Preheat the oven to 350 degrees F. Spread the almonds on a rimmed baking sheet and bake, tossing occasionally, until golden brown, 8 to 10 minutes.
Meanwhile, bring a pot of salted water to a boil. Add the pasta and cook as the label directs, then drain and rinse under cold water. Transfer to a serving bowl and toss with the olive oil, parmesan, lemon juice, shallot, thyme, 1 teaspoon salt and about half of the almonds. Season with salt and pepper. Top with the remaining almonds and the red pepper flakes.