Amanda Capes‐Davis
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View article: Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications
Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications Open
Reproducible laboratory research relies on correctly identified reagents. We have previously described gene research papers with wrongly identified nucleotide sequence(s), including papers studying miR‐145 . Manually verifying reagent iden…
View article: Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications
Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications Open
Reproducible laboratory research relies on correctly identified reagents. We have previously described human gene research papers with wrongly identified nucleotide sequence reagent(s), including papers studying miR-145 . Manually verifyin…
View article: Data from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Data from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Continuous cell lines are widely used, but can result in invalid, irreproducible research data. Cell line misidentification is a common problem that can be detected by authentication testing; however, misidentified cell lines continue to b…
View article: Supplementary Tables from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Supplementary Tables from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Contains the following Supplementary material: Supplementary Table 1: Examples of KB Terminology Supplementary Table 2: "Correct" Dataset, n=57 Supplementary Table 3: "Incorrect" Dataset, n=574 Supplementary Table 4: Sample articles from "…
View article: Supplementary Methods and Table Legends from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Supplementary Methods and Table Legends from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Contains the Supplementary Methods and the legends to accompany the Supplementary Tables.
View article: Supplementary Tables from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Supplementary Tables from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Contains the following Supplementary material: Supplementary Table 1: Examples of KB Terminology Supplementary Table 2: "Correct" Dataset, n=57 Supplementary Table 3: "Incorrect" Dataset, n=574 Supplementary Table 4: Sample articles from "…
View article: Supplementary Methods and Table Legends from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Supplementary Methods and Table Legends from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Contains the Supplementary Methods and the legends to accompany the Supplementary Tables.
View article: Data from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Data from Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Continuous cell lines are widely used, but can result in invalid, irreproducible research data. Cell line misidentification is a common problem that can be detected by authentication testing; however, misidentified cell lines continue to b…
View article: Lessons learned from automated screening of COVID-19 preprints
Lessons learned from automated screening of COVID-19 preprints Open
Preprints occupied the spotlight early in the pandemic, as scientists, the media and the public sought information on the evolving pandemic. While some in the scientific community embraced this shift, others were concerned about the qualit…
View article: Identification of human gene research articles with wrongly identified nucleotide sequences
Identification of human gene research articles with wrongly identified nucleotide sequences Open
Nucleotide sequence reagents underpin molecular techniques that have been applied across hundreds of thousands of publications. We have previously reported wrongly identified nucleotide sequence reagents in human research publications and …
View article: Human gene function publications that describe wrongly identified nucleotide sequence reagents are unacceptably frequent within the genetics literature
Human gene function publications that describe wrongly identified nucleotide sequence reagents are unacceptably frequent within the genetics literature Open
Nucleotide sequence reagents underpin a range of molecular genetics techniques that have been applied across hundreds of thousands of research publications. We have previously reported wrongly identified nucleotide sequence reagents in hum…
View article: Cross contamination meets misclassification: Awakening of <scp>CHP</scp>‐100 from sleeping beauty sleep—A reviewed model for Ewing's sarcoma
Cross contamination meets misclassification: Awakening of <span>CHP</span>‐100 from sleeping beauty sleep—A reviewed model for Ewing's sarcoma Open
A human cell line of neuroblastic tissue, which was believed to have been lost to science due to its unavailability in public repositories, is revived and reclassified. In the 1970s, a triple set of neuroblastoma (NB) cell lines became ava…
View article: Automated screening of COVID-19 preprints: Can we help authors to improve transparency and reproducibility?
Automated screening of COVID-19 preprints: Can we help authors to improve transparency and reproducibility? Open
The COVID-19 pandemic has thrust preprints into the spotlight, highlighting their advantages and disadvantages. The lack of peer review allows publication to occur with unprecedented speed, but this has raised concerns among biomedical sci…
View article: Identifying biomedical research papers with incorrect nucleotide sequence reagents using targeted and screening approaches
Identifying biomedical research papers with incorrect nucleotide sequence reagents using targeted and screening approaches Open
Biomedical literature describing erroneous nucleotide sequence reagents could reduce research reproducibility. We therefore developed the semi-automatic fact-checking tool Seek & Blastn (SB) to verify the targeting/non-targeting status of …
View article: CLASTR: The Cellosaurus STR similarity search tool ‐ A precious help for cell line authentication
CLASTR: The Cellosaurus STR similarity search tool ‐ A precious help for cell line authentication Open
Despite an increased awareness of the problematic of cell line cross‐contamination and misidentification, it remains nowadays a major source of erroneous experimental results in biomedical research. To prevent it, researchers are expected …
View article: Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines
Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines Open
The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by ale…
View article: Authenticating Hybrid Cell Lines
Authenticating Hybrid Cell Lines Open
Hybrid (both intra-species and inter-species) cell lines arise through intentional or nonintentional fusion of somatic cells having different origins. Hybrid cell lines can pose a problem for authentication testing to confirm cell line ide…
View article: The Possibility of Systematic Research Fraud Targeting Under-Studied Human Genes: Causes, Consequences, and Potential Solutions
The Possibility of Systematic Research Fraud Targeting Under-Studied Human Genes: Causes, Consequences, and Potential Solutions Open
A major reason for biomarker failure is the selection of candidate biomarkers based on inaccurate or incorrect published results. Incorrect research results leading to the selection of unproductive biomarker candidates are largely consider…
View article: Authentication of M14 melanoma cell line proves misidentification of MDA‐MB‐435 breast cancer cell line
Authentication of M14 melanoma cell line proves misidentification of MDA‐MB‐435 breast cancer cell line Open
A variety of analytical approaches have indicated that melanoma cell line UCLA‐SO‐M14 (M14) and breast carcinoma cell line MDA‐MB‐435 originate from a common donor. This indicates that at some point in the past, one of these cell lines bec…
View article: Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature
Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature Open
Continuous cell lines are widely used, but can result in invalid, irreproducible research data. Cell line misidentification is a common problem that can be detected by authentication testing; however, misidentified cell lines continue to b…
View article: The need for a worldwide consensus for cell line authentication: Experience implementing a mandatory requirement at the International Journal of Cancer
The need for a worldwide consensus for cell line authentication: Experience implementing a mandatory requirement at the International Journal of Cancer Open
Cell lines are used in life science research worldwide as biological surrogates. All cell lines are subject to major limitations when used as research tools, including (i) cross-contamination with other cells cultured in the same laborator…
View article: Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line
Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line Open
Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms…