Multi-omics studies that combine genomics, transcriptome, proteome and other modalities are increasingly common in fundamental biology research and biomedicine. Using multi-omics experimental designs at bulk or single-cell resolution can help identifying novel biomarkers or reveal insights into biological mechanisms. This course addresses the conceptual and mathematical foundations of state-of-the-art methods for analyzing the data that results from multi-omics studies. The course will provide an overview of advanced applications of multi-omics methods, provide insights into how to select the most appropriate methods and convey practical experiences by providing participants with hands-on training. Finally, we will provide opportunities for participants to apply the taught principles to their own problems and data.