Preheat the oven to 375 degrees F.
Generously season the short ribs with salt and pepper.
Put the flour in a wide, shallow bowl and dredge the ribs, coating each side evenly; shake off the excess flour.
Put the oil into a large, heavy oven-proof pot or Dutch oven and heat on medium high heat.
Place the ribs into the pot and brown all sides of the meat.
Transfer the meat to a plate.
Add the onions, carrots and fennel to the pot and season with salt and pepper and cook for 3-4 minutes. Add in the garlic and cook for another minute.
Pour in the wine and the tomato paste, bring to a boil and cook over medium high heat for 2-3 minutes.
Add the beef short ribs back to the pot.
Pour in the stock.
Add the thyme and bay leaf.
Bring to a boil; cover the pot with the lid, remove the pot from the stove and transfer the pot to the oven.
Bake for 2 hours or until the meat is very tender.
Carefully remove the short ribs from the pot and set aside. Discard the herbs and skim the excess fat. Simmer the sauce until thickened, 8-10 minutes.
Spoon some of the sauce over the ribs and serve with the vegetables.