For the Cupcakes:

1. Preheat oven to 350°F. Prepare two 12-cup muffin trays with cupcake liners.
2. In a large bowl, whisk together the dry ingredients. Set aside.
3. In a separate bowl, combine all of the wet ingredients. Add this to the flour mixture all at once and whisk until completely combined. Do not overmix. The batter will be thick and a little lumpy.
4. Divide the batter evenly among the muffin cups, filling each a little more than halfway full. Bake for 20-25 minutes, or until a toothpick inserted in the middle comes out clean and free of crumbs. Let cool for a few minutes in the pan before transferring the cupcakes to a wire cooling rack to cool completely before decorating with ganache.

For the Ganache:

1. Place chocolate chips in a medium-sized heatproof bowl. Set aside.
2. Combine the heavy cream and juice in a medium saucepan. Place over medium heat. As soon as the mixture begins to simmer, immediately remove from the heat and pour over the chocolate. Allow to stand for 5 minutes. Lightly stir with a whisk until all of the chocolate has melted and the mixture is smooth.
3. Add the butter and stir until it has melted and is completely incorporated.

To Assemble:

1. Cool the ganache slightly at room temperature for about 10 minutes.
2. Dip the top of each cupcake in the ganache, lightly shaking off any excess. Allow the ganache to set slightly at room temperature for another 10 minutes before applying the final garnish of pomegranate seeds.
3. Chill the cupcakes in the refrigerator to completely set and harden the ganache before serving, about 30 minutes.