Algorithms in Bioinformatics

BIOINF2110 Vorlesung Grundlagen der Bioinformatik

Online lecture

Lecturers  Prof. Daniel Huson,  Anupam Gautam, Timo Lucas, Dr. Monika Zeller and Wenhuan Zeng
Lectures

Start date: April 20th, 2020

(Was: Mondays 10:15-12h, Wednesdays 10:15-12h, Hörsaal 2, Sand 6/7)

Lectures will be made available via Ilias on Mondays.

Assignments will be made available via Ilias on Wednesdays.

Prof Daniel Huson is available online Wednesdays 10:15h for questions about the lecture.

Tutorials Mondays 10-12h via Zoom, participation is mandatory.
Grading Your grade will be based on an exam. (Whether this will take place online or at university will be decided later).
Admission to exam

You must achieve at least 50% of all assignment points and attend 8 (of 12) tutorials.

 You can work on and hand in assignment sheets in groups of up to two people.

If you attain 60%, 75% oder 90% of all assignment points, then you will be given 2, 5, or 8 (out of 50), respectively, bonus points in the final exam.

Language English
Links Alma Ilias

Content and script:

This course discusses some of the foundations of bioinformatics, focusing on how "how stuff works".  Many of the assignments will involve implementing key algorithms in Java, so knowledge of Java is required to take this course.

Schedule

This is a tentative schedule that might well change during the course.

Date Topic Assignments
20.4.  1. General Introduction and Java setup  
22.4.   1
27.4.  2. Pairwise Alignment  
29.4.   2
4.5. 3. Multiple Sequence Alignment  
6.5.   3
11.5. 4. Phylogenetics  
13.5.   4
18.5. Phylogenetics continued, 5. Genome comparison  
20.5.   5
25.5. 6. Blast and 7. RNA secondary structure  
27.5.   6
1.6. holiday  
3.6. holiday  
8.6. 8. Sequencing and Assembly  
10.6.   7
15.6. 9. HMMs  
17.6.   8
22.6. 10. Population Genetics  
24.6.   9
29.6. 11. Protein Secondary Structure  
1.7.   10
6.7. 12. Protein Tertiary Structure  
8.7.   11
13.7. 13. Microbiome Analysis  
15.7. 14. Cancer Genomics Pratice exam
20.7.    
22.7.  Final exam? (Online or in person, to be discussed)  

Makeup exam Wednesday, 28.9., 10-12h, either online or in person (to be decided.)