Are you breathing efficiently? Breathing while running is completely different from cycling.
I like to breathe in three steps/out two at a sustained hard pace like the early part of a race or mile repeats; in three/out three or slower at long run pace; in two/out two for sprints and steep hills. YMMV, but it was gratifying to read the recommendation for 3/2 in the Chi Running book.
Try inhaling through your nose and exhaling through your mouth. There are a lot of reasons to do that, but one of them is that nasal passages release nitric oxide which, if you inhale it, helps bring more oxygen to your muscles. If you have narrow nasal passages and/or allergies, try a nasal strip - they really help me. It takes some practice if you're used to inhaling through your mouth, but it's another way to help breathe more efficiently.
Speed comes from what you put behind you. - Judi Ketteler