M.Sc. Tizian Schulz
Seminar: Wednesday, 10.15-11.45 in U10-146
Office hours: by arrangement
Office: U10-141
Based on original research papers, the participants will give oral presentations (20-45 min, optimally about 25 min's) and write short summaries (ca. 5 pages), both in English, about current algorithmic problems in computational pangenomics and their solutions. Deadline for the written summary is one week after the presentation.
| 12.10. | Preliminaries, topic selection | Tizian |
| 19.10. | Computational pan-genomics: status, promises and challenges | Tizian |
| 26.10. | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage | Lisa |
| 02.11. | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs | ALL (Malte) |
| 09.11. | Bifrost (continued) | ALL (Malte) |
| 16.11. | Sequence variation aware genome references and read mapping with the variation graph toolkit (see also Tarjan, 1972 & Farrar, 2007) | ALL (Louisa) |
| 23.11. | (Tizian away) | |
| 30.11. | (Tizian away) | |
| 07.12. | (Tizian away) | |
| 14.12. | (Tizian away) | |
| 21.12. | (Tizian away) | |
| 11.01. | Bit-parallel sequence-to-graph alignment | ALL (Lisa) |
| 18.01. | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs | Louisa |
| 25.01. | Alignment- and reference-free phylogenomics with colored de Bruijn graphs | Jamie |
| 01.02. | Viral quasispecies reconstruction via contig abundance estimation in variation graphs | Malte |
The topic of the talk/report should be recent algorithmic problems in computational pangenomics and their solutions.
The students are encouraged to suggest their own topics.
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