Third q-bio Summer School: Stochastic Signal Processing in Biomolecular Systems

Back to The Third q-bio School.

In this theme, we will explore stochasticity in biochemical and systems biology modeling. As the subject is immense in its scope, we will be limited necessarily to exploring just a small section of the related topics. Specifically, we will review experimental manifestations of stochastic effects in biology, the methods used to treat them analytically and numerically, and effects of the stochasticity on behavior of biomolecular signal processing systems.

This section of the summer school is organized by Ilya Nemenman. Please address all questions about this section of the summer school to its organizer.

Lecture 1

Scope

Stochastic effects in systems biology: Theoretical Foundations and Experimental Results, Part I

Lecturer

Brian Munsky, Slides:File:Munsky Slides QBIO 09.pdf

Topics

Introduction to Stochasticity and the Master Equation.

The importance of stochasticity in gene regulatory networks. Discussion of a couple key examples.

The physics behind stochastic chemical kinetics.

Connection between deterministic reaction rates and propensity functions.

Derivation of the Master Equation for discrete stochastic processes.

Analysis of the master equation for a simple transcription process.

Discussion of the importance of stochasticity in small populations.

Lecture 2

Scope

Stochastic effects in systems biology: Theoretical Foundations and Experimental Results, Part II

Lecturer

Brian Munsky

Topics

Solving the Chemical Master Equation.

Solution of the master equation for systems with affine linear propensity functions.

Discussion of the effect of feedback.

Discussion of Kinetic Monte Carlo algorithms. Tau Leaping. Chemical Langevin equation. Time separation schemes. Hybrid methods.

Finite State projections techniques. Switch rate analysis.

Moment Closure techniques.

Homework

Homework 1: File:QBIO HWK1.pdf

Homework 2: Stochastic Analysis of a toggle Switch: File:Toggle HWK.pdf

Lecture 3

Scope

Methods of generating functional in stochastic kinetics: enzymatic reactions and molecular motors

Lecturer

Nikolai Sinitsyn

Lecture 4

Scope

Signal processing in biochemical networks: Fourier transforms, central limit heorem, linear feedback, and all that, Part I

Lecturer

Ilya Nemenman

Lecture 5

Hour I

Stochastic processes in population genetics and evolution

Lecturer

Anton Zilman

Topics

First passage problems in Master equation: importance of the outliers

Fisher model: genetic drift and fixation as a gambling problem

Hour II

Bioinfiormatics and evolution of HIV

Lecturer

Bette Korber

Topics

Introduction to phylogenetic inference

Applications to HIV infection

Lecture 6

Scope

Signal processing in biochemical networks: Information theory, noise suppression, form and function, and all that. Part II

Lectures

Ilya Nemenman

Lecture 7

Scope

Bacterial chemo- and thermo-taxis as examples of stochastic signal processing systems

Lecturer

Will Ryu

Lecture 8

Scope

Bacterial chemo- and thermo-taxis as examples of stochastic signal processing systems

Lecturer

Will Ryu