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teaching:2024winter:algbi [2024/09/16 15:09]
lucas created 		teaching:2024winter:algbi [2024/10/11 08:56] (current)
lucas [Schedule]
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 Topics include, but are not limited to, stringology in bioinformatics,​ sequence analysis, breakpoint distances, and other topics the participants find interesting. Topics include, but are not limited to, stringology in bioinformatics,​ sequence analysis, breakpoint distances, and other topics the participants find interesting.
 +
 +===== Deadlines =====
 +
 +  * The written summary is to be handed in **at most two weeks** after the presentation.
 +  * If you are unsure whether your presentation fits the format, you should make an appointment with me //​approximately one week// before the presentation.
 +  * You can do your "​practical implementation"​ presentation the same week you do your presentation on the algorithm or during the last seminar.
 +===== Schedule =====
 +| **Date** | **Topic** ​ | **Presenting** |
 +| 2024-10-07 | Introduction/​Organizational matters/​Topic selection |  |
 +| 2024-10-14 | | |
 +| 2024-10-21 | | |
 +| 2024-10-28 | <​del>​kmer counting</​del>​ | <​del>​Fabian Molls</​del>​ |
 +| 2024-11-04 | Phylogenetics:​ Maximum likelihood | Mathis Wuelperm |
 +| 2024-11-11 | Genome r. | Daniel Prib |
 +| 2024-11-18 | Haplotype matching | Victoria |
 +| 2024-11-25 | Compression | Jasper M. |
 +| 2024-12-02 | suffix arrays | Evelin Lanert |
 +| 2024-12-09 | Blast | Joyce Abigail Funk |
 +| 2024-12-16 | <​del>​Barcoding</​del>​ | <​del>​Luca Schmidt</​del>​ |
 +| 2024-12-23 | holidays | |
 +| 2024-12-30 | holidays | |
 +| 2025-01-06 | holidays | |
 +| 2025-01-13 | | |
 +| 2025-01-20 | | |
 +| 2025-01-27 | algo presentations ​ | |
 +
 +===== Literature =====
 +| k-mer counting | [[https://​doi.org/​10.1093/​bioinformatics/​btv022 | Deorowicz et al.]] |
 +| Phylogenetics:​ Neighbor-Joining | [[https://​doi.org/​10.1093/​oxfordjournals.molbev.a040454 | Saitou & Nei]] |
 +| Genome rearrangement | [[https://​doi.org/​10.1007/​11851561_16 | Bergeron et al.]] |
 +| Haplotype matching: PBWT | [[https://​doi.org/​10.1093/​bioinformatics/​btu014 | Durbin]] |
 +| Compression | [[https://​doi.org/​10.1089/​cmb.2016.0151 | Al-Okaily et al.]] |
 +| Suffix ararys | [[https://​doi.org/​10.1137/​0222058 | Manber & Myers]] |
 +| BLAST | [[https://​doi.org/​10.1016/​S0022-2836(05)80360-2 | Altschul et al.]] |
 +| Barcoding | [[https://​doi.org/​10.1098/​rspb.2002.2218 | Herbert et al.]] |