Algorithms of Bioinformatics is a specialization module (Vertiefungsmodul) covering the theoretical foundations of algorithms used in bioinformatics.

The module will introduce students in computer science and related programs to the context in molecular biology, in which algorithmic techniques are an essential tool, but our focus will always be on the abstract algorithmic problems and their theoretical solutions. Prior knowledge of biology is not required; a solid foundation in algorithms and data structures is expected.

Planned Content

  • sequence alignments
  • string algorithms and indexing
  • genome assembly
  • signal detection in biological data
  • phylogenetic trees
  • RNA secondary structure prediction

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Lectures

There will be synchronous interactive lectures, starting from October 16. Live participation is expected. Recordings and livestreams will be made available on a best-effort basis; you can find the livestream on the Live page.

Our regular lecture slot is

Units

The module will consist of the following units; each will have a unit subpage (linked in the table) with slides, lecture notes, and video recordings for that unit.

Week w/c (Mon) Lecture Exercises
1 2025-10-13 Unit 0: Administrativa —
2 2025-10-20 Unit 1: Puzzle from the Lab Sheet 1
3 2025-10-27 Unit 2: Hidden Messages Sheet 2
4 2025-11-03 Unit 3: Comparing Sequences Sheet 3
5 2025-11-10 Unit 3: Comparing Sequences Sheet 4
6 2025-11-17 Unit 4: Assembling Genomes Sheet 5
7 2025-11-24 Unit 5: String Matching Sheet 6
8 2025-12-01 Unit 6: Suffix Trees Sheet 7
9 2025-12-08 Unit 6: Suffix Trees Sheet 8
10 2025-12-15 Unit 7: Googling Genomes Sheet 9
— 2025-12-22 Xmas break  
— 2025-12-29 Xmas break  
— 2026-01-05 Xmas break  
11 2026-01-12 Unit 7: Googling Genomes Sheet 10
12 2026-01-19 Unit 8: RNA Secondary Structure Prediction Sheet 11
13 2026-01-26 Unit 9: Phylogenetic Trees Sheet 12
14 2026-02-02 Unit 9: Phylogenetic Trees  
15 2026-02-09 Recap, Exam Q&A —

Tutorials (Übungen)

There will be exercises sheets with practice problems and group submissions. Further details will be given in class.

Solutions will be discussed in the tutorial sessions, Fridays, noon to 2pm, in Seminar Room V (05D09).

Online Tools

We will use several tools and services that have proven effective in this module.

Campuswire

Campuswire is our main online communication channel.
Any questions relating to the module should be posted on Campuswire on the question & answer forum, the “class feed”.
You can post anonymously if you prefer, and you are strongly encouraged to answer each other’s questions, as well!

You can also use the platform for (social or topical) discussions in the chat rooms.

ILIAS

We will use the university’s official learning management system ILIAS for announcements and examination-related information.

Slido

During the live lectures, I will use Slido for interactive parts.

We maintain a collaborative exam question gallery.

Join us in making this a great resource for preparation for the exam – the better your questions, the more likely they are going to be asked in the actual exam!

Exam & Assessment

The module mark is based on the final examination. To be admitted to the exam, you must achieve a passing grade in the tutorials.

More details will be given in class.

Further reading

The module combines parts from several sources. Key texts are the following.

Other resources