facilitate negotiation on how to collectively improve the process of scholarly communications not only for preprints but other forms of scholarly contributions.

scientific communication and education↗

bioRxiv2020

Peer review and preprint policies are unclear at most major journals

Clear and findable publishing policies are important for authors to choose appropriate journals for publication. We investigated the clarity of policies of 171 major academic journals across disciplines regarding peer review and preprinting. 31.6% of journals surveyed do not provide information on the type of peer review they use. Information on whether preprints can be posted or not is unclear in 39.2% of journals. 58.5% of journals offer no clear information on whether reviewer identities are revealed to authors. Around 75% of journals have no clear policy on co-reviewing, citation of preprints, and publication of reviewer identities. Information regarding practices of Open Peer Review is even more scarce, with <20% of journals providing clear information. Having found a lack of clear information, we conclude by examining the implications this has for researchers (especially early career) and the spread of open research practices.View Full Text

scientific communication and education↗

bioRxiv2020

Attitudes and Practices of Open Data, Preprinting, and Peer-review - a Cross Sectional Study on Croatian Scientists

Attitudes towards open peer review, open data and use of preprints influence scientists engagement with those practices. Yet there is a relatively small number of validated questionnaires that measure these attitudes. The goal of our study was to construct and validate such a questionnaire. Using a sample of Croatian scientists (N=541), from a wide range of disciplines, we developed a questionnaire titled Attitudes towards Open data sharing, preprinting, and peer-review (ATOPP). The questionnaire has 21 item with a four-factor structure (attitudes towards: open data, preprint servers, open peer-review and open peer-review in small scientific communities). Based on the questionnaire, the attitudes of Croatian scientists towards these topics were generally neutral, with a median of 3.3 out of 5 of the total attitude score. Croatian scientist attitudes were lowest for open peer-review in small scientific communities (Md 2.0) and highest for open data (Md 3.9).

scientific communication and education↗

bioRxiv2020

The impact of preprint servers in the formation of novel ideas

We study whether novel ideas in biomedical literature appear first in preprints or traditional journals. We develop a Bayesian method to estimate the time of appearance for a phrase in the literature, and apply it to a number of phrases, both automatically extracted and suggested by experts. We see that presently most phrases appear first in the traditional journals, but there is a number of phrases with the first appearance on preprint servers. A comparison of the general composition of texts from bioRxiv and traditional journals shows a growing trend of bioRxiv being predictive of traditional journals. We discuss the application of the method for related problems.

scientific communication and education↗