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Step 1
Preheat the oven to 350 degrees F. Spread the pecans in a single layer on an ungreased rimmed baking sheet. Bake for 8 to 10 minutes until the pecans are fragrant and toasted, tossing once halfway through. Set a timer—nuts love to burn.
Step 2
Bring a large pot of salted water to a boil. Cook the pasta to al dente, according to package directions. Drain and set aside.
Step 3
Meanwhile, in a very large deep skillet or Dutch oven, heat the olive oil over medium high. Once hot, add the butternut squash, salt, and pepper. Sauté until the squash is just barely beginning to soften, about 2 minutes.
Step 4
Add the Brussels sprouts. Cook until the sprouts are starting to crisp at the edges and are crisp-tender, 5 to 6 minutes more. Stir periodically but not constantly so that the sprouts have time to crisp on each side.
Step 5
While the vegetables cook, brown the butter: Set a bowl large enough to hold the butter once melted by the stove. Place the butter in a small/medium light-colored saucepan and heat over medium-low. Let the butter melt slowly; it will take several minutes. Continue to heat until butter melts completely, foams and crackles, turns clear golden (the crackling will stop), then turns toasty brown. Swirl the pan periodically as it melts and foams. This entire process will take 3 to 5 minutes, depending upon your pan. Once the butter begins to smell lightly nutty, stir it frequently, scraping up the browned bits from the bottom. Watch the pan carefully in the last few minutes to ensure that the bits at the bottom do not burn (the color will change fast). As soon as the bits turn the color of a pecan, remove the butter from the heat and pour it, along with the toasted bits that are at the bottom of the saucepan, into the bowl to prevent the butter from burning.
Step 6
To the pan with the vegetables, add the cooked pasta. Pour the brown butter over the top. Add the thyme, nutmeg, lemon juice, cherries, toasted pecans, and half of the Parmesan. Stir to combine. Taste and add more salt and pepper as desired.
Step 7
Serve warm, sprinkled with remaining Parmesan cheese.