Special-topic Lecture Bioinformatics: Modeling Cell Fate

Lecturer:

Prof. Dr. Volkhard Helms

Tutors:

Maryam Nazarieh, Thorsten Will

Lecture:

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

Tutorial:

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

Information:

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

Requirements:

no formal requirements, but solid prior knowledge about

  • cellular networks
  • genetics
  • omics technologies
  • programming experience

Content:

  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.

Schein/Certification:

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.

Leistungspunkte/Credits:

5 (2 V + 1 Ü)

Language

This course is taught in English language.

Lectures:

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
ppt		 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
ppt		 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