An in-depth analysis of MD5 collisions used in Flame was published by the Co-Founder and Chief Scientist at Trail of Bits (Trail of Bits is an independent information security company) and can be found here – http://www.trailofbits.com/resources/flame-md5.pdf
Also, the European Network and Information Security Agency (ENISA) has published a paper called ‘The threat from Flamer – Flamer, a state of the art spying virus, reminds us of the weaknesses in our cyber defenses.’
Read more here – https://www.enisa.europa.eu/media/news-items/The-threat-from-Flamer.pdf#