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The translation of mRNA into protein lies at the heart of gene expression. The precise determination of translation initiation sites is crucial because it affects how mRNA codes for proteins and is also critical for ensuring timely and accurate protein production in plants. Intriguingly, a single transcript can have multiple initiation sites, both at the AUG codon and other non-AUG codons. Thus, our laboratory is dedicated to studying how translation is controlled, with a particular focus on uncovering these less-explored translation initiation sites and exploring hidden protein-coding genes. These investigations are aimed at unraveling the intricacies of how plants defend themselves and respond to viral infections and how plant viruses induce disease. To achieve this, we employ multidisciplinary approaches integrating molecular techniques, data mining, and predictive biology to establish an experimental and computation-driven discovery platform. Our goal is to illuminate the intricate mechanisms through which plant ribosomes determine where translation begins and unravel the yet unexplored biological significance of these hidden genes in the context of plant-virus interactions.