Course details
The instructor for this course is Omer Karin. The course will be held from 10:00 to 12:00 on Wednesdays, with the exception of May 3rd. It is held as part of the Taught Course Center (TCC) and is aimed at PhD students from Univs. of Bristol, Imperial, Oxford and Warwick. If you are interested in signing up for the course, please contact the TCC at tcc@maths.ox.ac.uk.
In this course, we will provide an overview of the systems biology approach to modeling biological systems. Our goal would be to understand how interactions between biological components such as genes, proteins, and cells, give rise to the functional properties of biological systems. We will cover topics ranging from simple genetic circuits to higher-level emergent properties that arise from the interactions of many molecules and cells. The course does not assume any background in biology and will be largely self-contained.
Schedule (tentative):
Week 1 (26/4): Background on cell biology and systems biology
In this week, we will provide a brief overview of molecular cell biology and introduce the systems biology approach to modeling biological systems. We will explore the issue of modularity in biological regulation. We will also introduce the concept of network motifs and how they are used to understand compelx biological networks.
Week 2 (10/5): Autoregulation and Negative Feedback
We will analyze the simple motif of negative autoregulation, and explore the implications of negative feedback in biological circuits. Lecture Notes
Week 3 (17/5): Positive feedback
We will discuss positive feedback and its effects on stability, as well as bifurcations, hysteresis, and oscillations.
SlidesWeek 4 (24/5): Robustness in the glucose-insulin system; dynamical compensation
We introduce the fundamental concept of robustness and explore how it can be used to understand human physiology and disease susceptibility, specifically focusing on the glucose-insulin system.
Lecture NotesWeek 5 (31/5): Robustness in bacterial chemotaxis; fold-change detection
Here we will study robustness through the lens of classic studies and experiments in bacterial navigation.
Week 6 (7/6): Chemotaxis and sampling
We will use chemotaxis to explore the relation between genetic circuits and higher-level biological properties, by considering the random-walk behavior of bacteria.
Week 7 (14/6): Self-tuning of long transients in biology
We will consider the topic of long-transients in biological systems and how they can be implemented through collective behavior.
Week 8 (8/6): Cell state as a high-dimensional attractor
In the final talk we will consider how the concept of high-dimensional attractors can be used to understand cell-state and cell-fate dynamics. We will present Hopfield networks as toy models for high-dimensional attractors and explore their applicability to biology. Lecture Notes