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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 19 recordsLinked to original sources
bioRxiv2022

Phase 1 of the NIH Preprint Pilot: Testing the viability of making preprints discoverable in PubMed Central and PubMed

IntroductionThe National Library of Medicine (NLM) launched a Pilot in June 2020 to: 1) explore the feasibility and utility of adding preprints to PubMed Central (PMC) and making them discoverable in PubMed, and 2) to support accelerated discoverability of National Institutes of Health (NIH)-supported research without compromising user trust in NLMs widely used literature services. MethodsThe first phase of the Pilot focused on archiving preprints reporting NIH-supported SARS-CoV-2 virus and COVID-19 research. To launch Phase 1, NLM identified eligible preprint servers and developed processes for identifying NIH-supported preprints within scope in these servers. Processes were also developed for the ingest and conversion of preprints in PMC and to send corresponding records to PubMed. User interfaces were modified for display of preprint records. NLM collected data on the preprints ingested and discovery of preprint records in PMC and PubMed and engaged users through focus groups and a survey to obtain direct feedback on the Pilot and perceptions of preprints. ResultsBetween June 2020 and June 2022, NLM added more than 3,300 preprint records to PMC (viewed 4 million times) and PubMed (viewed 3 million times) Nearly one-quarter of preprints in the Pilot were not associated with a peer-reviewed published journal article. User feedback revealed that the inclusion of preprints did not have a notable impact on trust in PMC or PubMed. DiscussionNIH-supported preprints can be identified and added to PMC and PubMed without disrupting existing operations processes. Additionally, inclusion of preprints in PMC and PubMed accelerates discovery of NIH research without reducing trust in NLM literature services. Phase 1 of the Pilot provided a useful testbed for studying NIH investigator preprint posting practices, as well as knowledge gaps among user groups, during the COVID-19 public health emergency, an unusual time with heightened interest in immediate access to research results.

scientific communication and education↗
bioRxiv2020

Preprinting a pandemic: the role of preprints in the COVID-19 pandemic

The world continues to face a life-threatening viral pandemic. The virus underlying the COVID-19 disease, SARS-CoV-2, has caused over 98 million confirmed cases and 2.2 million deaths since January 2020. Although the most recent respiratory viral pandemic swept the globe only a decade ago, the way science operates and responds to current events has experienced a paradigm shift in the interim. The scientific community has responded rapidly to the COVID-19 pandemic, releasing over 125,000 COVID-19 related scientific articles within 10 months of the first confirmed case, of which more than 30,000 were hosted by preprint servers. We focused our analysis on bioRxiv and medRxiv, two growing preprint servers for biomedical research, investigating the attributes of COVID-19 preprints, their access and usage rates, as well as characteristics of their propagation on online platforms. Our data provides evidence for increased scientific and public engagement with preprints related to COVID-19 (COVID-19 preprints are accessed more, cited more, and shared more on various online platforms than non-COVID-19 preprints), as well as changes in the use of preprints by journalists and policymakers. We also find evidence for changes in preprinting and publishing behaviour: COVID-19 preprints are shorter and reviewed faster. Our results highlight the unprecedented role of preprints and preprint servers in the dissemination of COVID-19 science, and the impact of the pandemic on the scientific communication landscape.

scientific communication and education↗
bioRxiv2020

Publishing of COVID-19 Preprints in Peer-reviewed Journals, Preprinting Trends, Public Discussion and Quality Issues

IntroductionCOVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals. We aimed to evaluate: (i) whether COVID-19-related preprints were favored for publication, (ii) preprinting trends and public discussion of the preprints, and (iii) the relationship between the publication topic (COVID-19-related or not) and quality issues. MethodsManuscripts deposited at bioRxiv and medRxiv between January 1 and September 27 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data. The Retraction Watch Database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. ResultsWith adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR=2.04, 95%CI 1.87-2.23) as well as over the entire observed period (OR=1.42, 95%CI 1.33-1.52). Submission-to-acceptance was by 38.67 days (95%CI 34.96-42.39) shorter for COVID-19 articles. Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. ConclusionCurrent data suggest a preference for publication of COVID-19-related preprints over the observed period.

