Pat 4 pounds English-cut bone-in beef short ribs dry with paper towels. Season all over with 2 teaspoons kosher salt and 1 teaspoon black pepper.
Heat 1 tablespoon olive oil in a Dutch oven or large heavy-bottomed pot over medium-high heat until shimmering. Working in 2 batches, add the short ribs and sear until all 4 sides are browned, 2 to 3 minutes per side. Transfer all the short ribs to a large plate.
Reduce the heat to medium. Add 2 diced medium carrots, 4 diced medium celery stalks, and 1 diced large yellow onion to the pot. Sauté until the vegetables are softened, about 7 minutes. Add 4 minced garlic cloves and 2 tablespoons tomato paste. Cook, stirring frequently, until fragrant and the tomato paste darkens in color, about 1 minute.
Add 1 ½ cups dry red wine and scrape up any browned bits from the bottom of the pot. Vigorously simmer until reduced slightly, about 5 minutes.
Stir in 28 ounces passata, 2 cups beef broth, 2 tablespoons soy sauce, 2 fresh thyme sprigs, and 1 dried bay leaf. Return the short ribs and their accumulated juices to the pot, arranging the ribs in an even layer. Bring to a boil.
Reduce the heat to maintain a simmer. Partially cover and cook, stirring once or twice, until the short ribs are very tender, about 3 hours.
Using tongs, transfer the short ribs to a rimmed baking sheet. Remove and discard the thyme stems and bay leaves. Remove the meat from the bones and shred into large pieces with two forks. Discard the bones and return the meat to the pot.
If serving immediately, skim off the excess fat from the surface, then stir in ½ cup heavy cream and ½ cup grated Parmesan cheese. If not serving immediately, let cool completely, then cover and refrigerate overnight. Scrape off and discard the hardened layer of fat from the surface before reheating over medium heat; stir in the cream and Parmesan cheese before serving.
When ready to serve, bring a large pot of heavily salted water to a boil. Add 1 pound dried pappardelle pasta and cook according to package directions until al dente. Drain.
Add the pasta to the pot with the short ribs and sauce and toss to combine. Serve garnished with chopped fresh parsley leaves and more Parmesan cheese if desired.
