Preheat the oven to 350°F. Lightly spray a 12 cup muffin tin (or 24 cup mini muffin tin) with cooking spray, or line with paper liners.
In a large bowl, whisk together the all-purpose flour, whole wheat flour, brown sugar, cocoa powder, baking soda and salt until well combined. Add the chocolate chips and dried cherries and toss to combine.
In a medium bowl, whisk together the buttermilk, egg, egg yolk, oil and vanilla until well combined. Pour this mixture into the dry ingredients and stir until just mixed, do not over-mix.
Fill the prepared muffin tin with the batter, dividing it equally between the muffin cups, they will be almost full. Bake for 23-25 minutes for full size muffins, and 16-18 minutes for mini muffins, or until a toothpick inserted in the center of a muffin comes out clean.
Muffins are best the first couple of days after baking them, but store well in an airtight container at room temperature for up to 5 days. They also freeze well for up to 3 months.