Fall 2012 SB 200 - A Systems Approach to Biology
Co-taught with Johan Paulsson.
This is a completely revised course, that tries to develop a more conceptual basis for systems biology. It was started in 2010 and evolved further in Cambridge in Spring 2011 (for which, see below).
Lectures:
Introduction: why mathematical models? – 12-1
Homeostasis & microscopic cybernetics – 12-2, 12-3, 12-4
Evolution, modularity & weak linkage – 12-5
Time-scale separation & the linear framework – 12-6
Regulatory networks & dynamical systems – 12-7, 12-8, 12-9
Signal transduction & information processing – 12-10, 12-11, 12-12
Metabolic economics (from 2011) – 11-7, 11-8, 11-9
Nullcline theorem handout.
Matrix algebra for beginners: 1, 2, 3.
Spring 2011 Six Lectures on Systems Biology
Delivered in the Department of Genetics, University of Cambridge, as part of the Physics of Medicine initative.
This series covers a mixture of topics from SB200 below and from work in my own lab, loosely following three themes: (1) post-translational modification, (2) microscopic cybernetics, (3) modularity and evolution.
Fall 2008 SB 200 - A Systems Approach to Biology
Co-taught with Walter Fontana and Johan Paulsson.
(Of historical interest only.) This course was a development of MCB195 below. My segment introduced some of the mathematical techniques needed for mechanistic systems biology, with a focus on deterministic dynamical systems.
Lectures: 1, 2, 3, 4, 5, 6, 7, 8.
Production-consumption handout.
Nullcline theorem handout.
Matrix algebra for beginners: 1, 2, 3.
See also "Models in systems biology: the parameter problem and the meanings of robustness".
Spring 2005 MCB 195 - A Systems Approach to Biology
(Of historical interest only.) This was a pioneering undergraduate course co-taught with Lew Cantley, Walter Fontana and Marc Kirschner and a heroic group of TAs led by Mike Springer. We each taught one segment of ~6 lectures: Jeremy (dynamical systems in biology), Walter (motifs and networks), Marc (spatial organisation), Lew (bacterial and eukaryotic chemotaxis).
Lectures: 1, 2, 3, 4, 5, 6.
Prion model handout.