Our paper on the impact and extent of outdated pathway information on current biomedical research was just published in Nature Methods. Congratulations to Lina Wadi who led this project!
Our new paper shows that 67% of 3,900 publications in 2015 used outdated software that only captured 26% of biological processes and pathways apparent in current resources (http://rdcu.be/j1Z8).
free ePDF – http://rdcu.be/j1Z8
Pathway enrichment analysis is a common technique for interpreting gene lists derived from high-throughput experiments. Its success depends on the quality of gene annotations. We analyzed the evolution of pathway knowledge and annotations over the past seven years and found that the use of outdated resources has strongly affected practical genomic analysis and recent literature: 67% of ~3,900 publications we surveyed in 2015 referenced outdated software that captured only 26% of biological processes and pathways identified using current resources.