I know I'm a little late for this discussion, but I thought it was still worth mentioning -- at least for future reference.

Recently I bumped into the same issue and asked in Chatterbox. It turns out that, at least if you use the BioPerl modules, there are a few peer-reviewed articles that cover the module. In their Wiki page they explicitly tell which articles should be cited whenever the BioPerl modules are used in published scientific articles.