Many journals accept manuscripts that have been previously posted as preprints.
To check if a journal allows preprints, the best source of information is always the journal website. But you can also search SHERPA/RoMEO or a crowd-sourced list of journal policies on preprints on Wikipedia.
More detailed descriptions of innovative practices are below.
Preprints under consideration
Nature Communications offers authors of papers that have been sent out for review the option to have the corresponding preprint included in a public list.
An editorial describes the process and intended outcomes:
We hope that by offering additional visibility to preprints that are under consideration in our journal, we will not only be able to accelerate the dissemination of potentially exciting science, but also complement our peer review process by promoting wider scrutiny of preprints and thus a more holistic review procedure. Preprint servers provide a means for scientists to solicit informal feedback on their work, and we anticipate that our authors will continue to take such feedback into account to strengthen their findings during the peer review process.
— Casey Brown (@casey6r0wn) October 4, 2016
Encourage submission of manuscripts of broad interest, fast track them into peer review with an appropriate editor. 2/
— Casey Brown (@casey6r0wn) October 4, 2016
Proceedings of the Royal Society B
This role and intentions for related developments (including “Preprint” and “Preprint Editor” flags) were described in an editorial. The preprint editor is assisted by a team of early career researchers at her university. The authors of a paper published via this route shared their experience in a post on the Royal Society’s Publishing Blog.
Inviting submissions from preprint servers
Several other journals report looking for papers on preprint servers.
For some time now we have been scanning new posts on bioRxiv to look for papers that we might want to invite into the journal, guaranteeing peer review.
– Louise Flintoft, editor of Genome Biology
— THERY Manuel (@ManuelTHERY) May 26, 2016
— Les Loew (@lesloew) May 26, 2016
One week later (Feb 6th) I received an unexpected — indeed, quite astonishing — email, from the editors of Biostatistics. It said that they had seen my preprint, thought it could be suitable for Biostatistics, had had it reviewed by two referees (reports attached), and that they would like to offer conditional acceptance for publication in Biostatistics if I could satisfactorily address the referee concerns.
Extended scoop protection
EMBO Journal has long offered scoop protection – an assurance that any competing articles published after the submission date of a manuscript under consideration would not be “considered relevant to the editorial assessment” of the manuscript. In December 2016, they announced that this protection will also extend backwards to the date of preprint posting. More details can be found in their submission policy on preprint servers.
This policy is described in an April 6, 2017 press release.
Link to previous versions
“Now, to document and help readers trace the complete publication record, authors are invited to voluntarily provide a footnote for their BJ article referencing their preprint in bioRxiv or arXiv, including the DOI number and the date the initial manuscript was deposited.”
PLOS links backwards to preprints as well:
Am excited that as of today we are linking to preprints posted to @biorxivpreprint from the published article itself. This also applies to previously published papers. https://t.co/1CPAMRWABh pic.twitter.com/YjFCtfPp7g
— Joerg Heber (@joergheber) July 20, 2018
“Authors submitting directly to the journal who upload a preprint of their paper to BioRxiv receive a 10% discount on the publication charge.”
ICMJE (International Committee of Medical Journal Editors)
On page 8 of their December 2016 recommendations, ICMJE has clarified that their recommendation against dual publication does not prevent consideration of preprints.
On page 9 of their December 2018 recommendations, ICMJE has added that authors should select preprint servers that collect COI statements and clearly disclose that the papers are not peer reviewed. Furthermore, ICMJE recommends that authors notify editors of the existence of a preprint and ensure that the preprint links to the final published article.