Hi YehiaZ,
We don't know for sure how Express Entry would affect the PhD stream, or how it would affect FSWP in general, really.
There may still be PhD stream, but instead of getting capped the way it currently is, they may put applicants onto the pool like everybody else within FSWP, rank them, and invite only those very close to the top. They have yet to announce the criteria to register under Express Entry.
We hardly know anything about Express Entry, except for, partially, that it will be a ranking system and PR invitations will be given NOT based on first-come-first-serve, but rather on how you are ranked.