I see the ads being added by the Agents such as Amazon. They have the information needed to target the customer, such as ereader model, buying habits, etc. They have access to genre information outside of the specific publisher.
The only thing that would be necessary for this to occur would be the right contracts between the publishers and the agents and a sufficient standardization to the ePub format. The standardization of the ePub format would allow the Publishers and Authors to determine the type and location of inserted ads ( if any) to be included in the eBooks. The Agents would be given access to apply ads to the pre-formatted locations according to their Publishing Contract. The agents would use the Point Of Sale to personalize which set of ads to apply before delivery according to eReader, likes, etc.
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