If you plan on using frozen blackberries, just be sure to toss with 1 tablespoon of flour before adding to the batter — this will help prevent them from sinking straight to the bottom of the muffin and staining the batter.
Preheat the oven to 375 F, and grease two muffin pans.
Whisk together the first six ingredients in a large bowl. Stir together the yogurt, oil, agave syrup, vanilla and eggs in a separate bowl. Fold wet ingredients into dry mixture with a rubber spatula or wooden spoon until combined. Gently fold in berries.
Fill muffin cups to the top and bake for 10 minutes. Rotate pans and bake 10-12 minutes longer or until muffins are slightly golden and a toothpick comes out clean when inserted into the center. Cool muffins in pans for 5 minutes before transferring to a cooling rack.