Efficient Data Structures in Computational Biology for Computer Scientists

This is a block proseminar covering topics related to efficient data structures in computational biology. It is intended for Computer Science students only.

Tutor: Cedric Laczny


Registration From October 25th to November 1st, 2016 – HERE
De-registration deadline Februar 1st, 2017
Kick-off meeting January 18th, 2017 – 15:00 s.t – E2.1 room 206
Deadline for the 1st version of slides February 13th, 2017
Presentations March 13th, 2017 – 13:00 s.t – E2.1 room 206
Summary submission deadline March 20th, 2017

Place and Time:

  • E2.1, room 206, 13:00 s.t.

Requirements for participation:

  • at least in 3rd semester

Certificate requirements:

  • Submitting the first version of the slides (see presentation guidelines and presentation guidelines checklist)
  • Successful presentation:
    • Talk: 30 minutes (proseminar)
    • Questions from the audience after the presentation
  • Attendance to all presentations
  • Submitting a summary (ca. 2 pages)

Topics: As indicated by the title of this course, the emphasis is on the efficient data structures, rather than any detailed biological results.

Nr. Presentation Topic Participant
1 Proseminar Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning Jillian C.
2 Proseminar Fast search of thousands of short-read sequencing experiments Maksim S.
3 Proseminar Fast and sensitive taxonomic classification for metagenomics with Kaiju Carsten K.
4 Proseminar MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph TBD
5 Proseminar Accelerating t-SNE using Tree-Based Algorithms TBD