The main theme of this dissertation is the study of the lattice points in a rational convex polyhedron and their encoding in terms of Barvinok's short rational functions. The first part of this thesis looks into theoretical applications of these rational functions to Optimization, Statistics, and Computational Algebra. The main theorem on Chapter 2 concerns the computation of the \emph{toric ideal} $I_A$ of an integral $n \times d$ matrix $A$. We encode the binomials belonging to the toric ideal $I_A$ associated with $A$ using Barvinok's rational functions. If we fix $d$ and $n$, this representation allows us to compute a universal Gröbner basis and the reduced Gröbner basis of the ideal $I_A$, with respect to any term order, in polynomial time. We derive a polynomial time algorithm for normal form computations which replaces in this new encoding the usual reductions of the division algorithm. Chapter 3 presents three ways to use Barvinok's rational functions to solve Integer Programs. The second part of the thesis is experimental and consists mainly of the software package {\tt LattE}, the first implementation of Barvinok's algorithm. We report on experiments with families of well-known rational polytopes: multiway contingency tables, knapsack type problems, and rational polygons. We also developed a new algorithm, {\em the homogenized Barvinok's algorithm} to compute the generating function for a rational polytope. We showed that it runs in polynomial time in fixed dimension. With the homogenized Barvinok's algorithm, we obtained new combinatorial formulas: the generating function for the number of $5\times 5$ magic squares and the generating function for the number of $3\times 3 \times 3 \times 3$ magic cubes as rational functions.