Possibly coinciding with the "Atlus" and "Index" brand division officially happening today (in Japan) that was announced on February 17 (Sega press release, for reference), Atlus has changed their old logo on several places such as the Persona Channel and their Twitter account to a new one:
New logo
Old logo
Edit:
New logo
Old logo
Edit:
The spun off Index company also has a new logo: http://indexweb.jp/
Atlus as a proper company now has their own corporate website at last: http://www.atlus.co.jp/
The press release has a high res version of their new logo too: