Journal retracts 31 papers, bans authors and reviewers after losing its impact factor

A journal that lost its impact factor and spot in a major index this year has made good on a promise to retract dozens of papers with “compromised” peer review.  

Genetika, a publication of the Serbian Genetics Society, did not receive an updated impact factor this year after Clarivate, the company behind the closely-watched but controversial metric, identified signs of citation stacking, a practice in which authors or journals seem to trade citations. Clarivate also dropped Genetika from its Web of Science index for failing to meet editorial quality criteria. 

Clarivate’s actions followed a blog post by scientific sleuth Elisabeth Bik about what she called the “Iranian Plant Paper Mill, which included 31 papers published in Genetika

Snežana Mladenović Drinić, the editor of Genetika, previously told Retraction Watch the journal would retract “papers for which it was determined that the peer review was not done validly.” Jelena Milasin, president of the Serbian Genetics Society, also said Genetika had offered to retract 32 “suspicious papers” published in 2021 and 2022, in the hopes of salvaging their standing with Clarivate.

In its latest issue, Genetika published a notice retracting 31 articles and a corrigendum “due to evidence indicating that the peer review of this paper was compromised, using of frauted [sic] data, high number of unfitting citation, overoll [sic] general misconduct related to professional codes of ethics.” 

The list largely overlaps with Bik’s, and includes five papers for which Clarivate had provided “evidence of inappropriate manipulation of citations.” 

The authors and reviewers of the retracted papers, as well as “authors who misused the papers published in Genetika by citing them unjustifiably” will be blacklisted from publishing in the journal in the future, according to the notice. It stated: 

We would like to apologize [sic] authors, readers and all scientific community that we are having to make those retractions, and we will take all necessary steps to ensure our editorial and peer review processes keep pace with the evolving threat and advancements in scientific fraud. 

Drinić and Milasin have not responded to our request for comment.

The five papers with manipulated citations all included M. Khayatnezhad as a coauthor. Khayatnezhad previously held a position in the environmental science and engineering department at the Islamic Azad University’s Ardabil branch in Iran, and also was managing editor of the university’s journal Anthropogenic Pollution. The journal now has a different managing editor, and an email we sent to Khayatnezhad’s university address bounced back. He did not respond to our request for comment sent to another address.

Hat tip: Alexander Magazinov

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Guest post: Genomics has a spreadsheet problem

Mandhri Abeysooriya

Surveys show spreadsheets are the most widely used analytical tool in academic research. But they are prone to errors. During the height of the COVID-19 pandemic, Public Health England lost 16,000 test results after using an old Excel file format to handle data. Whether this mix-up hampered local infection control is anybody’s guess, but it certainly could have. 

The software is causing trouble for other lines of research, too, as our team and others have shown: Genomics studies that rely on Excel spreadsheets to manage data turn out to be riddled with erroneous gene names, or gene-name errors, and the issue is affecting more and more journals.

A persistent problem

Gene-name errors were discovered by Barry R. Zeeberg and his team at the National Institutes of Health in 2004. Their study first showed that when genomic data is handled in Excel, the program automatically corrects gene names to dates. What’s more, Riken clone identifiers – unique name tags given to pieces of DNA – can be misinterpreted as numbers with decimal points.

In 2016, we conducted a more extensive search, showing that in more than 3,500 articles published between 2005 and 2015, 20% of Excel gene lists contained errors in their supplementary files. 

There are no documented cases in which gene-name errors have affected the conclusions of a study. But if a researcher unknowingly saved a spreadsheet containing such errors, someone importing those data for further analysis would face a reproducibility problem. 

In response to these issues, the HUGO Gene Nomenclature Committee (HGNC) has made changes to some gene names prone to errors. This includes converting the SEPT-1 gene to SEPTIN1 and the MARCH1 gene to MARCHF1. 

The widespread adoption of these new names is a lengthy process: Our latest study, of more than 11,000 articles published between 2014 and 2020, found that 31% of supplementary files that included gene lists in Excel contained errors. This percentage is higher than in our previous 2016 study

We also found some novel errors. Some were connected to the local language setting. For example, the AGO2 gene was converted to Aug-02, perhaps due to “Ago” being short for “August” in Spanish. Similarly, MEI1 was switched to May-01 (“Mei” is “May” in Dutch), and TAMM41 to Jan-41 (“Tammikuu” is “January” in Finnish).

One of the significant findings in our study was the five-digit conversion. When saving a gene name converted to a date and importing it into a new Excel spreadsheet, the dates will change into a five-digit number. Software packages like HGNChelper and Gene Updater can help in fixing gene-name errors, but not once they have been converted to numbers.

Mark Ziemann

More and more journals affected

Despite increased recognition of gene-name errors, scientific journals have taken no significant initiatives to mitigate the problem. Our continuous tracking of these errors, the data for which is publicly accessible at https://ziemann-lab.net/public/gene_name_errors/, reveals a steady rate of gene-name errors and a rising number of affected journals until recently. 

This spread may be due to the expansion of omics into different branches of biology and medicine, coupled with the growth of second-tier journals.

But the problem isn’t limited to lesser-known journals. We found the journals with the highest numbers of affected articles were Nature Communications, PLOS ONE, Scientific Reports, BMC Genomics, PLOS Genetics and Oncotarget, with at least 100 affected publications each. Clearly, journals need to produce guidelines about how to filter for and address gene-name errors that can affect data reproducibility.

A substantial number of genes may be misnamed when the computer is set to a non-English language. Our studies only scratch the surface of this problem, but they plainly show Excel and other non-specialised spreadsheet programs are not designed to handle big data. 

Although gene-name errors may seem like small fry in the grand scheme of scientific data analysis, they are a symptom of broader issues like over-reliance on spreadsheets and lack of consensus on how large genomic datasets should be reviewed and disseminated. These issues need to be addressed to improve the reliability of genomics research.

Mandhri Abeysooriya is a second-year PhD student at Deakin University in Melbourne, Australia; Mark Ziemann is the head of the bioinformatics team at the Burnet Institute in Melbourne. 

Abeysooriya would like to thank Severine Lamon, an associate professor at Deakin University, and Danielle Hiam, a postdoctoral fellow at Deakin University, for their invaluable insights, feedback and endless support in writing this article.

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