scientific communication and education↗
bioRxiv2020

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

ABSTRACTObjectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms. We also aim to provide a searchable database to enable relevant stakeholders to compare between platforms.Study Design and Setting Preprint platforms that were launched up to 25th June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot-tested and used to collect data from each preprint platform’s webpage(s). Data collected were in relation to scope and ownership; content-specific characteristics and information relating to submission, journal transfer options, and external discoverability; screening, moderation, and permanence of content; usage metrics and metadata. Where possible, all online data were verified by the platform owner or representative by correspondence.Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, six (14%) were provided by F1000 Research Ltd (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. The three most common screening checks related to the scope of the article, plagiarism and legal/ethical/societal issues and compliance. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read-access, and most have a policy regarding reasons for retraction and the sustainability of the service. Forty-one (93%) platforms currently have usage metrics, with the most common metric being the number of downloads presented on the abstract page.Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility. However, the process by which content is screened before online posting and withdrawn or removed after posting varies between platforms, which may be associated with platform operation, ownership, governance and financing.In concurrence with an increase in the number of preprint servers and platforms supporting biomedical and medical sciences research since 2013, there has been substantial growth in the number of preprints posted in this research area.The significant benefits of accelerated dissemination of research that preprints offer has attracted the support of many major funders.The raised profile of preprints has led to their wider acceptance in institutional and individual level assessment.This is the first full examination of the characteristics and policies of 44 preprint platforms with biomedical and medical scope. We use a robust methodological approach to extract relevant information from web-based material with input from preprint platform owners.Despite concerns regarding the permanence and quality of preprints, most preprint platforms have long-term preservation strategies and many have screening checks (for example, a basic check for the relevance of content) in place. For some platforms, these checks are performed by researchers with content expertise.We provide a searchable database as a valuable resource for researchers, funders and policymakers in the biomedical and medical science field to determine which preprint platforms are relevant to their research scope and which have the functionality and policies that they value most.Competing Interest StatementJessica Polka is Executive Director of ASAPbio.View Full Text

scientific communication and education↗
bioRxiv2024

Enabling preprint discovery, evaluation, and analysis with Europe PMC

Preprints provide an indispensable tool for rapid and open communication of early research findings. Preprints can also be revised and improved based on scientific commentary uncoupled from journal-organised peer review. The uptake of preprints in the life sciences has increased significantly in recent years, especially during the COVID-19 pandemic, when immediate access to research findings became crucial to address the global health emergency. With ongoing expansion of new preprint servers, improving discoverability of preprints is a necessary step to facilitate wider sharing of the science reported in preprints. To address the challenges of preprint visibility and reuse, Europe PMC, an open database of life science literature, began indexing preprint abstracts and metadata from several platforms in July 2018. Since then, Europe PMC has continued to increase coverage through addition of new servers, and expanded its preprint initiative to include the full text of preprints related to COVID-19 in July 2020 and then the full text of preprints supported by the Europe PMC funder consortium in April 2022. The preprint collection can be searched via the website and programmatically, with abstracts and the open access full text of COVID-19 and Europe PMC funder preprint subsets available for bulk download in a standard machine-readable JATS XML format. This enables automated information extraction for large-scale analyses of the preprint corpus, accelerating scientific research of the preprint literature itself. This publication describes steps taken to build trust, improve discoverability, and support reuse of life science preprints in Europe PMC. Here we discuss the benefits of indexing preprints alongside peer-reviewed publications, and challenges associated with this process.

scientific communication and education↗
bioRxiv2024

Exploring Neuroscience Researchers' Trust in Preprints through Citation Analysis

Preprints have emerged as efficient tools for fast and free dissemination of scientific findings. The present study explores the evolving landscape of preprints among the field of neuroscience and examines patterns and evolution of citations to preprints over time in this field. Leveraging bibliometric methods, we identified over 33,000 citations (1993-2022) to preprints within neuroscience publications indexed in Scopus. The findings elucidate a significant temporal increase in the number of documents citing preprints, reaching a peak of around 60 per 1,000 Scopus documents in 2021. Diverse document types, particularly reviews, exhibit a growing reliance on preprints as references. The most frequently cited preprint servers include bioRxiv, ArXiv, medRxiv, and PsyArXiv. Leading journals such as eLife and PLOS Computational Biology have cited preprints more than others. The United States takes the lead in citing preprints, followed by the United Kingdom and Germany. Using Scite.ai, motivations underlying preprint citations and the context in which they were cited were explored and the results are indicative of the "mentioning" nature of 93% of citations to preprints. Furthermore, the introduction and discussion sections have shown to include the highest number of citations to preprints. The findings highlight the dynamic transformation of preprints in neuroscience field.

neuroscience↗
bioRxiv2021

Linguistic Analysis of the bioRxiv Preprint Landscape

Preprints allow researchers to make their findings available to the scientific community before they have undergone peer review. Studies on preprints within bioRxiv have been largely focused on article metadata and how often these preprints are downloaded, cited, published, and discussed online. A missing element that has yet to be examined is the language contained within the bioRxiv preprint repository. We sought to compare and contrast linguistic features within bioRxiv preprints to published biomedical text as a whole as this is an excellent opportunity to examine how peer review changes these documents. The most prevalent features that changed appear to be associated with typesetting and mentions of supplementary sections or additional files. In addition to text comparison, we created document embeddings derived from a preprint-trained word2vec model. We found that these embeddings are able to parse out different scientific approaches and concepts, link unannotated preprint-peer reviewed article pairs, and identify journals that publish linguistically similar papers to a given preprint. We also used these embeddings to examine factors associated with the time elapsed between the posting of a first preprint and the appearance of a peer reviewed publication. We found that preprints with more versions posted and more textual changes took longer to publish. Lastly, we constructed a web application (https://greenelab.github.io/preprint-similarity-search/) that allows users to identify which journals and articles that are most linguistically similar to a bioRxiv or medRxiv preprint as well as observe where the preprint would be positioned within a published article landscape.

bioinformatics↗
bioRxiv2023

Unreviewed science in the news: The evolution of preprint media coverage from 2014-2021

It has been argued that preprint coverage during the COVID-19 pandemic constituted a paradigm shift in journalism norms and practices. This study examines whether, in what ways, and to what extent this is the case using a sample of 11,538 preprints posted on four preprint servers--bioRxiv, medRxiv, arXiv, and SSRN--that received coverage in 94 English-language media outlets between 2014-2021. We compared mentions of these preprints with mentions of a comparison sample of 397,446 peer reviewed research articles indexed in the Web of Science to identify changes in the share of media coverage that mentioned preprints before and during the pandemic. We found that preprint media coverage increased at a slow but steady rate pre-pandemic, then spiked dramatically. This increase applied only to COVID-19-related preprints, with minimal or no change in coverage of preprints on other topics. In addition, the rise in preprint coverage was most pronounced among health and medicine-focused media outlets, which barely covered preprints before the pandemic but mentioned more COVID-19 preprints than outlets focused on any other topic. These results suggest that the growth in coverage of preprints seen during the pandemic period may imply a shift in journalistic norms, including a changing outlook on reporting preliminary, unvetted research.

scientific communication and education↗
bioRxiv2021

Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors

Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find weak evidence that authors preferentially select their highest quality, most novel or most significant research to post as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.

