Can bitcoin transaction data be used to study markets? The nice thing about bitcoin is that it generates partially anonymous data about every single transaction. Can this data be used to gain insight about real-world markets? Or are there some fundamental differences that cannot be accounted for? If this data can be used, does anybody have any references on academic papers that use the bitcoin data?
There are no academic papers on Bitcoin market behavior.

If Bitcoin or another peer-to-peer currency ever develops a significant closed economy, then it would be a rich source of information on the behavior of markets and economies, as the transaction timing, value and locations (for both the sender and receiver in a transaction) of Bitcoin transactions is publicly broadcasted -and in the case of timing and value, already being recorded in the block chain. 

Furthermore, information about the full Bitcoin transaction history of each pseudonymous individual can be deduced through network analysis techniques.

While Bitcoin is reserved for niche use and doesn't form a closed economy though, the data from the transaction history is of limited use for studying real world market and economic behavior.

Also, in the future the visibility of Bitcoin transaction data could be reduced if many participants in the Bitcoin economy begin to rely on private layers built on top of the Bitcoin network to conduct their transactions through, which is likely to happen given the implications for privacy that visible transactions create.