====== Classic and Cutting-Edge Algorithms in Bioinformatics (2S) ======


| [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=423647608 | 392131]]| Kobert, Bohnenkämper | Summer 2023 | (Monday, 16-18 in U10-146) |


===== Contents =====
In this seminar, we will explore influential research papers on Algorithms in Bioinformatics. We will have a 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, for instance on 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.

For the module "(Special) Algorithms in Bioinformatics", the seminar is combined with "Implementation of Algorithms". Our seminar is particularly well suited for this, as the student can choose to re-implement, and/or adapt, one of the algorithms they read about here for "Implementation of Algorithms".

Students can also use this seminar for the modules "Algorithmen und Programmierung" or "Computational Life Sciences". In this case, it is mandatory to also present software using the algorithm(s) from the chosen paper or implement (parts of) the algorithm. In turn, the seminar counts for more credit points in these modules.




===== 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.

===== Schedule =====
| **Date** | **Topic**  | **Presenting** |
| 16.10. | Introduction/Organizational matters/Topic selection | Kassian&Leonard |
| 23.10. | Scheduling/Introduction to Scientific Writing | Kassian & Leonard |
| 30.10. | | |
| 06.11. | | |
| 13.11. | | Fabian |
| 20.11. | | Lennart |
| 27.11. | | Niclas & Melissa  |
| 04.12. | | Wanja & Olívia |
| 11.12. | | |
| 18.12. | | |
| **Winter break** |||
| 08.01. | | |
| 15.01. | | |
| 22.01. | | |
| 29.01. | | |
=====Suggested Literature=====

|**Classic** |||
| Barcoding | [[https://doi.org/10.1098/rspb.2002.2218 | Herbert et al.]] |
| Genome rearrangement | [[https://doi.org/10.1007/11851561_16 | Bergeron et al.]] |
| deBruijn Graph assembly | [[https://doi.org/10.1073/pnas.171285098 | Pevzner et al.]] |Melissa L. |
| Alignment | [[https://doi.org/10.1016/0022-2836(82)90398-9 | Gotoh]] |Fabian F.|
| Phylogenetics: Neighbor-Joining | [[https://doi.org/10.1093/oxfordjournals.molbev.a040454 | Saitou & Nei]] | Lennart F. |
| Suffix ararys | [[https://doi.org/10.1137/0222058 | Manber & Myers]] |
| BLAST | [[https://doi.org/10.1016/S0022-2836(05)80360-2 | Altschul et al.]] | Olívia K. |
| Suffix trees | [[https://doi.org/10.1007/BF01206331 | Ukkonen]] |
| **Cutting-edge** |||
| Compression | [[https://doi.org/10.1089/cmb.2016.0151 | Al-Okaily et al.]] |Niclas T. |
| Pathway inference via Hypergraphs | [[https://doi.org/10.1007/978-3-031-29119-7_10 | Krieger & Kececioglu ]] | |
| k-mer counting | [[https://doi.org/10.1093/bioinformatics/btv022 | Deorowicz et al.]] | |
| Phylogenetics: Maximum likelihood | [[https://doi.org/10.1093/bioinformatics/btz305 | Kozlov et al.]] | |
| Haplotype matching: PBWT | [[https://doi.org/10.1093/bioinformatics/btu014 | Durbin]] |Wanja K.| 
| Sequence similarity searching (HMMer) | [[https://doi.org/10.1371/journal.pcbi.1002195 | Eddy ]] |
===Your own ideas?===
You might be inspired by
  * [[teaching:alggrliterature | the Algorithms in Genome Research Literature ]]
  * [[teaching:2021winter:cg |  the Algorithms in Comparative Genomics Literature ]]
  * [[teaching:2023summer:sa| the Sequence Analysis Literature]]
  * reading the references of the papers listed here
  * ...