ORIGINAL ARTICLE

(wileyonlinelibrary.com) doi: 10.1002/leap.1265 Received: 4 September 2019 | Accepted: 16 October 2019

bioRxiv: Trends and analysis of five years of preprints

Kent R. Anderson

Founder, Caldera Publishing Solutions, Westborough,

Abstract
MA, USA bioRxiv was founded on the premise that publicly posting preprints would
allow authors to receive feedback and submit improved papers to journals.
ORCID: 0000-0002-5458-6735
This paper analyses a number of trends against this stated purpose,
E-mail: kent@caldera-publishing.com namely, the timing of preprint postings relative to submission to accepting
journals; trends in the rate of unpublished preprints over time; trends in
the timing of publication of preprints by accepting journals; and trends in
the concentration of published, reviewed preprints by publisher. Findings
show that a steady c.30% of preprints remain unpublished and that the
majority is posted onto bioRxiv close to or after submission – therefore
giving no time for feedback to help improve the articles. Four publishers
(Elsevier, Nature, PLOS, and Oxford University Press) account for the pub-
lication of 47% of bioRxiv preprints. Taken together, it appears that bio-
Rxiv is not accomplishing its stated goals and that authors may be using
the platform more to establish priority, as a marketing enhancement of
papers, and as functional Green OA, rather than as a community-driven
source of prepublication review.

INTRODUCTION To evaluate bioRxiv, we can be more specific. The stated pur-

The preprint server bioRxiv was developed at Cold Spring Harbor
Labs (CSHL) and its Press (CSHLP) and has become the largest
such platform in the biological sciences since its launch in
November 2013, hosting more than 40,000 preprints to date. Its
preprint base has since been used to catalyse the launch of a
related preprint initiative, medRxiv, which was launched in 2019
through a collaboration of CSHLP, the BMJ Publishing Group,
and Yale University.
Preprint servers have been established under various aus-
pices, including as temporary documents to bridge the time gap
between submission and publication (Goldschmidt-Clermont,
1965) to fixed papers intended to fundamentally supplant formal
journals (Brooks, 2009). There is little agreement about their
function, from the durability of preprints themselves in the record
to their function for authors. Numerous concerns about preprint
management have been articulated (Kling, 2005), especially in the
biological and medical sciences.
pose of bioRxiv is to serve as a useful way station as papers
move along to journals:
By posting preprints on bioRxiv, authors are able to make
their findings immediately available to the scientific com-
munity and receive feedback on draft manuscripts before
they are submitted to journals.
This paper examines data acquired from a number of sources,
including bioRxiv web pages and published article pages. Overall,
more than 37,000 preprints from bioRxiv were analysed for this
paper, and more than 1,200 published, peer reviewed articles
with associated preprints were included in the final data set.
Data were gathered using the Web Scraper plugin for Google
Chrome (https://www.webscraper.io/), and data were down-
loaded via CSV and then converted to Microsoft Excel. All calcu-
lations were performed in Excel. Data included the date of
preprint posting, the digital object identifier (DOI) of the preprint,

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2 K.R. Anderson
Key points
• Of the preprints related to papers published in Nature
journals, 57% were posted on bioRxiv after the paper was
submitted to the journal that would ultimately publish it.
• Approximately 30% of bioRxiv preprints remain un-
published, similar to the publication rate of ArXiv.org.
• Almost half of bioRxiv preprints that are ultimately publi-
shed are found in journals from four publishers: Elsevier,
Nature, PLOS, and Oxford University Press.
• Authors posting preprints on bioRxiv rarely publish in meg-
ajournals: only 3–9% of published articles appear in the
four main megajournals (PLOS One, Nature Communica-
tions, Scientific Reports, and Science Advances.
and any associated journal publication emanating from the pre-
print. A sub-analysis conducted later used the same tool to assess
the use and reach of Twitter relative to bioRxiv preprints. Pub-
lishers and journals associated with published papers emanating
from preprints were determined via DOI lookup. These data cor-
respond strongly with a prior analysis published earlier this year
by researchers from the University of Minnesota (Abdill &
Blekham, 2019). However, my analysis varies, and I have added
other data sets to test pre-publication posting behaviour and
other factors that those authors did not test.
