Preheat your oven to 375°F (190°C).
In a large bowl, combine the whole wheat flour, bran flakes, brown sugar, baking soda, and salt.
In another bowl, whisk together the milk, vegetable oil, eggs, and vanilla extract.
Pour the wet ingredients into the dry ingredients and stir until just combined.
Fold in the raisins or nuts, if using, to incorporate evenly.
Spoon the batter into a greased muffin tin, filling each cup about two-thirds full.
Bake for 18-22 minutes or until a toothpick inserted in the center comes out clean.
Remove the muffins from the oven and let them cool in the tin for 5 minutes before transferring to a wire rack.
