Principles of Complex Networked Systems

This course introduces and develops the mathematical theory of complex nonlinear interaction networks, such as biological, epidemiological, and social networks, with applications to systems biology, drug and gene therapy research, epidemiological studies of human infectious diseases, social studies, and ecology, among others. By employing fundamental concepts from diverse areas of research, such as statistics, signal processing, biophysics, biochemistry, cell biology, and epidemiology, we introduce a multidisciplinary and rigorous approach to the modeling and computational analysis of complex interaction networks. Topics to be covered include: overview of complex nonlinear interaction networks and their applications, graph-theoretic representations of network topology and stoichiometry, stochastic modeling of dynamic processes on complex networks and master equations, Langevin, Poisson, Fokker-Plank, and moment closure approximations, exact and approximate Monte Carlo simulation techniques, time-scale separation approaches, deterministic and stochastic sensitivity analysis techniques, network thermodynamics, and reverse engineering approaches for inferring network models from data.  We will use biochemical reaction systems as the prototypical networks of study. Emphasis is placed on mathematical rigor and computational efficiency.


Computational Functional Genomics

This course provides an introduction to mathematical and computational techniques for Functional Genomics, a growing area of research in cell biology and genetics whose objective is to understand the biological function of genes and their interactions. Computational functional genomics focuses on the problems of collecting, processing and analyzing data related to genome-wide patterns of gene expression with the objective to discover mechanisms by which a cell’s gene expression is coordinated. This has become feasible with the development of DNA microarray technology, which allows the simultaneous measurement of gene expression levels of thousand of genes. Topics covered include: an introduction to cell biology (cells, genome, DNA, transcription, translation, control of gene expression, DNA and RNA manipulation), DNA microarray technology and experimental design, processing and analysis of microarray data (data reduction, filtering, clustering), and computational models for genetic regulatory networks (Boolean networks, Bayesian networks, ODE-based networks).