This course is held in English.

Based on selected book chapters from Genome-Scale Algorithm Design (Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu), the participants will give oral presentations (20-45 min) and write a short summary (5-10 pages) about the an algorithmic problem in bioinformatics and their solutions. Talks and essays must be done in English. The first day covers an overview of possible topics, which will then be distributed to the students. Aspects of scientific writing and presenting will be covered as well.

The overarching topic of this semester are string algorithms for genome-scale data, with a focus on fundamental algorithmic techniques underlying modern bioinformatics tools, including indexing, pattern matching, compressed data structures, and graph-based genome representations.

To practice algorithm design and presentation, each participant will present one core algorithmic idea from the assigned book chapter using pseudocode (in LaTeX). Afterwards, they will implement the algorihtm as a basic prototype in a programming language of their choice (esoteric programming languages are accepted, as long as accompanied by a proper explanation ;)).

Possible concrete chapters/topics to be presented and discussed in the seminar include:

5. Network flows

7. Hidden Markov models

8. Classical indexes

9. Burrows-Wheeler indexes

10. Alignment-based genome analysis

11. Alignment-free genome analysis and comparison

12. Compression of genome collections

13. Fragment assembly

14. Haplotype analysis

15. Pangenomics

Timetable