Bioinformatics 3

Tutors

Markus Hollander, Thorsten Will, Nicolas Künzel, Andreas Denger, Dr. Pratiti Bhadra

Lecture:

Tuesday and Thursday, 2:15 pm - 4:00 pm, building E2 1, room 001

Tutorial:

Thursday, 12:00 -2:00 pm, E2 1, room 007

Exam:

Tuesday, February 11th, 10:00 am - 1:00 pm, E1 3, HS 001

Re-exam

to be announced

Requirements:

Familiarity with contents of Bioinformatik I and II. The students will have to complete programming assignments with Python. This course can be taken as part of the Master program Bioinformatics.

Content:

The course will cover methodological aspects of integrated biology and systems biology:

  • protein-protein interaction networks (mathematical graphs, Bayesian networks)
  • analysis of protein complexes (density fitting, Fourier transformation)
  • transcriptional regulatory networks (Boolean networks) including epigenetic processes and micro RNAs
  • dynamic simulation of cellular processes (differential equation solvers, stochastic simulations)
  • metabolic networks (linear algebra)

Schein/Certification:

Students need to pass the written final exam that will be scheduled near the end of the winter semester or the re-exam that will be scheduled at the beginning of the following summer semester.

Condition for participation in the final exam:

At least half of the points of the assignments. Solutions have to be returned at the beginning of the following Friday`s lecture. In addition each student has to solve one of these problems on the blackboard.

Textbook:

V. Helms, Principles of Computational Cell Biology, Wiley (2019)

Leistungspunkte/Credits:

9 (4 V + 2 Ü)

Language

This course is taught in English language.

Lectures:

Lecture Slides (pdf) Slides (ppt) Assignments Supplements
Lecture 1, October 18  pdf ppt Assignment 1 Supplement
Lecture 2, October 21 pdf ppt    
Lecture 3, October 25 pdf ppt  Assignment 2  Supplement 2
Lecture 4, October 29 (Tuesday) pdf ppt    
Lecture 5, October 31 (Thursday) pdf ppt  Assignment 3 Supplement 3 
Lecture 6, November 5 pdf ppt    
Lecture 7, November 7 pdf ppt Assignment 4 Supplement 4
Lecture 8, November 12 pdf ppt    
Lecture 9, November 14 pdf ppt Assignment 5 Supplement 5
Lecture 10, November 19 pdf ppt    
no lecture on November 21        
Lecture 11, November 26 pdf ppt    
Lecture 12, November 28 pdf ppt Assignment 6 Supplement 6
Lecture 13, December 3 pdf ppt    
Lecture 14, December 5 pdf ppt Assignment 7 Supplement 7
Lecture 15, December 10 pdf ppt    
Lecture 16, December 12 pdf ppt Assignment 8  Supplement 8 
Lecture 17, December 17        
Lecture 18, December 19        
Lecture 19, January 7        
Lecture 20, January 9        
Lecture 21, January 14        
Lecture 22, January 16        
Lecture 23, January 21        
Lecture 24, January 23        
 Lecture 25, January 28        
Lecture 26, January 30        
Lecture 27, February 4        
Lecture 28, February 6