Are you a horizontal or vertical runner?
Vertical runners tend to get more up and down movement when they run compared to a more efficient horizontal runner. See this video comparing horizontal versus vertical running.
If you are more of a vertical runner, your breathing pattern may be part of the problem. Vertical runners tend to breath by elevating or lifting their shoulders and ribs when they breath. A more efficient breathing pattern is one that focuses on using the diaphragm and expanding your ribs outward. Check out this video for a simple exercise to work on your breathing and become a more efficient runner.
If you are looking for a more comprehensive training program, contact Dr. Terry Gebhardt at Colorado In Motion at Terry@ColoradoInMotion.com.