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As this year draws to a close, we’re looking back at some of our most popular research of 2021. Which research outputs have made the most-read list? Find out below!

It’s been another busy year for F1000Research! With almost 900 articles published this year to date, we’re proud to see the benefits of our pioneering open research model in action.

Research Articles remain our most popular article type, representing 57% of the published work. However, many researchers continue to use our non-traditional article types to tell the full story of their research. Case Reports, Systematic Reviews, and Study Protocols are all popular choices among our authors.

Moreover, we expect to see further uptick in the publication of novel article types in 2022. Both Data Notes and Clinical Practice Articles make up a larger portion of our published work this year compared to last. Additionally, our recent introduction of Policy Briefs, Genome Notes, and Case Studies will give authors even more options to make real world impact next year. We’re proud to offer so many solutions to suit the needs of today’s researchers across all disciplines.

And now down to details! Our most-read articles of 2021 are those that received the highest number of views across F1000Research and PubMed Central, where they are also indexed. Articles must have already passed peer review to be considered.  Without further ado, here are our top 5 research outputs this year!

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#1: Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology

Mauro Petrillo, Carlo Brogna, Simone Cristoni, Maddalena Querci, Ornella Piazza, Guy Van den Eede

This ground-breaking Research Article revealed that SARS-CoV-2 (COVID-19) replicates in our gut bacteria, potentially making the disease more severe. With almost 19,000 views and over 600 downloads, the study has made quite an impact on the scientific community.

 “We observed something completely unexpected,” said author Mauro Petrillo. “The bacteriophage-like behavior of SARS-CoV-2. A bacteriophage is a type of virus that infects bacteria.”

To the authors’ knowledge, this type of behavior has never been observed before. “We must now look at COVID-19 and long-term COVID-19 from new perspectives to better understand the disease and to develop more targeted therapies, including in the presence of comorbidities,” notes Petrillo. “The same applies to other diseases in case such a phage-like behavior is not limited to SARS-CoV-2.”

The authors continue to work on further evidence of what they observed, in parallel with the activities of another paper recently published on F1000Research. Read our full interview with Petrillo and stay tuned for further updates.

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#2: Sustainable data analysis with Snakemake

Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster

This Method Article received over 13,000 views and 1332 downloads. The authors describe Snakemake, a text-based pipeline execution system that builds on the principles of the Unix ‘make’ utility.

“The authors balance the conceptual overview with well-chosen usage examples that are simple enough to understand and make clear how the example can generalize to other cases”, notes one peer reviewer, Michael Reich.

“This paper provides a comprehensive introduction and overview of Snakemake and serves as an effective entry point to this popular system.”

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#3: Current market rates for scholarly publishing services

Alexander Grossmann, Björn Brembs

In this Research Article, the authors “assume the role of a newcomer to the academic publishing market” and break down article publication costs. The authors cover all aspects of the publishing process, from submission, through peer review, to publication, indexing, and archiving.

The article has almost 7000 views and 690 downloads. What’s more, Version 1 of this article has an Altmetric score of 181 and 302 mentions on Twitter. Version 2, however, has an even higher Almetric score of 215, with over 348 mentions on Twitter.

“There is no doubt therefore that this is an extremely valuable report that should be widely disseminated”, commends one peer reviewer, Pandelis Perakakis.

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#4: Defining and validating regenerative farm systems using a composite of ranked agricultural practices

Tommy L.D. Fenster, Claire E. LaCanne, Jacob R. Pecenka, Ryan B. Schmid, Michael M. Bredeson, Katya M. Busenitz, Alex M. Michels, Kelton D. Welch, Jonathan G. Lundgren

This Research Article proposes a regenerative agriculture matrix scoring system to evaluate the extent to which a farming system has adopted regenerative practices.

With almost 5000 views and 438 downloads, the authors have successfully exemplified the benefits of practicing regenerative agriculture.

“This review of regenerative agriculture in many parts of US is the most comprehensive and thorough I have yet seen on the subject,” says reviewer Richard W. Teague. “It covers a wide array of biological disciplines to assess the various biodiversity elements required to assess the efficacy of regenerative agriculture relative to conventional agriculture.”

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#5: SARS-CoV-2 and the role of fomite transmission: a systematic review

Igho J. Onakpoya, Carl J. Heneghan, Elizabeth A. Spencer, Jon Brassey, Annette Plüddemann, David H. Evans, John M. Conly, Tom Jefferson

The final of our top 5 is a Systematic Review article with 4668 views and 784 downloads. The authors compiled and summarized many scientific publications that surveyed SARS-CoV-2 on surfaces. As one peer reviewer, Ana Karina Pitol Garcia notes, “Surface contamination is an essential piece of information needed to understand the role of fomites in disease transmission.”

The authors aimed to identify, appraise, and summarize the evidence from primary studies and systematic reviews assessing the role of fomites in COVID-19 transmission. The comparison is comprehensive and provides useful insights into the development of our understanding of COVID-19.

Congratulations to all our most-read authors of 2021!

We want to take this opportunity to thank all our authors and reviewers who have published and reviewed with us this year. We look forward to reading even more of your articles and reports in 2022!

New to F1000Research? We welcome your submissions for publication next year. Check out our ‘How It Works’ page and our article guidelines, to learn what to expect when submitting your research.