Design Principles for Genetic Circuits (2015)

In 2015, I TA’d Caltech’s BE 150 course. We covered design principles for genetic circuits, and various simulation and modeling frameworks. You can access the web archive link to the course webpage here

ME: Michael Elowitz, JB: Justin Bois, AS: Anandh Swaminathan, VS: Vipul Singhal. | Date| Class / Instructor| Description | | ———– | ———– | ———————————————————————– | | M 03/30 | L1 (ME) | Introduction to systems biology and gene circuit dynamics | |W 04/01 | L2 (ME)| Small genetic circuits provide powerful functionality | |F 04/03 | R1 (JB)| Introduction to Python for scientific computing and programming preliminaries | |M 04/06 | L3 (ME)| Key functional modules can be identified as circuit motifs; The feed-forward loop (FFL) motif provides several dynamic functions | |W 04/08 | L4 (ME)| Some circuit architectures enable key properties of genetic circuits to be robust to variations in parameter values and fluctuations in component concentrations | |F 04/10 | R2 (AS)| Toggles and C1-FFLs | |M 04/13 | L5 (ME)| Robustness in co-substrate competition | |W 04/15 | L6 (JB)| Multiple binding sites can enable sharp and complex regulation by one or more transcription factors | |F 04/17 | R3 (VS)| Discussions on robustness | |M 04/20 | L7 (JB)| Noise in genetic circuits comes from the expression machinery and the global cellular environment | |W 04/22 | L8 (JB)| Bursty gene expression enables cells to regulate mean and cell-cell variability of protein levels | |F 04/24 | R4 (JB)| Stochastic simulation algorithms for simulating master equations | |M 04/27 | L9 (ME)| Futile cycles in kinase systems can enable switch-like responses and perfect linear amplification | |W 04/29 | L10 (ME)| Paradoxial regulation enables bistable homeostatic states | |F 05/01 | R5 (AS)| Dynamical systems applied to two-component regulation | |M 05/04 | L11 (JB)| Looped repression enables multistate oscillations | |F 05/08 | L12 (JB)| Delayed and combined positive-negative feedback loops enable oscillations in cells | |M 05/11 | L13 (JB)| Excitable gene circuits enable probabilistic, transient differentiation | |W 05/13 | L14 (SN)| Dynamic multiplexing enables multiple types of information to be transmitted through a single pathway | |F 05/15 | R6 (VS)| Background on the KaiABC circuit | |M 05/18 | L15 (ME)| Time-based regulation enables coordinated activation of targets | |W 05/20 | L16 (JB)| Cis interactions enable heterotypic signaling to facilitate developmental patterning | |W 05/27 | L17 (JB)| Feedbacks in morphogenetic patterning systems enable robust length-scale specification and scaling | |F 05/29 | R7 (VS)| Scaling of morphogen gradients | |M 06/01 | L18 (JB)| Example of data analysis: frequencies of nuclear localization pulses in yeast | |W 06/03 | L19 (ME and JB)| Course recap and “How will we think about genetic circuits in the future?” | |———–|———–|———————————————————————–|