Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente, about 10-12 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the chopped onion and cook until softened, about 4 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Add the ground beef to the skillet and cook, breaking it apart with a spoon, until browned and cooked through, about 7-8 minutes. Drain excess fat if necessary.
Stir in the crushed tomatoes, tomato paste, dried oregano, dried basil, salt, black pepper, and red pepper flakes. Bring the sauce to a simmer and cook for 10 minutes, stirring occasionally.
Preheat the oven to 375°F (190°C).
In a large mixing bowl, combine the cooked pasta with the meat sauce and grated Parmesan cheese. Mix well.
Transfer the pasta mixture to a 9×13 inch baking dish and spread evenly.
Sprinkle the shredded mozzarella cheese evenly over the top.
Bake in the preheated oven for 15 minutes, or until the cheese is melted and bubbly.
Remove from the oven and let cool for 5 minutes. Garnish with chopped fresh parsley before serving.