The best way to do this now is to follow the guide on the following page.
I tried to build markdown files to use for publication section of my blog programmatically using r. I came close, but not all the way there.
The following code takes a bibtex file, reads it into r, formats the output and splits each citation out to a separate markdown file. Unfortunately, there were som spaces and formatting errors that I was not able to get rid of, so I had to go through some manual cleaning up afterwards.