This thesis consists of two projects in which various machine learning approaches and statistical analysis for the integration of biomedical data analysis were explored, developed and tested. Integration of different biomedical data sources allows us to get a better understating of human body from a bigger picture. If we can get a more complete view of the data, we not only get a more complete view of the molecule basis of phenotype, but also possibly can identify abnormality in diseases which were not found when using only one type of biomedical data. The objective of the first project is to find biological pathways which are related to Duechenne Muscular Dystrophy(DMD) and Lamin A/C(LMNA) using the integration of multi-omics data. We proposed a novel method which allows us to integrate proteins, mRNAs and miRNAs to find disease related pathways. The goal of the second project is to develop a personalized recommendation system which recommend cancer treatments to patients. Compared to the traditional way of using only users' rating to impute missing values, we proposed a method to incorporate users' profile to help enhance the accuracy of the prediction. / Master of Science