A telescope for the RNA universe : novel bioinformatic approaches to analyze RNA sequencing data

In this thesis I focus on the application of bioinformatics to analyze RNA. The type of experimental data of interest is sequencing data generated with various Next Generation Sequencing technique: nuclear RNA, cytoplasmic RNA, captured polyadenylated RNA fragments, etc. I highlight the necessity in developing new tools (e.g., to analyze nuclear RNA) and give a showcase example of implementing such tool and showing its usability on a real biological experiment. The thesis also covers existing tools to perform various types of RNA analysis and shows how these tools can be twigged and expanded to answer certain biological questions (e.g., studying changes in RNA specific to human aging). I also show how current bioinformatic approaches can be used in a particularly complex study such as investigating cancer (in this thesis, breast cancer) pathogenesis