Preheat oven to 350°.
Pat short ribs dry and season with salt and pepper.
Heat oil in dutch oven. Sear until browned all over, in batches if necessary and transfer to plate.
Add onion, thyme, salt and pepper and cook until onions start to soften.
Sprinkle with flour and cook one minute more.
Add stock, bay leaves, and browned short ribs and let come to a simmer.
Cover and place in the oven until tender, about 2 hours.
Serve.