Preheat the oven to 250 degrees F.
Season the short ribs on all sides with salt and pepper. Heat about two tablespoons of oil in a large Dutch oven with a lid or stockpot over medium high heat. Working in batches, brown ribs on all sides. Set aside. Do not drain grease from the pan.
Puree the onion, carrots, celery, garlic and ½ cup of fresh cranberries in a food processor. Add the puree to the pot along with the remaining whole cranberries. Sauté until tender, about 5-7 minutes.
Add the tomato paste and sauté for another five minutes.
Add one cup of hearty red wine and scrape up any food that’s stuck on the bottom of the pan. Continue to simmer until liquid is reduced by half, about 10 minutes.
If using a Dutch oven, nestle the short ribs into the vegetable mixture. If not using a Dutch oven, transfer vegetables to roasting pan or casserole dish with a lid. Add a fresh thyme bundle tied with kitchen twine and two whole bay leaves.
Nestle the short ribs in the mixture. Cover the pan. Roast the short ribs for three hours, until the meat is tender and falling off the bone.
Remove and discard the thyme bundle and the bay leaves before serving.