Season short ribs with salt and pepper. Heat olive oil in a Dutch oven over medium-high, and sear the ribs until browned on all sides. Set them aside.
In the same pot, sauté onion, carrots, celery, and garlic for 3-5 minutes. Deglaze with red wine, scraping up browned bits, and cook for 3 minutes.
Add beef broth, bouillon, crushed tomatoes, tomato paste, cheese rind (optional), salt, pepper, oregano, basil, bay leaves, and thyme. Place the ribs back in, bring to a boil, then simmer covered on low for 2 ½ - 3 hours.
Discard bay leaves, thyme, and cheese rind. Remove ribs, shred the meat, and return it to the pot. Simmer uncovered for 30-45 minutes to thicken. For a thicker sauce, mix ½ tsp cornstarch with a little sauce, then stir it back in.
Cook pasta in salted water until just shy of al dente, then toss directly into the ragu. Simmer together for 5 minutes.
Serve topped with parmesan and fresh basil.
