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This paper develops a general framework for communication over doubly dispersive fading channels via an orthogonal short-time Fourier (STF) basis. The STF basis is generated from a prototype pulse via time-frequency shifts. In general, the orthogonality between basis functions is destroyed at the receiver due to channel dispersion. The starting point of this work is a pulse scale adaptation rule first proposed by Kozek to minimize the interference between the basis functions. We show that the average signal-to-interference-and-noise (SINR) ratio associated with different basis functions is identical and is maximized by the scale adaptation rule. The results in this paper highlight the critical impact of the channel spread factor, the product of multipath and Doppler spreads, on system performance. Smaller spread factors result in lesser interference such that a scale-adapted STF basis serves as an approximate eigenbasis for the channel. A highly effective iterative interference cancellation technique is proposed for mitigating the residual interference for larger spread factors. The approximate eigendecomposition leads to an intuitively appealing block-fading interpretation of the channel in terms of time-frequency coherence subspaces: the channel is highly correlated within each coherence subspace whereas it is approximately independent across different subspaces. The block-fading model also yields an approximate expression for the coherent channel capacity in terms of parallel flat-fading channels. The deviation of the capacity of doubly dispersive channels from that of flat-fading channels is quantified by studying the moments of the channel eigenvalue distribution. In particular, the difference between the moments of doubly dispersive and flat-fading channels is proportional to channel spread factor. The results in this paper indicate that the proposed STF signaling framework is applicable for spread factors as large as 0.01.