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Over the last decade, numerical solutions of Quantum Chromodynamics (QCD) using the technique of lattice QCD have developed to a point where they are beginning to connect fundamental aspects of nuclear physics to the underlying degrees of freedom of the Standard Model. In this review, the progress of lattice QCD studies of nuclear matrix elements of electroweak currents and beyond-Standard-Model operators is summarized, and connections with effective field theories and nuclear models are outlined. Lattice QCD calculations of nuclear matrix elements can provide guidance for low-energy nuclear reactions in astrophysics, dark matter direct detection experiments, and experimental searches for violations of the symmetries of the Standard Model, including searches for additional CP violation in the hadronic and leptonic sectors, baryon-number violation, and lepton-number or flavor violation. Similarly, important inputs to neutrino experiments seeking to determine the neutrino-mass hierarchy and oscillation parameters, as well as other electroweak and beyond-Standard-Model processes can be determined. The phenomenological implications of existing studies of electroweak and beyond-Standard-Model matrix elements in light nuclear systems are discussed, and future prospects for the field toward precision studies of these matrix elements are outlined.