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Experiments have shown that flow in compliant microchannels can become unstable at a much lower Reynolds number than the corresponding flow in a rigid conduit. Therefore, it has been suggested that the wall's elastic compliance can be exploited towards new modalities of microscale mixing. While previous studies mainly focused on the local instability induced by the fluid--structure interactions (FSIs) in the system, we derive a one-dimensional (1D) model to study the FSI's effect on the global instability. The proposed 1D FSI model is tailored to long, shallow rectangular microchannels with a deformable top wall, similar to the experiments. Going beyond the usual lubrication flows analyzed in these geometries, we include finite fluid inertia and couple the reduced flow equations to a novel reduced 1D wall deformation equation. Although a quantitative comparison to previous experiments is difficult, the behaviors of the proposed model show qualitative agreement with the experimental observations, and capture several key effects. Specifically, we find the critical conditions under which the inflated base state of the 1D FSI model is linearly unstable to infinitesimal perturbations. The critical Reynolds numbers predicted are in agreement with experimental observations. The unstable modes are highly oscillatory, with frequencies close to the natural frequency of the wall, suggesting that the observed instabilities are resonance phenomena. Furthermore, during the start-up from an undeformed initial state, self-sustained oscillations can be triggered by FSI. Our modeling framework can be applied to other microfluidic systems with similar geometric scale separation under different operating conditions.