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NOTE: The Friday lectures will include discussing a paper related to the week topic. Papers will be announced about a week prior to the discussion.
Course Objectives: Biology and Control Theory
Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology.
The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating field offers a wide range of challenging open questions, which the students will be encouraged to critically discuss.
Course Schedule
| Week |
Date |
Lecture Topic |
Papers considered in class |
BioControl Journal Club
|
| 1
|
Introduction, Modeling biological systems
|
| 29 March (M)
|
Course overview and objectives, layers of control of gene expression. Slides
|
Syllabus
|
NA
|
| 2 April (F)
|
Modeling: Ordinary Differential Equations. Slides
|
Review on modeling genetic regulatory networks and Modeling the trp operon
|
Model-based redesign of transcriptional networks
|
| 2
|
Deterministic and stochastic modeling
|
| 6 April (T)
|
CDS methods for dynamic performance and periodic behaviors. The case of Negative Auto-Regulation. Slides
|
Detection of multistability, bifurcations and hysteresis in biological positive-feedback systems , Negative Autoregulation Speeds the Response Times of Transcription Networks
|
NA
|
| 9 April (F)
|
Modeling: Stochastic methods, Gillespie algorithm. Slides
|
Gillespie's fundamental paper
|
Defining bifurcations in stochastic systems
|
| 3
|
Model identification in biology
|
| 13 April (T)
|
Overview of system identification methods. Slides
|
|
NA
|
| 16 April (F)
|
Experimental approaches to identification of biological networks Slides
|
Using noise for parameter identification, Identification of network connectivity, Experimental identification of network topologies, Using dynamic correlation to reveal regulatory activity
|
NA
|
| 4
|
Theory of Chemical Reaction Networks
|
| 20 April (T)
|
General introduction and examples. Structural properties of CRNs. Slides
|
M. Feinberg, original notes , H. Othmer, Theory of Complex Reaction Networks
|
NA
|
| 23 April (F)
|
Proof of the Deficiency Zero Theorem
|
|
|
| 5
|
Monotone systems
|
| 27 April (T)
|
Definitions and basic theorems
|
|
NA
|
| 30 April (F)
|
Applications, predicting oscillations
|
|
|
| 6
|
Synthetic biology: design principles
|
| 4 May (T)
|
Design of molecular control systems and demand for gene expression
|
|
NA
|
| 7 May (F)
|
Network motifs, structural and dynamical properties
|
|
|
| 7
|
Synthetic biology: design principles
|
| 11 May (T)
|
Transcriptional and translational control
|
|
NA
|
| 14 May (F)
|
Ultrasensitivity
|
|
|
| 8
|
Robustness
|
| 18 May (T)
|
Theoretical aspects of robustness
|
|
NA
|
| 21 May (F)
|
Robustness in experimental biology
|
|
|
| 8
|
Modularity in control theory and biology
|
| 25 May (T)
|
Time-scale separation principle and dynamical systems approaches to modularity
|
|
NA
|
| 28 May (F)
|
Modularity in experimental biology
|
|
|
Course Administration
This course is a special topics course in which the lecture material has been prepared by a senior graduate student. The class is P/F only and there is no required homework and no midterm or final exam. Students will be required to work on an individual or team course project.
Course Project
Project proposals are due at 5pm on the last day of the Midterm examination period (May 4) and are due by 5pm on the last day of the final examination period (June 7). Project theme: select a cellular regulatory mechanism, define a list of important features of the system, come up with a modeling framework and carry out an analysis of its properties (e.g. stability, robustness, modularity...).
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