This thesis consists of two parts. In the first we prove that the Khovanov-Lauda-Rouquier algebras $R_\alpha$ of finite type are (graded) affine cellular in the sense of Koenig and Xi. In fact, we establish a stronger property, namely that the affine cell ideals in $R_\alpha$ are generated by idempotents. This in particular implies the (known) result that the global dimension of $R_\alpha$ is finite. In the second part we use the presentation of the Specht modules given by Kleshchev-Mathas-Ram to derive results about Specht modules. In particular, we determine all homomorphisms from an arbitrary Specht module to a fixed Specht module corresponding to any hook partition. Along the way, we give a complete description of the action of the standard KLR generators on the hook Specht module. This work generalizes a result of James. This dissertation includes previously published coauthored material.