Earlier this month, Bernd Pulverer, chief editor of The EMBO Journal, reflected on two years of transparency in peer review at the journal (Nature 468, 29-31, subscription required).  The journal now publishes referees' reports, authors' responses and editors' comments alongside papers.  

Despite initial concerns about changing the long-established peer review system, he reports the shift to transparency as "overwhelmingly positive", with steady submission volumes, and no significant impact on quality of referees' reports or rate of acceptance of invitations to review papers.  The huge amount of effort that goes into peer review is now more visible too - benefiting everyone involved in the process.

In the two years since EMBO began their transparent peer review experiment, the subject has come up several times, with a particular focus on stem cell biology.

At a conference in June 2009, 14 leading stem cell scientists sent an open letter to leading journals via this site expressing their strong concerns about the lack of transparency in peer review. They suggested that comments from reviewers should be published alongside the research, as The EMBO Journal does with its peer review process files.

Then in June this year, New Scientist published an analysis of "publication dynamics" in the field of induced pluripotentⁱ stem (iPS) cell research, finding that researchers in the US get their papers published faster, and in higher-profile journals, than rivals elsewhere.  Based on these findings, they echoed the call in the letter from leading stem cell scientists to lift the veil of secrecy over peer review.

It seems that other journals are beginning to heed the call - recently, the European Journal of Cell Biology announced that it would follow The EMBO Journal's footsteps and publish peer review process files alongside research papers.

Reference: Nature http://dx.doi.org/10.1038/468029a