This course introduces the foundational principles of biological data analysis, with a strong emphasis on understanding how core bioinformatic algorithms work. Rather than focusing on tool usage or software development, this course explores the underlying concepts, strengths and limitations of key analytical methods, and the critical parameters that influence results. Topics include sequence alignment, database searching, phylogenetic reconstruction, genome annotation, gene prediction, and the analysis of gene expression data. This is not an applied bioinformatics course or a course in tool development—it is designed for students who want to understand the theory and logic behind genome-scale analyses.