We study representations of Khovanov-Lauda-Rouquier (KLR) algebras of affine Lie type. Associated to every convex preorder on the set of positive roots is a system of cuspidal modules for the KLR algebra. For a balanced order, we study imaginary semicuspidal modules by means of `imaginary Schur-Weyl duality'. We then generalize this theory from balanced to arbitrary convex preorders for affine ADE types. Under the assumption that the characteristic of the ground field is greater than some explicit bound, we prove that KLR algebras are properly stratified. We introduce affine zigzag algebras and prove that these are Morita equivalent to arbitrary imaginary strata if the characteristic of the ground field is greater than the bound mentioned above. Finally, working in finite or affine affine type A, we show that skew Specht modules may be defined over the KLR algebra, and real cuspidal modules associated to a balanced convex preorder are skew Specht modules for certain explicit hook shapes.

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.