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Spring 2018  Five Lectures on A Systems Approach to Biology

I gave these lectures as part of a School organised by Alicia Dickenstein and Alejandra Ventura at the University of Buenos Aires in Argentina. Stas Shvartsman gave the other five lectures. The School involved participants from across Latin America. Some photographs are here. The lectures are based on those I have been giving at Harvard, as below, but have been substantially revised to reflect several new ideas, arising from a book on systems biology which I am struggling to write.

    The role of mathematics in biology – 1
    Homeostasis of the organism – 2
    The complexity of evolution – 3
    Weak linkage and learning – 4
    Timescale separation and the linear framework – 5

Some comments from two of the Chilean participants (in Spanish).

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).

    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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