Research Integrity and Peer Review-past highlights and future directions.

In May 2016, we launched Research Integrity and Peer Review, an international, open access journal with fully open peer review (reviewers are identified on their reports and named reports are published alongside the article) to provide a home for research on research and publication ethics, research reporting, and research on peer review. As the journal enters its third year, we reflect on recent events and highlights for the journal and explore how the journal is faring in terms of gender and diversity in peer review. We also share the particular interests of our Editors-in-Chief regarding models of peer review, reporting quality, common research integrity issues that arise during the publishing process, and how people interact with the published literature. We continue to encourage further research into peer review, research and publication ethics and research reporting, as we believe that all new initiatives should be evidence-based. We also remain open to constructive discussions of the developments in the field that offer new solutions.

Why articles are retracted: a retrospective cross-sectional study of retraction notices at BioMed Central.

OBJECTIVES: To assess why articles are retracted from BioMed Central journals, whether retraction notices adhered to the Committee on Publication Ethics (COPE) guidelines, and are becoming more frequent as a proportion of published articles. DESIGN/SETTING: Retrospective cross-sectional analysis of 134 retractions from January 2000 to December 2015. RESULTS: 134 retraction notices were published during this timeframe. Although they account for 0.07% of all articles published (190 514 excluding supplements, corrections, retractions and commissioned content), the rate of retraction is rising. COPE guidelines on retraction were adhered to in that an explicit reason for each retraction was given. However, some notices did not document who retracted the article (eight articles, 6%) and others were unclear whether the underlying cause was honest error or misconduct (15 articles, 11%). The largest proportion of notices was issued by the authors (47 articles, 35%). The majority of retractions were due to some form of misconduct (102 articles, 76%), that is, compromised peer review (44 articles, 33%), plagiarism (22 articles, 16%) and data falsification/fabrication (10 articles, 7%). Honest error accounted for 17 retractions (13%) of which 10 articles (7%) were published in error. The median number of days from publication to retraction was 337.5 days. CONCLUSIONS: The most common reason to retract was compromised peer review. However, the majority of these cases date to March 2015 and appear to be the result of a systematic attempt to manipulate peer review across several publishers. Retractions due to plagiarism account for the second largest category and may be reduced by screening manuscripts before publication although this is not guaranteed. Retractions due to problems with the data may be reduced by appropriate data sharing and deposition before publication. Adopting a checklist (linked to COPE guidelines) and templates for various classes of retraction notices would increase transparency of retraction notices in future.

A new forum for research on research integrity and peer review.

This editorial explains why we are launching Research Integrity and Peer Review, a new open-access journal that will provide a home to research on ethics, reporting, and evaluation of research. We discuss how the idea to launch this journal came about and identify the gaps in knowledge where we would like to encourage more research and interdisciplinary discussion. We are particularly keen to receive submissions presenting actual research that will increase our understanding and suggest potential solutions to issues related to peer review, study reporting, and research and publication ethics.

Retrospective analysis of the quality of reports by author-suggested and non-author-suggested reviewers in journals operating on open or single-blind peer review models.

OBJECTIVES: To assess whether reports from reviewers recommended by authors show a bias in quality and recommendation for editorial decision, compared with reviewers suggested by other parties, and whether reviewer reports for journals operating on open or single-blind peer review models differ with regard to report quality and reviewer recommendations. DESIGN: Retrospective analysis of the quality of reviewer reports using an established Review Quality Instrument, and analysis of reviewer recommendations and author satisfaction surveys. SETTING: BioMed Central biology and medical journals. BMC Infectious Diseases and BMC Microbiology are similar in size, rejection rates, impact factors and editorial processes, but the former uses open peer review while the latter uses single-blind peer review. The Journal of Inflammation has operated under both peer review models. SAMPLE: Two hundred reviewer reports submitted to BMC Infectious Diseases, 200 reviewer reports submitted to BMC Microbiology and 400 reviewer reports submitted to the Journal of Inflammation. RESULTS: For each journal, author-suggested reviewers provided reports of comparable quality to non-author-suggested reviewers, but were significantly more likely to recommend acceptance, irrespective of the peer review model (p<0.0001 for BMC Infectious Diseases, BMC Microbiology and the Journal of Inflammation). For BMC Infectious Diseases, the overall quality of reviewer reports measured by the Review Quality Instrument was 5% higher than for BMC Microbiology (p=0.042). For the Journal of Inflammation, the quality of reports was the same irrespective of the peer review model used. CONCLUSIONS: Reviewers suggested by authors provide reports of comparable quality to non-author-suggested reviewers, but are significantly more likely to recommend acceptance. Open peer review reports for BMC Infectious Diseases were of higher quality than single-blind reports for BMC Microbiology. There was no difference in quality of peer review in the Journal of Inflammation under open peer review compared with single blind.

Open, single-blind, double-blind: which peer review process do you prefer?

BMC Pharmacology and Toxicology was created from the merger of two journals within the BMC series published by BioMed Central: BMC Pharmacology and BMC Clinical Pharmacology. BMC Pharmacology operated anonymous peer review whereas BMC Clinical Pharmacology operated a fully open peer review policy where the identity of the reviewers was known to the editors, authors and readers. The merged journal also adopted a fully open peer review policy. Two years on we discuss the views and experiences of our Editorial Board Members towards open peer review on this biomedical journal.

Unpublished genomic data-how to share?

The field of genomics is often cited as the branch of biology that has led the way in data sharing. In most cases, sequencing data are made publicly available immediately after generation and often before the data generators have completed their analyses. Although the pros of such openness cannot be denied, problems can arise when unpublished genomic data are shared. In this editorial we touch on these issues and discuss the roles and responsibilities of the data generators, data users and journal editors.

Expression of concern: Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances.

After publication of this article (Fernandez et al., BMC Genomics 2011, 12:604) it was brought to the Editors' attention that the data generated by the first author, Ariel Fernandez, seemed anomalous. One of the author's institutions found that the data were not reproducible from the described methods, but an investigation by the author's other institution did not find the data or their interpretation suspicious. Given the conflicting conclusions of these investigations, the Editors advise the readers to interpret the data with due caution. We apologize to all affected parties.