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The formation of sub-structures within an atomic nucleus, appropriately termed nuclear clustering, is one of the core questions of nuclear many-body physics. In this thesis, we put forward a new method for the study of nuclear clustering relying on the completely microscopic Configuration Interaction approach. We construct reaction cluster channels in a Harmonic Oscillator many-body basis that respect the symmetries of the Hamiltonian, are fully antisymmetrized, and carry a separable and controlled Center of Mass component. Such channels are then used to explore cluster signatures in Configuration Interaction many-body wavefunctions. The Resonating Group Method is then applied, utilizing the reaction channels as a basis to capture the essential cluster characteristics of the system. We investigate the emergence of nuclear clustering in 2α, 2α+n, 2α+2n and 3α systems using a No Core Shell Model approach from first principles, and traditional Shell Model studies of clustering in heavier nuclei.