To evaluate bioRxiv’s success relative to its stated purpose, I
have interrogated the data along several related dimensions:
• The timing of preprint posting relative to publication in accepting
journals. If the premise of bioRxiv is proving successful, most
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preprints should be posted well ahead of submission to the
final journal accepting the paper in order for community feed-
back to accumulate, so authors can improve the paper prior to
submission.
• The rate of unpublished preprints remaining on the bioRxiv
servers. If bioRxiv is helping move manuscripts through an
improvement process and into journals, the rate of preprints
remaining unpublished should consistently trend towards zero,
and this rate of decrease should be accelerating as the service
proves more mainstream and successful.
The null hypothesis is therefore that bioRxiv is doing what it
purports – helping authors improve papers prior to submission to
journals. One sign of success would be a high and increasing per-
centage of papers successfully passing peer review and resulting
in journal publication. This outcome would satisfy all stake-
holders. By extension, if the null hypothesis is contradicted by
the data, it would be reasonable to assume that bioRxiv is serving
purposes other than those stated.
TIMING OF PREPRINT POSTING RELATIVE TO
PUBLICATION IN ACCEPTING (FINAL)
JOURNALS
To evaluate whether preprints are being mainly used to gather
community feedback in order to improve papers prior to submis-
sion, I constructed a sample of more than 1,200 papers published
from 2016 to 2018 across a variety of Nature journals. Journals
from Nature were selected as they cover a wide variety of sub-
ject areas and reliably include publication event data, such as date
of submission, date of acceptance, and date of publication. In
addition, Nature journals were generally the most active for
authors posting preprints in bioRxiv during the timeframe of this
FIGURE 1 This scattergram shows
1,220 papers from Nature journals.
The 0 date is the date the paper
was submitted to the journal. The
distance above this point is the
number of days prior to submission
the preprint was posted. The dis-
tance below this point is the number
of days after submission when the
preprint was posted. As you can see,
the trend is for more preprints to be
posted after submission, fewer to be
posted prior to submission, and the
times to shift towards being closer
to submission if done before or fur-
ther beyond if done after.
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analysis, accounting for 14% of all published preprints (Elsevier
was second, with 13%). Papers were matched across bioRxiv and
the Nature journals by digital object identifier (DOI).
The data show that 57% of the preprints related to papers
published in Nature journals were posted on bioRxiv after the
paper was submitted. A total of 5% of papers were posted after
acceptance, while 0.2% were posted after publication.
The time afforded to posting before submission was gener-
ally brief. Only 29% of published papers were posted as a pre-
print more than 10 days before the paper was submitted to the
journal that published it, while 26% of preprints were posted
within 10 days before or after submitting it to that journal. The
remainder were posted more than 10 days after submission.
Figure 1 shows the data for each paper from 1 to 1,220 (X-axis).
Negative values connote days after submission, meaning the pre-
print was posted after submission.
The trend in the data was towards a longer period occurring
between submission and posting, doubling from 20 days post-
submission for 2016 preprints to 40 days post-submission for
2018 preprints. The overall effect of the data suggests fewer
postings prior to submission and more postings after (the data
are from 2016 to 2018, reading left to right, with the spread of
papers distributed evenly from 0 to 1,220). This suggests that
authors are increasingly using the platform for purposes other
than receiving pre-submission feedback.
Overall and on average, the preprints related to Nature jour-
nal articles were posted slightly more than a month (34 days) after
being submitted to the journal that would ultimately publish the
work. This timing may have some significance. In general, for many
journals, 30 days is enough time for a paper to clear initial editorial
review and, in some cases, to have cleared initial peer review.
Given these data, it appears that, instead of a pre-submission
system, bioRxiv may be viewed as a pre-publication system by
the authors using it. This shift in author utilization of bioRxiv may
be accelerating as well.
