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First-principles calculations of defects and electron–phonon interactions play a critical role in the design and optimization of materials for electronic and optoelectronic devices. The late Audrius Alkauskas made seminal contributions to developing rigorous first-principles methodologies for the computation of defects and electron–phonon interactions, especially in the context of understanding the fundamental mechanisms of carrier recombination in semiconductors. Alkauskas was also a pioneer in the field of quantum defects, helping to build a first-principles understanding of the prototype nitrogen-vacancy center in diamond, as well as identifying novel defects. Here, we describe the important contributions made by Alkauskas and his collaborators and outline fruitful research directions that Alkauskas would have been keen to pursue. Audrius Alkauskas’ scientific achievements and insights highlighted in this article will inspire and guide future developments and advances in the field.