J'ai brièvement évoqué l'excellente présentation d'un collègue français, C Labbé, lors du congrès sur le peer-review début septembre 2017. Cette communication a été remarquée, par exemple sur Scholarly Kitchen en citant d'abord ce travail dans le compte rendu du congrès.
Avec une collègue australienne, ils ont appliqué un logiciel appelé "seek and blastn" pour analyser les séquences de nucléotides des gènes dans les publications. Cet outil nécessite encore des développements, mais les premiers résultats sont intéressants. Il s'agit d'extraire automatiquement dans une publication des "gene identifiers and nucleotide sequences (15 to 90 bases) using named entity recognition techniques (thesaurus and rules). The sentence containing each sequence is automatically analyzed (using finite-state machines) to assign a claimed status (targeting or nontargeting) that is compared with the most likely status according to blastn analysis."
Des séquences de nucléotides incorrectes ont été mises en évidence dans des articles… Ce travail a permis de rétracter des articles comme expliqué sur RetractionWatch et d'autres rétractations pourraient suivre…
Leur analyse d'articles en provenance de Chine, publié dans Scientometrics en décembre 2016 est inquiétante.. Voici le résumé de leur article :
Comparing 5 publications from China that described knockdowns of the human TPD52L2 gene in human cancer cell lines identified unexpected similarities between these publications, flaws in experimental design, and mis-matches between some described experiments and the reported results. Following communications with journal editors, two of these TPD52L2 publications have been retracted. One retraction notice stated that while the authors claimed that the data were original, the experiments had been out-sourced to a biotechnology company. Using search engine queries, automatic text-analysis, different similarity measures, and further visual inspection, we identified 48 examples of highly similar papers describing single gene knockdowns in 1–2 human cancer cell lines that were all published by investigators from China. The incorrect use of a particular TPD52L2 shRNA sequence as a negative or non-targeting control was identified in 30/48 (63%) of these publications, using a combination of Google Scholar searches and visual inspection. Overall, these results suggest that some publications describing the effects of single gene knockdowns in human cancer cell lines may include the results of experiments that were not performed by the authors. This has serious implications for the validity of such results, and for their application in future research.
