Systems Biology

Lecture Notes

LEC #	TOPICS
Part I: Systems Microbiology - ‘The Cell as a Well-stirred Bioreactor’
1	Introduction (PDF) Michaelis-Menten Kinetics
2	Equilibrium Binding Cooperativity
3	Lambda Phage (PDF) Multistability Associated MATLAB® Code File (M)
4	Multistability (cont.) (PDF)
5	Synthetic Genetic Switches
6	Stability Analysis (PDF)
7	Introduction E. coli Chemotaxis (PDF - 1.3 MB)
8	Fine-tuned versus Robust Chemotaxis Models (PDF) Associated MATLAB® Code File (M)
9	Wrapping up Chemotaxis (PDF)
10	Genetic Oscillators (PDF) Associated MATLAB® Code File (M)
11	Genetic Oscillators (cont.)
12	Stochastic Chemical Kinetics
13	Stochastic Chemical Kinetics (cont.)
Part II: Cell Systems Biology - ‘The Importance of Diffusion and Gradients for Cellular Regulation’
14	Introduction Cell Systems Biology (PDF) Fick’s Laws
15	Local Excitation Global Inhibition Theory
16	Local Excitation (cont.) (PDF) Global Inhibition Theory (cont.)
17	Rapid Pole-to-pole Oscillations in E. coli (PDF) Associated MATLAB® Code File (M - 1 of 2) (M - 2 of 2)
18	Rapid Pole-to-pole Oscillations in E. coli (cont.) (PDF)
19	Models for Eukaryotic Gradient Sensing
20	Models for Eukaryotic Gradient Sensing (cont.) (PDF)
21	Modeling Cytoskeleton Dynamics
22	Modeling Cytoskeleton Dynamics (cont.)
Part III: Developmental Systems Biology - ‘Building an Organism Starting From a Single Cell’
23	Quorum Sensing (PDF)
24	Final Problem Set Question Hour
25	Drosophila Development (PDF)