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Autumn 2016  SB 200 - Dynamic Processes in Cells (also known as 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, UK in Spring 2011 (for which, see below).

Lectures:
    Introduction: why mathematics? – 16-1
    Homeostasis & microscopic cybernetics – 16-2, 16-3, 16-4
    Evolution, modularity & weak linkage – 16-5, 16-6
    Time-scale separation & the linear framework – 16-7
    Cellular identity & gene regulatory networks– 16-8, 16-9, 16-10
    Information processing in signal transduction – 16-11, 16-12
    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.

Lectures: 1, 2, 3, 4, 5, 6.


Autumn 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.

 

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