Season short ribs all over with salt and pepper. Heat the oil in a Dutch oven over medium high heat. Sear the short ribs, rotating every minute or so, until browned and seared on all sides. Remove from pot and set aside.
Reduce heat to medium. Add onion, carrots, celery and garlic and sauté for 3-5 minutes. Add red wine to deglaze the pan and cook for 3 minutes, scraping up browned bits from the bottom of the pan.
Add beef broth, boullion, tomatoes (crush them with your hands or a potato masher), tomato paste, cheese rind, salt, pepper, oregano, basil, bay leaves and crushed red pepper. Nestle short ribs on top and top with fresh thyme sprigs.
Bring to a boil, reduce heat, cover pot and simmer for 2 hours.
Remove bay leaves, thyme sticks and cheese rind. Remove short ribs and shred meat (discard bones).
Return meat to the pot and continue to simmer for 30 minutes, to reduce some of the sauce. (If you like the sauce to be a thicker gravy consistency, scoop some into a cup and mix with ½ teaspoon cornstarch, then return to pot).
Cook pasta according to package instructions in salted water. Once pasta is almost al dente, use tongs to remove it from the hot pasta water and add it to the ragu sauce. Toss to combine and cook for 5 more minutes.
Spoon ragu and noodles into shallow bowls and garnish with fresh shredded parmesan cheese, for serving. (Or, if you're feeling fancy top each bowl with a pinch of fresh burrata, sprinkle of flake sea salt and fresh chopped basil.)