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teaching:2024winter:algbi [2024/09/16 15:13] lucas |
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 ===== | ===== Schedule ===== | ||
| **Date** | **Topic** | **Presenting** | | | **Date** | **Topic** | **Presenting** | | ||
- | | 2024-10-07 | Introduction/Organizational matters/Topic selection | Kassian&Leonard | | + | | 2024-10-07 | Introduction/Organizational matters/Topic selection | | |
- | | 2024-10-14 | | | | + | |
- | | 2024-10-14 | | | | + | |
- | | 2024-10-14 | | | | + | |
| 2024-10-14 | | | | | 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.]] | |