ArticlePLoS computational biology2021
Gene name errors: Lessons not learned.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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.
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Who cites it
17 citing papers in PubMed.
- Reproducible Data Analysis With R in Laboratory Hematology.International journal of laboratory hematology · 2026Review
- Protein-coding genes in humans and model mammals (mouse, rat and pig): gene identifiers and disambiguation of gene nomenclature retrieved from the Ensembl genome browser.BMC genomics · 2025Article
- Relational Databases for Behavior Science.Perspectives on behavior science · 2025Article
- Reporting Chemical Data in the Environmental Sciences.ACS environmental Au · 2025Review
- Catalyzing computational biology research at an academic institute through an interest network.PLoS computational biology · 2025Article
- Datavzrd: Rapid programming- and maintenance-free interactive visualization and communication of tabular data.PloS one · 2025Article
- What is the real value of omics data? Enhancing research outcomes and securing long-term data excellence.Nucleic acids research · 2024Article
- Eleven quick tips for properly handling tabular data.PLoS computational biology · 2024Article
- Two subtle problems with overrepresentation analysis.Bioinformatics advances · 2024Article
- The five pillars of computational reproducibility: bioinformatics and beyond.Briefings in bioinformatics · 2023Article
- Metadata integrity in bioinformatics: Bridging the gap between data and knowledge.Computational and structural biotechnology journal · 2023Review
- A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes.Plant methods · 2022Article
- Towards comprehensive integration and curation of chloroplast genomes.Plant biotechnology journal · 2022Article
- Gene Updater: a web tool that autocorrects and updates for Excel misidentified gene names.Scientific reports · 2022Article
- Radiolucent Lesions of the Jaws: An Attempted Demonstration of the Use of Co-Word Analysis to List Main Similar Pathologies.International journal of environmental research and public health · 2022Article
- Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse.Harvard data science review · 2022Article
- Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% (3,436/11,117) of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.
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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.