Proteins are among the central elements in every living cell as these ultimately determine how the cell functions. The protein abundances can be regulated at many levels, such as transcription, translation and degradation. As the complexity increases when considering the large number of components involved in the system (eg. mRNA, tRNA, ribosomes and their interactions), some computational study is needed for the analysis of the global regulation related to protein synthesis. Here we will present three projects that demonstrate how mathematical modeling and computational analysis can be used for fundamental analysis and analysis of omics data: • a study of genome-scale properties of Escherichia coli; • an analysis of translatome data of a bacteria, Lactococcus lactis; • an analysis of proteomics data related to drug target identification.