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Systems Biology >> Content Detail



Study Materials



Readings

MATLAB® software is required to run the .m files in this section.

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Suggested Readings in Biology

The following sections from Amazon logo Alberts, Bruce, et al. Molecular Biology of the Cell. 4th ed. New York: Garland Science, 2002. ISBN: 9780815332183, are suggested:

  • RNA and Protein Synthesis
  • Overview of Gene Control
  • How Genetic Switches Work
  • General Principles of Cell Signaling
Downloadable course notes are included courtesy of Prof. Alexander van Oudenaarden as well as any additional authors noted in the table below.
LEC #TOPICSREADINGS
Part I: Systems Microbiology - 'The Cell as a Well-stirred Bioreactor'
1Introduction

Michaelis-Menten Kinetics
2Equilibrium Binding

Cooperativity
Michaelis-Menten Kinetics (PDF)

Associated MATLAB® code file (M)
3Lambda Phage

Multistability
A Genetic Switch in Lamba Phage (PDF)

Associated MATLAB® code file (M)

Hasty, Jeff, Joel Pradines, Milos Dolnik, and J. J. Collins. "Noise-based Switches and Amplifiers for Gene Expression." Proc. Natl. Acad. Sci. USA 97, no. 5 (Feb 29, 2000): 2075-80.
4Multistability (cont.)Isaacs, Farren J., Jeff Hasty, Charles R. Cantor, and J. J. Collins. "Prediction and Measurement of an Autoregulatory Genetic Module." PNAS 100, no. 13 (June 24, 2003): 7714-19.
5Synthetic Genetic SwitchesSynthetic Genetic Switches (PDF)

Gardner, Timothy S., Charles R. Cantor, and James J. Collins. "Construction of a Genetic Toggle Switch in Escherichia coli." Nature 403, no. 6767 (January 20, 2000): 339-42.
6Stability AnalysisStability Analysis (PDF)
7Introduction E. coli Chemotaxis
8Fine-tuned versus Robust Chemotaxis ModelsModeling Escherichia coli chemotaxis (PDF)

Associated MATLAB® code file (M)

Spiro, Peter A., John S. Parkinson, and Hans G. Othmer. "A Model of Excitation and Adaptation in Bacterial Chemotaxis." Proc. Natl. Acad. Sci. USA 94, no. 14 (July, 1997): 7263–68.
9Wrapping up ChemotaxisBiological Oscillators (PDF)
10Genetic OscillatorsBiological Oscillators (PDF)

Associated MATLAB® code file (M)

Elowitz, Michael B., and Stanislas Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403, no. 6767 (January 20, 2000): 335-8.
11Genetic Oscillators (cont.)Routh-Hurwitz (PDF)

Associated MATLAB® code file (M)

Atkinson, Mariette R., Michael A. Savageau, Jesse T. Myers, and Alexander J. Ninfa. "Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli." Cell 113, no. 5 (May 30, 2003): 597-607.
12Stochastic Chemical KineticsThe Origin and Consequences of Noise in Biochemical Systems (PDF) (Courtesy of Alexander van Oudenaarden and Mukund Thattai. Used with permission.)
13Stochastic Chemical Kinetics (cont.)
Part II: Cell Systems Biology - 'The Importance of Diffusion and Gradients for Cellular Regulation'
14Introduction Cell Systems Biology

Fick's Laws
15Local Excitation

Global Inhibition Theory
Local Excitation, Global Inhibition Model (PDF)
16Local Excitation (cont.)

Global Inhibition Theory (cont.)
17Rapid Pole-to-pole Oscillations in E. coliHoward, Martin, Andrew D. Rutenberg, and Simon de Vet. "Dynamic Compartmentalization of Bacteria: Accurate Division in E. Coli." Physical Review Letters 87, no. 27 (December 31, 2001).
18Rapid Pole-to-pole Oscillations in E. coli (cont.)
19Models for Eukaryotic Gradient SensingModels for Eukaryotic Gradient Sensing (PDF)

Associated MATLAB® code file (M)

Narang, Atul, K. K. Subramanian, and D. A. Lauffenburger. "A Mathematical Model for Chemoattractant Gradient Sensing based on Receptor-regulated Membrane Phospholipid Signaling Dynamics." Annals of Biomedical Engineering 29, no. 8 (2001): 677-91.
20Models for Eukaryotic Gradient Sensing (cont.)Postma, Marten, and Peter J. M. Van Haastert. "A Diffusion–Translocation Model for Gradient Sensing by Chemotactic Cells." Biophysical Journal 81, no. 3 (September, 2001): 1314-23.
21Modeling Cytoskeleton DynamicsDogterom, Marileen, and Stanislas Leibler. "Physical Aspects of the Growth and Regulation of Microtubule Structures." Physical Review Letters 70, no. 9 (March 1, 1993).
22Modeling Cytoskeleton Dynamics (cont.)Cytrynbaum, E. N., V. Rodionov, and A. Mogilner. "Computational Model of Dynein-dependent Self-organization of Microtubule Asters." Journal of Cell Science 117, no. 8 (March 15, 2004): 1381-97.
Part III: Developmental Systems Biology - 'Building an Organism Starting From a Single Cell'
23Quorum SensingYou, Lingchong, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold. "Programmed Population Control by Cell-Cell Communication and Regulated Killing." Nature 428, no. 6985 (April 22, 2004): 868-71.
24Final Problem Set Question Hour
25Drosophila DevelopmentHouchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler. "Establishment of Developmental Precision and Proportions in the Early Drosophila embryo." Nature 415, no. 6873 (February 14, 2002): 798-802.

 








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