Table 1.

Outline of the topics and principles presented in the Systems Biomedicine and Systems Biology courses in the Pharmacology and Systems Biology program

Course	Module or topic	Subtopics and principles
Systems Biomedicine: Molecules, Cells, and Networks	Module	Representative concept areas
	Module 1: General Mechanistic Principles and Introduction to MATLAB	Protein structure, nucleic acid structure Introduction to MATLAB enzyme kinetics (and MATLAB workshop) Receptor function and ligand binding, cell signaling Cell cycle Design of metabolic pathways Physiological homeostasis Genetics and pedigrees, transcription Epigenetics Omics: Genomics and proteomics, including pitfalls and principles of error assessment
	Module 2: Diabetes	Protein processing Secretion and modulation of secretion Metabolic differentiation of different tissues and relationship to gene expression Modes of hormone-mediated signaling Protein processing, transporter-enzyme kinetics, organ crosstalk, ER stress and inflammation Learning from single-mutation-based diabetes SNPs and GWAS Epidemiology of diabetes/obesity Therapeutics and their mode of action, drug discovery
	Module 3: Cancer	Signaling pathways and networks Growth control Cell cycle and mutations in the cell cycle (and MATLAB workshop) Cancer pathology Cancer genetics and genomics The lymphatic system and metastasis Chemotherapeutics and their pitfalls Mechanism-based new therapeutics Cancer epidemiology and statistical models
	Module 4: Renal Disease	Anatomy of the kidney, its specialized cells Principles of filtration and uptake in the kidney Cell polarization and cytoskeleton Diseases of renal podocytes Systems approaches to understanding origins and progression of podocyte diseases vs. single-gene target approaches Channel and transporter structure–function; channelopathies, their systemic physiological effects, and therapeutics Personalized medicine for kidney disease and its systems basis
	Module 5: Drug Abuse	Clinical perspective on drug abuse and its biological underpinnings Neurocircuitry of addiction Receptors and transporters in the relevant brain regions Neuroimaging of receptors Elements of synaptic structure and function Learning and memory Current and potential therapeutic approaches Systems modeling of addiction
Systems Biology: Computational Modeling	Topic
	Graph theory and networks	Representation of biological systems as graphs Tools for building metabolic and signaling networks Quantitative statistical analysis Identification of motifs
	Statistical models for large data sets	Clustering Principal components analysis Partial least-squares regression
	Deterministic models, biochemical signaling models	Representing reactions as systems of ODEs Models in MATLAB Stability analysis of dynamical systems, oscillatory cell cycle models, bistable (all-or-none) Signaling models: multicompartment ODE models Modeling spatial regulation: partial differential equations models
	Physiological models	Action potential models, spatial propagation of electrical signals Calcium signaling models
	Practical considerations in signaling models	Extracting parameters from the literature Estimating unknown parameters Estimating errors
	Stochastic models	Waiting times Poisson probability distributions Gillespie’s algorithm Cell-to-cell variability

ER, endoplasmic reticulum; GWAS, genome-wide association studies; ODE, ordinary differential equation; SNP, single-nucleotide polymorphism.