Small non-coding RNAs such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs) play a big role in regulating gene expression in cells. In my work, I focus primarily on miRNAs, which represses the expression of the mRNA targets post-transcriptionally. For Drosophila melanogaster, I predicted the tissue-specific expression of several miRNAs based on the expression levels of the predicted mRNA targets in those tissues. The computational predictions are then followed up by quantitative PCR validation of miRNA expression levels in dissected fly tissues. For Stylophora pistillata (a species of coral found in the Red Sea) and Symbiodinium sp. (a photosynthetic, symbiotic algae present in the coral cell), my collaborators and I strived to study the genome, transcriptome and proteome of both organisms. At present, there is another coral genome available — from Acropora digitifera — but the large evolutionary distance between both corals (about 240 million years apart) warrants in-depth study of our coral of interest. On the other hand, our Symbiodinium genome will be the first of its kind for any dinoflagellate. My role in the project was to investigate the small RNAome of both organisms via small RNAseq. As the presence of a thick cell wall in Symbiodinium sp. poses a unique challenge to RNA extraction, and compounded by the dearth of literature regarding RNA extraction from the dinoflagellate, we optimised a procedure that consistently produced high quality RNA for downstream sequencing. From our draft proteome, I showed that the RNA interference (RNAi) machinery is very likely to be present in both organisms. Based on our short RNAseq data, I predicted miRNAs in both organisms. Two of the predicted miRNAs in S. pistillata have been identified in other organisms, while all of the predicted miRNAs in Symbiodinium sp. were novel