There are limitations to these data. We cannot tell from these
data if any papers were reviewed and rejected elsewhere prior
to the ultimately successful submission, review, and publication
FIGURE 2 Percentage of preprints not published in peer-reviewed format.
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Trends and analysis of five years of preprints 3
process. This was a sampling of articles submitted to a specific
publisher. The sample size was limited by the availability of
complete submission, acceptance, and publication data across many
publishers.
With the majority of preprints in this sample being posted after
submission to the journal that would ultimately publish them, and
usually after some editorial signal has been sent, if not complete
reviews, it seems bioRxiv is being used by authors for purposes
other than garnering community feedback. Given the potential for
posted preprints to reflect peer review or editorial review feedback,
and the increasing time between submission and posting, these
practices may have implications for publisher policies around Green
OA, preprints, and copyright transfer agreements.
TRENDS IN UNREVIEWED PREPRINTS ON
BIORXIV
(A note on terminology: I view preprints as published in the prac-
tical sense. However, where they have not been accepted and
published by a peer reviewed journal, what remains on bioRxiv is
the unreviewed assertions of the authors, which here are called
the ‘unreviewed preprint’. This term is used to differentiate these
articles from those that have been reviewed and subsequently
published in peer reviewed journals.)
Using data from more than 37,000 preprints posted on bio-
Rxiv between November 2013 and 31 December 2018, thou-
sands of unreviewed preprints remain on bioRxiv servers. I
consider these to be abandoned manuscripts – either abandoned
by the authors, who never intended to publish them in a peer
reviewed journal or who gave up after multiple unsuccessful
attempts, or abandoned by the scientific community via the peer
review and editorial review mechanisms the community uses to
accept or reject research findings. However defined, the rate of
unreviewed or abandoned manuscripts is steady – 2 years after
posting, approximately a third of preprints has not resulted in a
peer reviewed publication.
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4 K.R. Anderson
FIGURE 3 Preprints posted and not published in a peer-reviewed form.
As of 1 August 2019, for the years 2013–2019, 41.9% of bio-
Rxiv preprints have not been published in a peer reviewed journal.
The averages at the heart of the data are quite consistent (Fig. 2):
• 2013 – 40.3% (service started in November, 77 preprints
posted, 31 never published)
• 2014 – 31.9%
• 2015 – 32.2%
• 2016 – 31.3%
• 2017 – 32.4%
• 2018 – 50.0%
Focusing on the four complete years, when the service had a
full year for preprint posting and publication events can be
assumed to have had sufficient time to occur (2014–2017), the
average rate of abandoned manuscripts is 32%, or roughly 1 in
3. These data are not dissimilar to publication rates calculated
from arXiv preprints (Lariviere et al., 2014).
The rapid increase in the raw number of preprints means that
the steady percentage of abandoned preprints represents a grow-
ing number of preprints posted on bioRxiv that have never been
accepted in a peer reviewed journal (Fig. 3):
• 2013 – 31 preprints never published
• 2014 – 252
• 2015 – 509
• 2016 – 1,293
• 2017 – 3,339
• 2018 – 10,213
This rapid increase in preprints posted, combined with the
historical norms of unpublished or abandoned preprints, means
that the volume of unreviewed and unpublished manuscripts on
bioRxiv is growing, strongly indicating that the purpose of bioRxiv
as a platform allowing authors to share manuscripts for
community-based improvements prior to publication in a peer
reviewed journal is not being fulfilled.
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PUBLISHERS OF PAPERS WITH ASSOCIATED
PREPRINTS
Since 2013, Elsevier and Nature have published the largest per-
centage of papers initially posted on bioRxiv. These papers were
published in journals with a variety of business models, including
subscription journals. Over time, in fact, the percentage of papers
published by pure OA publishers (e.g. PLOS, BioMed Central,
eLife) has decreased.
As of 1 August 2019, Nature and Elsevier accounted for 27%
of the published papers based on preprints from 2013 to 2018.
