Welcome to the Lectures Wiki
"Regulation and control of molecular networks" WS 2014/15

News

We will have a double lecture (10-12, 12-14) on December 12 and no lecture on December 19.

General information

SWS: 3, ECTS: 5

Lectures: Alexander Bockmayr / Heike Siebert
Exercises: Therese Lorenz

Language: English / German

Dates

Lecture: Friday 10-12h SR E.31/A7
Exercise (every two weeks): Friday 12-14h SR E.31/A7

Contents

We will focus on modeling and analysis of molecular networks, using continuous, discrete and hybrid discrete/continuous formalisms. Motivated by applications in systems medicine and biotechnology, we will discuss methods to uncover the relation between system design and function, e.g. using modularization approaches or optimisation principles. We also discuss possibilities for network control, e.g. via gene knock-outs.
This course is complementary to the seminar Molecular Networks.

Schedule (subject to change)

Date Lecturer Type Topic MaterialSorted ascending
19.12.2014 H. Siebert no lecture    
28.11.2014 A. Bockmayr Lecture Temporal gene expression Article
05.12.2014 T. Lorenz
A. Bockmayr
Exercises
Lecture

Metabolism coupled to gene expression

Article
09.01.2015 T. Lorenz
H. Siebert
Exercises
Lecture

Logical modeling
exercise
slides
24.10.2014 T. Lorenz
A. Bockmayr
Exercises
Lecture
Simple network examples
Time-scale separation
Ingalls, Chap.2.1
Ingalls, Chap.2.2
31.10.2014 A. Bockmayr Lecture Michaelis-Menten kinetics
Tikhonov's theorem
Ingalls, Chap.3.1
Sontag, Chap.1.6.8 Slides
21.11.2014 T. Lorenz
A. Bockmayr
Exercises
Lecture

Metabolic pathways

Ingalls, Chap.5.1-5-2
12.12.2014 Heike Siebert Double Lecture ODEs and PLDEs, phase space analysis slides
16.01.2015 Heike Siebert
T. Lorenz
Lecture
Exercises
From logical to structure models slides
23.01.2015 Heike Siebert Lecture Graph modules slides
30.01.2015 Heike Siebert
Therese Lorenz
Lecture
Exercises
Statistical significance slides
06.02.2015 Heike Siebert Lecture Dynamical modules slides
13.02.2015 Heike Siebert
Therese Lorenz
Lecture
Exercises
Dynamical modules (cont.) slides
14.11.2014 T. Lorenz Lecture Chemostat Sontag, Chap.1.1.6-10, 1.2.4
17.10.2014 A. Bockmayr Lecture Chemical reaction networks Sontag, Chap.1.6.1-1.6.2
07.11.2014 T. Lorenz
A. Bockmayr
Exercises
Lecture

Inhibition, Cooperativity

Sontag, Chap.1.6.9-1.7.2

Materials

Ingalls B. Mathematical Modeling in Systems Biology MIT Press, 2013

Sontag ED. Lecture Notes on Mathematical Systems Biology Rutgers Univ., Apr 2014

H. De Jong et al., Qualitative simulation of genetic regulatory networks using piecewise-linear models , Bull. Math. Biol., 2004

Concepts from graph theory for analysing biological networks are introduced here

Minimum requirements

Active and regular attendance at exercises, passing the final exam

Tutorial

Comments

Topic revision: r30 - 11 Feb 2015, HeikeSiebert
 
  • Printable version of this topic (p) Printable version of this topic (p)