Category: genetics retractions

Sequence errors are ‘canaries in a coal mine’ in genetics studies, sleuth says 

A genetics researcher came across an interesting paper earlier this year on the gene he studies. The scientist, a doctoral candidate who asked not to be named, decided to take a closer look at which part of the gene, SNHG14, the authors targeted to measure its expression. He ran the sequence of the short strand of DNA, called a primer, given in the paper through a database and found the sequence matched with a completely different gene.

The scientist searched through similar papers and found 19 more across as many journals with the same problem: all their “SNHG14” primers matched with the gene MALAT1/TALAM1. There may be more, but he stopped looking.

Two of the papers he found have been retracted. One appeared in 2023 in Computational and Mathematical Methods in Medicine, a journal Wiley acquired from Hindawi that is no longer publishing. The notice cites inappropriate citations and peer review manipulation. The other article, published in 2022 in the International Journal of Oncology, was retracted for plagiarism. 

Continue reading Sequence errors are ‘canaries in a coal mine’ in genetics studies, sleuth says 

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. 

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

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.

Continue reading Guest post: Genomics has a spreadsheet problem

Journal to retract papers that cost its impact factor and spot in leading index

A journal that didn’t get an impact factor this year after Clarivate, the company behind the closely-watched but controversial metric, identified unusual citations in several articles will retract the offending papers, according to its editor. 

Genetika, a publication of the Serbian Genetics Society, did not receive an updated impact factor in Clarivate’s 2023 Journal Citation Reports due to citation stacking, a practice in which authors or journals seem to trade citations, also known as “citation cartels” or “citation rings.” 

Specifically, Clarivate identified five papers published in Genetika in 2021 that had been cited by 22 papers published in the journal Bioscience Research in 2022, Snezana Mladenovic Drinic, the editor of Genetika, told Retraction Watch. Clarivate also suppressed Bioscience Research this year, meaning that the journal did not receive a new impact factor either. 

Continue reading Journal to retract papers that cost its impact factor and spot in leading index

Almond, no joy: Plant geneticist in Iran up to at least six retractions

A plant geneticist in Iran is up to at least six retractions for misuse of figures and other material from previously published papers. 

The newest retraction involves a 2017 paper in Scientific Reports, a Springer Nature publication, titled “Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species.” PubPeer commenters have been discussing it for some seven months.

According to the notice: 

Continue reading Almond, no joy: Plant geneticist in Iran up to at least six retractions

Two years after student loses PhD, ORI concludes he committed misconduct

The U.S. Office of Research Integrity (ORI) announced today that a former graduate student committed research misconduct — nearly two years after his institution stripped him of his degree.

The ORI concluded that Shiladitya Sen committed misconduct in a PNAS paper (retracted six months ago), his PhD thesis, a poster presentation, and two grant applications to the National Institutes of Health (NIH). Sen has agreed not to seek federal funding for three years.

A spokesperson for The Ohio State University (OSU), where Sen was based, told us its investigation wrapped up in Spring 2016, and Sen’s PhD was revoked that June. It’s not clear why it took two years for the ORI to issue its own finding; the ORI did not immediately respond to requests for comment.

According to ORI’s notice, Sen:

Continue reading Two years after student loses PhD, ORI concludes he committed misconduct

Caught Our Notice: Hey peer reviewers — did you even read this paper??

What Caught Our Attention: A tree of life paper has been axed — and based on the information in the retraction notice, we’re wondering how it ever passed peer review.

Specifically, the notice states a review of the paper found “concerns regarding the study design, methodology, and interpretation of the data.” Overall, the research “contradict(s) a large body of existing literature and do(es) not provide a sufficient level of evidence to support the claims made in the paper.” Um, so what did it get right?

Continue reading Caught Our Notice: Hey peer reviewers — did you even read this paper??

Authors retract heart disease paper for “nonscientific reason”

Researchers have retracted a 2018 paper about the genetic underpinnings of heart disease from the FASEB Journal — and it’s not entirely clear why.

The paywalled retraction notice simply cites a “nonscientific reason.” Cody Mooneyhan, the director of publications at the journal, declined to provide further details, and the authors have provided different accounts of what happened: The paper’s corresponding author, John Yu, told Retraction Watch that he requested the retraction because the first author, Chia‐Ti Tsai, refused to sign the journal’s copyright agreement. Tsai, a professor in the Department of Internal Medicine at National Taiwan University in Taipei, told us he was “not notified before the paper was submitted.” Continue reading Authors retract heart disease paper for “nonscientific reason”

Caught Our Notice: 54 problems in three scientific images equals one expression of concern

Title: Effects of microRNA-223 on morphine analgesic tolerance by targeting NLRP3 in a rat model of neuropathic pain

What Caught Our Attention: Usually, an Expression of Concern (EOC) offers general language about “concerns regarding the validity of the data” or “concerns regarding the integrity of the study.” Here the language is anything but, saying that 54 Western blot bands within three figures have problems such as “visible pasted joints,” “square border,” and numerous “appear to be the same band.”  According to the notice, the authors have not responded to requests for the original blots, so the editors are allowing the article to remain intact, choosing instead “to alert readers to these issues and allow them to arrive at their own conclusions regarding the figures.” Continue reading Caught Our Notice: 54 problems in three scientific images equals one expression of concern

Author: “The retractions were about bureaucracy, not science”

A researcher has retracted two 2014 papers, after discovering they had not gone through the proper approval process before being submitted.

The papers were part of a collaboration funded by the U.S. National Institutes of Health, which focused on solving protein structures. Adam Godzik, the senior author, told Retraction Watch that all papers had to be approved by a special committee before being submitted to a journal. Given the scale of the collaboration, the committee for the Joint Center for Structural Genomics (JCSG) would assess whether researchers who had made a previous contribution to the work should be added as authors.

Proteins: Structure, Function, and Bioinformatics retracted both papers after Godzik informed the editor in August 2014 that neither article had undergone the required review before being submitted to the journal. Although Wiley agreed to the retractions in an email to Godzik in September 2014,  the papers were only pulled in January—more than three years later. Continue reading Author: “The retractions were about bureaucracy, not science”