Open access journal for long-form publication
Plos One do not have an explicit word count limit, and computational biology should be on-topic for them: 


  There are no explicit restrictions for the number of words, figures, or the length of the supporting information, although we encourage a concise and accessible writing style. 


For further info see http://plosone.org/static/guidelines

Also, have you seen that Plos Computational Biology has two types of articles, Research articles and Software articles, and that the 3500 word limit only applies to the latter (see http://www.ploscompbiol.org/static/guidelines). For Research articles they only say: 


  Although we have no firm length restrictions for the entire manuscript, we urge authors to present and discuss their findings concisely.