ArticlePloS one2019
Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
31 citing papers in PubMed.
- Estimating scientific coherence using population-level indicators and research production data: a longitudinal analytical proof-of-concept study.Frontiers in research metrics and analytics · 2026Article
- Tackling paper mills requires us to prevent future contamination and clean up the past - the case of the journalBioengineered · 2025Article
- Article
- Publication integrity: what is it, why does it matter, how it is safeguarded and how could we do better?Journal of the Royal Society of New Zealand · 2025Review
- How to fight fake papers: a review on important information sources and steps towards solution of the problem.Naunyn-Schmiedeberg's archives of pharmacology · 2024Review
- Misspellings or "miscellings"-Non-verifiable and unknown cell lines in cancer research publications.International journal of cancer · 2024Article
- Triangulating evidence in health sciences with Annotated Semantic Queries.Bioinformatics (Oxford, England) · 2024Article
- Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals.Naunyn-Schmiedeberg's archives of pharmacology · 2024Article
- Retracted: MicroRNA-124 Regulates the Proliferation of Colorectal Cancer Cells by Targeting iASPP.BioMed research international · 2023Article
- Protection of the human gene research literature from contract cheating organizations known as research paper mills.Nucleic acids research · 2022Review
- Is the future of peer review automated?BMC research notes · 2022Article
- Identification of human gene research articles with wrongly identified nucleotide sequences.Life science alliance · 2022Article
- Retraction: Exosome-derived PTENP1 suppresses cisplatin resistance of bladder cancer (BC) by suppressing cell proliferation, migration and inducing apoptosisRSC advances · 2021Article
- Retraction: LncRNA MALAT1 aggravates MPP-induced neuronal injury by regulating miR-212 in SH-SY5Y cells.RSC advances · 2021Article
- Retraction: LncRNA ZEB2-AS1 regulates the drug resistance of acute myeloid leukemiaRSC advances · 2021Article
- Retraction: LncRNA OIP5-AS1 contributes to ox-LDL-induced inflammation and oxidative stress through regulating the miR-128-3p/CDKN2A axis in macrophages.RSC advances · 2021Article
- Article
- Retraction: TRIM22 functions as an oncogene in gliomas through regulating the Wnt/β-catenin signaling pathway.RSC advances · 2021Article
- Retraction: Long noncoding RNA DLEU1 promotes cell proliferation and migration of Wilms tumor through the miR-300/HOXC8 axis.RSC advances · 2021Article
- Retraction: MicroRNA-135a alleviates lipid accumulation and inflammation of atherosclerosis through targeting lipoprotein lipase.RSC advances · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleotide sequence reagents are verifiable experimental reagents in biomedical publications, because their sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that incorrectly identified nucleotide sequence reagents are characteristic of highly similar human gene knockdown studies, some of which have been retracted from the literature on account of possible research fraud. Because of the throughput limitations of manual verification of nucleotide sequences, we developed a semi-automated fact checking tool, Seek & Blastn, to verify the targeting or non-targeting status of published nucleotide sequence reagents. From previously described and unknown corpora of 48 and 155 publications, respectively, Seek & Blastn correctly extracted 304/342 (88.9%) and 1066/1522 (70.0%) nucleotide sequences and a predicted targeting/ non-targeting status. Seek & Blastn correctly predicted the targeting/ non-targeting status of 293/304 (96.4%) and 988/1066 (92.7%) of the correctly extracted nucleotide sequences. A total of 38/39 (97.4%) or 31/79 (39.2%) Seek & Blastn predictions of incorrect nucleotide sequence reagent use were correct in the two literature corpora. Combined Seek & Blastn and manual analyses identified a list of 91 misidentified nucleotide sequence reagents, which could be built upon through future studies. In summary, incorrect nucleotide sequence reagents represent an under-recognized source of error within the biomedical literature, and fact checking tools such as Seek & Blastn may help to identify papers and manuscripts affected by these errors.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.