Absolutely. Hitting the 'O' key brings up the social menu and from that hit 'friends' and you can add or remove players as friends.
Its also possible to switch to whichever instance you all want to play in as well, though I cant remember the function for it atm. But I am routinely able to group up with friends online, and run missions together. Missions also increase in difficulty based on how many are in your group as well, so if your doing a 'patrol' mission which has about 5-7 sub-missions, you will end up with a boatload of experience by the time you finish the mission and call it back in to starfleet.
You can often finish missions up quicker as well by dividing tasks and proceeding accordingly. But doing this can often find a team member jumped and outnumbered pretty quick so ymmv.