Yesterday I have installed Ubuntu 16.04 LTS on my laptop to try it out.
While overall the experience is quite good, I found that notifications were broken for apps like slack and atom.
Following the issue found on github, I have found the following workaround to work for me:

Add the following line to /etc/environment ( edit as root ) and reboot ( or logout and login )

ELECTRON_USE_UBUNTU_NOTIFIER=1