Of the two, Elsevier is growing the fastest. Along with PLOS and
Oxford University Press (OUP), four publishers published 47% of
the papers based on bioRxiv preprints over the years mentioned
above:
• Nature – 14%
• Elsevier – 13%
• PLOS – 11%
• OUP – 9%
In the market overall (personal communication, 2019),
Elsevier accounts for 18% of the papers published (which puts
them short of market here), while SpringerNature accounts for
~12% (which means the Nature subset is strongly over-
performing in the market for these papers). Authors associated
with bioRxiv preprints may submit papers to Nature journals
more often due to its journals mix – there are many prominent
biology journals at Nature, as well as the flagship. Despite this,
Elsevier’s share appears to be overtaking Nature’s – up to
1 August 2019, for 2018 preprints, Elsevier had published 14% of
the published preprints to Nature’s 13%.
Two of the Top 4 are non-profit publishers. Overall, the mix
of the most active publishers of papers emanating from bioRxiv
preprints skews towards the non-profit space. This may have to
do with how biology and medical publishers skew overall, with
some of the most robust independent journals coming from
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biology and medicine. Non-profit biomedical publishers are usu-
ally affiliated with a society and have some of the most respected
journal brands – high-impact, central to communities, aspirational
– which may also explain the observation.
A total of ~100 publishers or journals have published
papers that first existed as bioRxiv preprints. This number
seems to be stabilizing, probably indicating the scope of interest
for authors of viable bioRxiv preprints. However, the papers are
not evenly distributed. The share of bioRxiv preprints published
with the 12 most active publishers of bioRxiv preprints
totals 72% of the papers resulting from preprints. These 12 are
(in order – those with a share of 10% or more are in bold
italic):
1. Nature
2. Elsevier
3. PLOS
4. OUP
5. BioMed Central
6. eLife
7. Wiley
8. PNAS
9. Genetics Society of America
10. Society for Neuroscience
11. Frontiers
12. PeerJ
The total share of papers published from bioRxiv preprints
for this dozen has been declining slowly; however, 80% of papers
based on 2015 preprints were published by these 12, and this
had dropped to 70% for 2018 preprints as of 1 August 2019.
Megajournals do not appear to appeal to authors posting
preprints on bioRxiv. For the preprint years 2015–2017, bioRxiv
preprints were only published as peer reviewed papers 3–9% of
the time in four of the major megajournals (PLOS One, Nature
FIGURE 4 Percentage of papers from pre-
prints published (by quarter).
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Trends and analysis of five years of preprints 5
Communications, Scientific Reports, and Science Advances). These
percentages declined over time.
OTHER OBSERVATIONS
Further analysis shows that publication events generally occur
more frequently in the final calendar quarter of each year, with
the lowest percentage published in the first calendar quarter
(16%) and the highest percentage (30%) published in the last cal-
endar quarter. Given the high probability of calendar quarters
aligning with fiscal year quarters, these data suggest that pub-
lishers accelerate publication of papers as the year ends. These
trends were independent of the overall growth of the number of
preprints on bioRxiv (Fig. 4).
The publishers most consistently publishing both more
papers and a higher percentage of papers in Q4 were Nature,
Elsevier, and OUP. This behaviour suggests that some calendar-
year incentive may drive the pace of paper acceptances and pub-
lication practices.
Papers emanating from preprints were published in journals
from exclusively OA publishers (PLOS, eLife, PeerJ, BioMed Cen-
tral, and Frontiers) and OA megajournals 51% of the time in
2014. This percentage dropped to 24% by 2017.
As the share of Nature and Elsevier journals publishing pre-
prints increased, there was an observable tendency for society
journals contracting for services with these large publishers to
publish articles using the Gold OA business model. Nature and
Elsevier’s proprietary titles appeared to do this far less commonly.
Twitter amplification of preprints is the most commonly asso-
ciated activity on the bioRxiv platform. However, its efficacy has
been declining. From 2014 to 2017, a tweet about a bioRxiv pre-
print on average reached 76,181 users. By the first half of 2019,
the average reach had declined to 53,967, a 29.2% decline. The
number of tweets per preprint also declined, from an average of
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6 K.R. Anderson
18 in the 2014–2017 time period to 13 in the first half of 2019.
