Gene Regulatory Networks Computational Studies

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Gene Regulatory Networks Computational Studies
Ronojoy Ghosh Aeronautics and Astronautics

• Modeling Biological Networks Journal Club
• Stanford University
• July 24, 2001

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Introduction

• Why?
• Modular description basic regulatory themes
• Gene network ? circuit diagram
• Prediction

3
Model Properties

• Multistable
• Natural biological switch
• Feedback
• Negative/Positive
• Degree of stability
• Oscillations

4
Modeling Methods

• Binary logic
• Chemical kinetics
• Ordinary differential equations
• Stochastic kinetics
• Completeness vs. Complexity

5
Bacteriophage-?

• Models
• Probabilistic
• Rate-equation
• Stochastic
• Similar system
• Phage T7
• lac/trp operon
• Fruitfly segmentation

6
Synthetic Networks

• Toggle switch
• Repressilator
• Autoregulation

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Bistable Toggle Switch
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Repressilator
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Autoregulation
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Hysteresis-based Oscillators
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Conclusion

• Experiment?hypothesis?model?experiment
• Equations
• Clear assumptions
• Contradictions
• Theoretical approach
• Could reduce trial-and-error in experimentation
• Testable predictions