Online application including Statement of Objectives, CV, 3 Letters of Recommendation, and short response questions about fairly basic things like research interests and summary of awards/recognition. Notified via email unofficially of acceptance on February 9th. No interview, however some applicants did require an interview. Seems to be a case by case basis for interviews.
I applied through university. The process took 5 months. I interviewed at MIT (Cambridge, MA) in Mar 2013
Interview
I had an interview with the professor I ended up working for. I discussed my research interests and previous work experience. I also discussed potential projects I could be involved in during my Phd.