The major contributing factor appears to be that Twitter users
with followers numbering in the hundreds of thousands boosted
preprints in the early days but have since moved on to other
things and no longer tweet about bioRxiv or preprints.
DISCUSSION
Overall, the null hypothesis – that bioRxiv helps authors improve
manuscripts prior to publication in peer reviewed journals – is
not supported by the data. Most authors who publish peer
reviewed articles based on preprints post the related preprint
after submission to the accepting journal, and more post within
10 days of submission. Taken together, these data indicate that
bioRxiv is not generally used as a source of pre-submission feed-
back. Trends also indicate that the rate of unpublished and ulti-
mately abandoned preprints remains steady, indicating that
bioRxiv is not scaling any effective and productive feedback
mechanism for authors, which one would reasonably expect
would lead to a decreasing percentage of unpublished preprints.
The practice of posting preprints close to or after submission,
and potentially after receiving a positive sign indicating likely
publication, is not unexpected. Good authors are cautious. They
do not want to be scooped or embarrassed. Therefore, it makes
sense they would only post a paper that has received some signal
about its fate, and perhaps some review and positive feedback,
maybe even a letter noting that only minor changes remain, bol-
stering their confidence that their paper is in decent shape and
bound for publication.
There are also data suggesting that papers posted as pre-
prints generate more citations (Davis & Fromerth, 2007). An
unknown proportion of authors may be placing preprints in bio-
Rxiv to realize this benefit. Depositing preprints also helps
authors establish priority. Finally, there is a distinct aspect of
social media promotion detectable on bioRxiv, with most ‘com-
ments’ linked from the tool the platform uses coming from article
promotion on Twitter and other social media platforms. In a more
competitive ‘publish or perish’ and funding environment, authors
may be using any and all methods they have to promote them-
selves and their work. While rational, author and paper promo-
tion is not a stated purpose of bioRxiv.
The observation that a steady percentage of bioRxiv pre-
prints are abandoned is more problematic. Operational assump-
tions – such as assigning permanent DOIs to preprints – were
made based on the notion that preprints would be tied to perma-
nent, validated journal articles. If the assumption had been other-
wise, a URL would be perfectly functional until and unless a peer
reviewed article was published based on the existing preprint.
Because this assumption was made, bioRxiv also lacks a policy to
retire or deprecate an inactive preprint after a reasonable period,
which the data indicate would be 2–3 years after posting.
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Overall, four publishers – Nature, Elsevier, PLOS, and OUP –
were responsible for publishing 72% of the papers emanating
from preprints posted to bioRxiv. The level of concentration
among these four is slowly decreasing over time. This may be
due to more society publishers establishing cascade systems and
launching Gold OA publications. The lack of interest in mega-
journals among authors posting bioRxiv preprints and successfully
pursuing publication may indicate that publication brand is an
important element of submission decisions. The erosion of pure
OA publishers as outlets for papers emanating from bioRxiv pre-
prints appears to confirm other findings that a business model is
not a primary way for authors to determine publication venue.
Preprint servers are an experiment and need to be measured
and assessed as such. To date, bioRxiv looks as if it adds little to
the experience of most authors, the fate of most papers, and the
overall health of the scholarly publishing ecosystem. The risks
and costs of leaving thousands of unreviewed and abandoned
preprints available to the general public, scientists, and practi-
tioners are not clear and may be sizable, especially as unrefereed
preprints are ported into medRxiv, a preprint server specifically
focused on medicine.
These data suggest that bioRxiv is being utilized by authors
more as a pre-publication, post-acceptance platform for article
promotion, career advancement, and protection of priority.
ACKNOWLEDGEMENTS
The author acknowledges the contributions of Eric Anderson,
which included the acquisition of key data elements about pub-
lishers’ utilization of preprints. The author also thanks Phil Davis
for discussions about similar findings for arXiv and for providing
useful references for the same.
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