Formal security analysis of Bitcoin
Currently I'm in the process of finishing my master thesis on the topic of Bitcoin security, and I know there is one more person making a similar master thesis. While it might not be as in-depth of an analysis as a professional cryptography expert might perform, it should be fairly extensive.

Over the course of working on the subject I haven't found any article more comprehensive than the Bitcoin wiki page on Weaknesses of Bitcoin. A lot of problems have been covered in depth on this Stackexchange, as well as some topics on the Bitcoin forum.

EDIT:

My master thesis is available to read in this thread on the Bitcoin forum. It covers a wide analysis of many aspects of Bitcoin, from its cryptography algorithms, through the protocol, the standard client, Bitcoin-related applications, and even users' behaviours. I hope that answers your question better.