Put the beans in a large pot and add enough cold water to cover by 3 to 4 inches. Set aside to soak overnight. Drain and rinse the beans with fresh water. Boil for 1½ hours.
In a large pot, heat the oil over medium heat, add the garlic, onion, carrots, fennel and prosciutto, and cook for 2 to 3 minutes, or until soft and golden. Add the red pepper flakes and tomatoes, and cook uncovered, for 20 to 25 minutes.
Add the beans and bring to a boil. Reduce the heat to a simmer, and cook, uncovered, for 15 minutes, or until the beans are very tender.
In a large pot of lightly salted boiling water, cook the pasta according to package directions, or until al dente. Drain.
Add the pasta to the beans and stir over medium heat for 1½ to 2 minutes to allow the pasta to combine with the sauce.
Garnish generously with grated cheese (about 2 tablespoons per serving) and serve.
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