@tommy @shiro I know what paper you're talking about:
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008984
Originally identified in 2004 as a problem, the entire field of computational biology still hasn't moved past this almost 20 years later.
I've dealt with this problem myself in my work. It's actually less work to change the gene's actual name than it is to get people to stop using it. But it's still extremely disruptive to do this.
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