As a robust system, cells can wisely choose and switch between different signaling programs according to their differentiation stages and external environments. Cancer cells can hijack this plasticity to develop drug resistance. For example, breast cancers that are initially responsive to endocrine therapy often develop resistance robustly. This process is dynamically controlled by interactions of genes, proteins, RNAs and environmental factors at multiple scales. The complexity of this network cannot be understood by studying individual components in the cell. Systems biology focuses on the interactions of basic components, so as to uncover the molecular mechanism of cell physiology with a systemic and dynamical view. Mathematical modeling as a tool in systems biology provides a unique opportunity to understand the underlying mechanisms of endocrine response and resistance in breast cancer. In Chapter 2, I focused on the experimental observations that breast cancer cells can switch between estrogen receptor α (ERα) regulated and growth factor receptor (GFR) regulated signaling pathways for survival and proliferation. A mathematical model based on the signaling crosstalk between ERα and GFR was constructed. The model successfully explains several intriguing experimental findings related to bimodal distributions of GFR proteins in breast cancer cells, which had been lacking reasonable justifications for almost two decades. The model also explains how transient overexpression of ERα promotes resistance of breast cancer cells to estrogen withdrawal. Understanding the non-genetic heterogeneity associated with this survival-signaling switch can shed light on the design of more efficient breast cancer therapies. In Chapter 3, I utilized a novel strategy to model the transitions between the endocrine response and resistance states in breast cancer cells. Using the experimentally observed estrogen sensitivity phenotypes in breast cancer (sensitive, hypersensitive, and supersensitive) as example, I proposed a useful framework of modeling cell state transitions on the energy landscape of breast cancer as a dynamical system. Grounded on the most possible routes of transitions on the breast cancer landscape, a state transition model was developed. By analyzing this model, I investigated the optimum settings of two intuitive strategies, sequential and intermittent treatments, to overcome endocrine resistance in breast cancer. The method used in this study can be generalized to study treatment strategies and improve treatment efficiencies in breast cancer as well as other types of cancer. / Ph. D.