The Ly$alpha$ forest provides one of the best means of mapping large-scale structure at high redshift, including our tightest constraint on the distance-redshift relation before cosmic noon. We describe how the large-scale correlations in the Ly$alpha$ forest can be understood as an expansion in cumulants of the optical depth field, which itself can be related to the density field by a bias expansion. This provides a direct connection between the observable and the statistics of the matter fluctuations which can be computed in a systematic manner. We discuss the way in which complex, small-scale physics enters the predictions, the origin of the much-discussed velocity bias and the `renormalization of the large-scale bias coefficients. Our calculations are within the context of perturbation theory, but we also make contact with earlier work using the peak-background split. Using the structure of the equations of motion we demonstrate, to all orders in perturbation theory, that the large-scale flux power spectrum becomes the linear spectrum times the square of a quadratic in the cosine of the angle to the line of sight. Unlike the case of galaxies, both the isotropic and anisotropic pieces receive contributions from small-scale physics.
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