This undergraduate course aims to provide students with an overview of current methods, applications, and analyses in systems biology. Another important purpose of this course is to highlight some of the design principles of biological systems and to provide a mathematical framework in which these principles can be used to understand biological networks. This course is an introduction to data integration and statistical methods used in contemporary Systems Biology, Bioinformatics, and Systems Pharmacology research. The course covers methods and tools for processing raw data from genome-wide mRNA expression studies (microarrays and RNA-sequencing) following the pipeline of data normalization, differential expression, clustering, enrichment analysis, and network construction. The ultimate purpose of the course is to enable participants to utilize the methods presented in this course for analyzing any mRNA-level omics data.