scientific communication and education↗
bioRxiv2019

Tracking the popularity and outcomes of all bioRxiv preprints

Researchers in the life sciences are posting their work to preprint servers at an unprecedented and increasing rate, sharing papers online before (or instead of) publication in peer-reviewed journals. Though the popularity and practical benefits of preprints are driving policy changes at journals and funding organizations, there is little bibliometric data available to measure trends in their usage. Here, we collected and analyzed data on all 37,648 preprints that were uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. We find that preprints on bioRxiv are being read more than ever before (1.1 million downloads in October 2018 alone) and that the rate of preprints being posted has increased to a recent high of more than 2,100 per month. We also find that two-thirds of bioRxiv preprints posted in 2016 or earlier were later published in peer-reviewed journals, and that the majority of published preprints appeared in a journal less than six months after being posted. We evaluate which journals have published the most preprints, and find that preprints with more downloads are likely to be published in journals with a higher impact factor. Lastly, we developed Rxivist.org, a website for downloading and interacting programmatically with indexed metadata on bioRxiv preprints.

scientific communication and education↗
bioRxiv2016

search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any website to be integrated with articles from preprint servers. The bioPreprint search engine is publicly available at http://www.hsls.pitt.edu/resources/preprint.

Scientific Communication and Education↗
bioRxiv2021

Publication practices during the COVID-19 pandemic: Biomedical preprints and peer-reviewed literature

The coronavirus pandemic introduced many changes to our society, and deeply affected the established in biomedical sciences publication practices. In this article, we present a comprehensive study of the changes in scholarly publication landscape for biomedical sciences during the COVID-19 pandemic, with special emphasis on preprints posted on bioRxiv and medRxiv servers. We observe the emergence of a new category of preprint authors working in the fields of immunology, microbiology, infectious diseases, and epidemiology, who extensively used preprint platforms during the pandemic for sharing their immediate findings. The majority of these findings were works-in-progress unfitting for a prompt acceptance by refereed journals. The COVID-19 preprints that became peer-reviewed journal articles were often submitted to journals concurrently with the posting on a preprint server, and the entire publication cycle, from preprint to the online journal article, took on average 63 days. This included an expedited peer-review process of 43 days and journals production stage of 15 days, however there was a wide variation in publication delays between journals. Only one third of COVID-19 preprints posted during the first nine months of the pandemic appeared as peer-reviewed journal articles. These journal articles display high Altmetric Attention Scores further emphasizing a significance of COVID-19 research during 2020. This article will be relevant to editors, publishers, open science enthusiasts, and anyone interested in changes that the 2020 crisis transpired to publication practices and a culture of preprints in life sciences.

scientific communication and education↗
bioRxiv2024

The Impact of Preprints on the Citations of Journal Articles Related to COVID-19

To investigate the impact of preprints on the citation counts of COVID-19-related papers, this study compares the number of citations received by drafts initially distributed as preprints and later published in journals with those received by papers directly submitted to journals. The difference in the median number of citations between COVID-19 preprint-distributed papers and COVID-19 directly submitted papers published in 184 journals was tested using the Mann-Whitney U test. The results showed that 129 journals had a statistically significant higher median citation count for COVID-19 preprint-distributed papers compared to directly submitted papers, with a p-value of less than 0.05. In contrast, no journals had a statistically significant higher median citation count for COVID-19 directly submitted papers. This indicates that 70.11% of the journals that published preprint-distributed papers experienced a significant increase in citations. We also identified that among the 184 journals, 13 journals garnered a substantial number of citations. Among the 74,037 COVID-19 papers, preprint-distributed papers (9,028) accounted for only 12.19%. However, among the 2,015,997 citations received by COVID-19 papers, preprint-distributed papers garnered 542,715 citations, representing a substantial 26.92%. These results suggest that distributing preprints prior to formal publication may help COVID-19 research reach a wider audience, potentially leading to increased readership and citations.

scientific communication and education↗
bioRxiv2019

The effect of bioRxiv preprints on citations and altmetrics

1.A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.

