Seminar on Statistical Biology: Stochastic models of gene expression and protein synthesis
The dynamics of
living cells is based on the expression of specific genes at specific times. Gene transcription is carefully controlled, allowing the cell to respond to
situations requiring different proteins: for instance, enzymes are produced when nutrients need to be processed
and repair proteins are assembled to respond to cell damage.
The cellular information processing to achieve this control can be
described a stochastic process out of equilibrium. In this seminar,
we discuss the basic elements of stochastic modelling and
nonequilibrium processes as well as models of gene transcription and translation.
Part A: Introduction
Part A: Introduction
- Introduction to nonequilibrium stochastic systems
- Introduction to stochastic gene expression
- Introduction to exclusion models of protein synthesis
- Nonequilibrium models of gene expression
- Elongation and termination in transcription
- Nonequilibrium models and network inference
- TASEP with open boundaries
- Ribosome profiling
- Inhomogeneous TASEP
- Ribosome recycling
- Ribosome dropoff and Langmuir kinetics
Schedule
Thursdays 12:00, Seminar Room 215 in the ITP (old building).
The first meeting is Thursday 17.10.
Please contact the faculty member in charge of your topic for literature pointers well in advance of your presentation.
The list of dates, as well as relevant literature can be found here.
Please contact the faculty member in charge of your topic for literature pointers well in advance of your presentation.
The list of dates, as well as relevant literature can be found here.
Literature
Introduction to stochastic systems:
R. Livi and P. Politi, Nonequilibrium Statistical Physics: A Modern Perspective, CUP
N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North Holland
Stochastic gene expression:
A. Raj and A. van Oudenaarden: Single-molecule approaches to stochastic gene expression. Annu. Rev. Biophys. 38:255 (2009)
Materials for the individual seminar topics will be provided separately.
R. Livi and P. Politi, Nonequilibrium Statistical Physics: A Modern Perspective, CUP
N.G. van Kampen, Stochastic Processes in Physics and Chemistry, North Holland
Stochastic gene expression:
A. Raj and A. van Oudenaarden: Single-molecule approaches to stochastic gene expression. Annu. Rev. Biophys. 38:255 (2009)
Materials for the individual seminar topics will be provided separately.
Picture credit:
Quelle National Human Genome Research Institute, via WikiMedia
Commons, see here for
details and licensing.
![here](https://de.wikipedia.org/wiki/Datei:DNA_transcription.svg"){kind=link}