BioE 42 - Physical Biology of Cells
Principles of transport, continuum mechanics, and fluids, with applications to cell biology. Topics include random walks, diffusion, Langevin dynamics, transport theory, low Reynolds number flow, and beam theory, with applications including quantitative models of protein trafficking in the cell, mechanics of the cell cytoskeleton, the effects of molecular noise in development, the electromagnetics of nerve impulses, and an introduction to cardiovascular fluid flow.
BioE 334 - Engineering Principles in Molecular Biology
Exploration of engineering principles in molecular biology through close reading of classic papers illustrating the achievements and difficulties that exemplify the interface of theory and quantitative experiment. Topics include: bistability, cooperativity, robust adaptation, kinetic proofreading, analysis of fluctuations, sequence analysis, clustering, phylogenetics, maximum likelihood methods, and information theory. During each 3-hour meeting, we will discuss key readings on a particular concept, often with one classic paper and one modern paper readdressing the concept. These sessions are designed to improve your critical reading of quantitative biology texts, along with your foundational knowledge of physics, computation, and engineering in biological contexts.
BioE 115 (previously BioE 45) – Computational Modeling of Microbial Communities
Provides biologists with basic computational tools and knowledge to confront large datasets in a quantitative manner. Students learn basic programming skills focused on Matlab, but also are introduced to Perl and Python. Topics include: image analysis, bioinformatics algorithms, reaction diffusion modeling, Monte Carlo algorithms, and population dynamics. Students apply computational skills to a miniature research project studying the human gut microbiota.
Taught with Justin Sonnenburg and Tiffany Vora.
BioE 221G - Gut Microbiota in Health and Disease
Our bodies are teeming with microbial life that influences human biology in myriad ways. This intimate connection between our microbes and our health is spurring a biomedical revolution, requiring both biomedical scientists and clinicians to extend our thinking of humans to human-microbial ecosystems. This course will provide a detailed account of how microbial and human biology intersect, focusing on foundational knowledge and principles, cutting-edge hypotheses and directions, and the technologies that are rapidly accelerating our knowledge. Challenges of dealing with large datasets and leveraging existing databases will be addressed in the optional computational component of the class.
Taught with Justin Sonnenburg, Ami Bhatt, and Stanley Falkow.
Introduction to Perl and Matlab for Biology
This course was taught from 2005-2007 at Princeton to members of the Departments of Molecular Biology, Chemistry, Chemical Engineering, and Computer Science. The course was held for four weeks, with three hours of lectures per week and one hour of labs. The goal of the course is to develop a foundation of basic tools that can be immediately utilized for biological research analysis. The lab problems are meant to emulate realistic biological scenarios and completion of the labs is highly encouraged if the student is to acquire a proficiency in programming.