The book "Transactions on Computational Systems Biology IX" is part of the LNCS journal series and focuses on interdisciplinary research at the intersection of computer science and life sciences. It supports a paradigm shift in the techniques of computer and information sciences to meet the new challenges arising from a systems-oriented approach to biological phenomena. This edition includes four detailed contributions that illuminate various aspects of systems biology, including quantitative analyses of gene operons, ecological transitions and their impact on phenotype expressions, as well as the application of stochastic calculus to describe microbiological systems. The diversity of topics reflects the complexity and interdisciplinary nature of modern biological research.