580.248 Systems Biology of the Cell
Living systems respond to their environments. Understanding cellular responses is important for diseases caused by aberrant responses and for engineering of new life with desired properties. This course develops quantitative models for cellular response functions. It begins with linear response models for protein signal transduction, including an introduction to complex analysis and contour integrals and examination of the MAP kinase signaling cascade. Laplace transforms are related to characteristic functions and moment-generating functions from probability theory. Next, non-linear effects from saturation and cooperative are introduced in the context of transcriptional regulation. Continuous models are related to stochastic dynamics for small numbers of regulatory proteins, with applications to Delta-Notch signaling and lateral inhibition. Finally, diffusion-based models are introduced for long-range patterning and morphogenesis.
550.450 Computational Molecular Medicine (Department of Applied Math and Statistics)
This course was developed by Prof. Don Geman and Prof. Laurent Younes in the Department of Applied Math and Statistics. It introduces machine learning methods used in biomedicine, begins with a foundation in information theory, uses the Kullback-Liebler divergence as motivation for likelihood ratio tests, considers aspects of statistical testing relevant for multiple testing in high-dimensional spaces, and then provides examples of classification and regression problems encountered in genomics.
580.420 Build-a-Genome (also 020.420 in Department of Biology)
This unique course was a cross between a synthetic biology research lab and life in a biotech company. Students were trained in the basics of synthetic biology and then given DNA oligomers and reagents to synthesize building blocks for a synthetic yeast chromosome as part of the Sc2.0 project. Students had keys to the lab for 24/7 access and had weekly lab meetings to present and discuss results and troubleshoot.
This course is no longer offered because it was too successful: all the synthesis for the synthetic yeast genome has been completed, and synthetic chromosomes are in various stages of debugging. Versions of this course have been taught around the world, and similar courses continue to be taught by former teaching assistants.
This full-semester course was the origin of Systems Biology of the Cell. It included additional material on simulating stochastic systems with the Gillespie algorithm, stability analysis and its relationship with transition state theory in chemical kinetics, and biological networks including flux-balance analysis, graph diffusion kernels, network motifs, and stochastic block models.