Special-topic Lecture Bioinformatics: Modeling Cell Fate


Prof. Dr. Volkhard Helms


Maryam Nazarieh, Thorsten Will


Tuesday, 10:15 am – 11:45 am, building E2 1, room 007


Tuesday, 12:45 am – 02:00 pm, building E2 1, room 007.


This course can be used as a “Spezialvorlesung der Bioinformatik/Special-topic Lecture Bioinformatics”


no formal requirements, but solid prior knowledge about

  • cellular networks
  • genetics
  • omics technologies
  • programming experience


  1. biological content
    • circadian rhythms
    • cell cycle
    • cell differentiation/cell reprogramming
    • development of cancer
  2. bioinformatics content
    • microarray expression analysis
    • DNA methylation analysis
    • time series analysis
    • GO and pathway annotation
    • interaction networks
    • application of clustering techniques
    • construction of gene-regulatory networks
    • stochastic simulations
  3. mathematics content
    • stochastic processes + noise
    • differential equations
    • non-linear systems, bifurcations

Conditions for certification:

There will be three 45-minutes tests on different parts of the lecture. (a) Students need to pass at least two out of the three tests. (b) There will be about six bi-weekly graded assignments and tutorial sessions. Students need to get at least 50% of the points from the assignments.


An averaged score will be computed from the best two results of the three tests and this yields the grade of certification (“Schein”). There will be no final exam.


5 (2 V + 1 Ü)


This course is taught in English language.


Lecture 1, April 21 ppt pdf home work:
read this paper
Lecture 2, April 28 ppt pdf read intro and methods
of this paper
Lecture 3, May 5 ppt pdf Assign1 Suppl1
Lecture 4, May 12 ppt pdf
Lecture 5, May 19 mini test 1
pdf Assign2
Lecture 6, May 26 ppt pdf
Lecture 7, June 2 ppt pdf Assign3
home work:
read this paper
Lecture 8, June 9 ppt pdf
Lecture 9, June 16 mini test 2
pdf Assign4 Suppl4
June 23 no lecture
June 30 no lecture Assign5 (new deadline) Suppl5
Lecture 10, July 7 ppt pdf
Lecture 11, July 10
(12.15 am – 2 pm)
ppt pdf
Lecture 12, July 14 ppt pdf Assign6 Suppl6
Lecture 13, July 21 mini test 3