===== Contents =====
In this seminar, we will explore influential research papers on Algorithms in Bioinformatics. We will look at both the ground-breaking (classic) publications from earlier periods, as well as the state-of-the-art cutting-edge modern algorithms. Besides theoretical aspects, we also focus on practical aspects, such as software implementing these algorithms.

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.]] |