scientific communication and education↗
bioRxiv2026

Faster science, penalties in evaluation, and concerns on quality and impact: Researchers' use and perceptions of preprints

The preprint ecosystem has expanded rapidly over the past decade, fundamentally altering science communication. Yet, the scholarly community's attitudes toward this shift remain underexplored. Through a large-scale survey of US and Canadian biomedical scholars, we provide a comprehensive analysis of preprint utilization, perceived impact, and integration into academic credit systems. We find robust engagement across reading, citing, and submitting preprints; however, this activity is driven primarily by a desire for rapid dissemination rather than a foundational commitment to open science. Furthermore, while preprints are valued as networking assets, perceived career penalties during formal academic evaluations stifle broader cultural adoption. Crucially, to navigate the absence of formal peer review, scholars report a heavy reliance on author reputation as a primary heuristic for evaluating a preprint's credibility and guiding their reading and citation decisions. Notably, despite acknowledging preprints' role in accelerating knowledge sharing, scholars express significant concerns regarding fraud and misinformation, particularly amid declining public trust in science and emerging threats to scientific integrity from artificial intelligence. To resolve these tensions, the preprint ecosystem must evolve beyond prioritizing speed to foster genuine academic dialogue. Simultaneously, evaluation frameworks must adapt to the realities of preprinting, and innovative quality-control mechanisms are urgently needed to balance rapid dissemination with rigorous scientific integrity.

scientific communication and education↗
bioRxiv2026

Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models

Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unreliable, yet how much those claims change before publication has so far been quantified only in smaller cohorts, with results that vary by field and topic. Here, we compiled every bioRxiv preprint posted between 2018 and 2025 that we could match by DOI to a peer-reviewed published version, yielding 72,644 preprint-publication pairs. Using a large language model (Claude Sonnet 4.6), we parsed every preprint-publication abstract pair into one primary and two secondary claims, and classified each pair for content change (unchanged, minor, major) and hedging shift (more cautious, more confident, unchanged). On a validation subsample, the model agreed with two independent domain experts about as well as the experts agreed with each other (Cohens kappa 0.63 to 0.66). The primary claim was unchanged in 39.9% of abstracts, minorly revised in 50.0%, and substantially revised in only 10.2%. Hedging shifts were uncommon and asymmetric, with twice as many claims becoming more cautious as more confident (8.4% vs 4.2%). Major revisions were more frequent after long peer review (14.1% in the slowest versus 7.0% in the fastest tertile of review time) and declined over the study period (17.0% in 2019 to 5.7% in 2024). Over the same period, biomedical papers that were never posted as preprints were retracted at roughly twice the rate of those that were. Together, these data show that the move from preprint to peer-reviewed publication leaves the central claims of most biomedical abstracts intact, indicating that preprints are a reliable source of biomedical research.

scientific communication and education↗
bioRxiv2022

Science in motion: A qualitative analysis of journalists' use and perception of preprints

This qualitative study explores how and why journalists use preprints -- unreviewed research papers -- in their reporting. Through thematic analysis of interviews conducted with 19 health and science journalists in the second year of the COVID-19 pandemic, it applies a theoretical framework that conceptualizes COVID-19 preprint research as a form of post-normal science, characterized by high scientific uncertainty and societal relevance, urgent need for political decision-making, and value-related policy considerations. Findings suggest that journalists approach the decision to cover preprints as a careful calculation, in which the potential public benefits and the ease of access preprints provided were weighed against risks of spreading misinformation. Journalists described viewing unreviewed studies with extra skepticism and relied on diverse strategies to find, vet, and report on them. Some of these strategies represent standard science journalism, while others, such as labeling unreviewed studies as preprints, mark a departure from the norm. However, journalists also reported barriers to covering preprints, as many felt they lacked the expertise or the time required to fully understand or vet the research. The findings suggest that coverage of preprints is likely to continue post-pandemic, with important implications for scientists, journalists, and the publics who read their work.

scientific communication and education↗