====== Algorithms in Genome Research ======

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=565899095|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=565903030|10]] | Stoye, Dias Vieira Braga | Winter 2025/26 | Fr 9:00-10:30 and 10:30-12:00 in U10-146 |

==== Contents ====
This class covers the basic algorithmic techniques used in the computational analysis of genome and post-genome data. This includes algorithms for genomic mapping and assembly, methods for functional genome annotation (gene finding and gene function prediction), algorithms for the analysis of DNA microarrays and mass spectra, methods and models for protein structure prediction, and algorithms for comparative genomics. 

==== Literature ====
The page [[teaching:alggrliterature|AlgGRLiterature]] contains many links to the original literature. 

==== Time table ====

| **Date**   | **Topic** | **Exercises** |
| 17.10.2025 | (no class) | -- |
| 24.10.2025 | Overview (MDVB/JS) | -- |
| 31.10.2025 | Physical Mapping (JS) | {{:teaching:2025winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| 07.11.2025 | Genome Assembly I (MDVB) | {{:teaching:2025winter:alggr:exercises02Assembly1.pdf|Exercises 2}} |
| 14.11.2025 | Genome Assembly II (MDVB) | {{:teaching:2025winter:alggr:exercises03Assembly2.pdf|Exercises 3}} |
| 21.11.2025 | Genome Annotation (JS) | {{:teaching:2025winter:alggr:exercises04GenomeAnnotation.pdf|Exercises 4}} |
| 28.11.2025 | Computational Transcriptiomics (JS) | {{:teaching:2025winter:alggr:exercises05RNASeq.pdf|Exercises 5}} |
| 05.11.2025 | Computational Proteomics (JS) | {{:teaching:2025winter:alggr:exercises06MassSpec.pdf|Exercises 6}} |
| 12.12.2025 | Haplotypes (JS) | {{:teaching:2025winter:alggr:exercises07Haplotypes.pdf|Exercises 7}} |
| 19.12.2025 | Association Mapping (JS) | {{:teaching:2025winter:alggr:exercises08AssociationMapping.pdf|Exercises 8}} |
| Winter break |||
| 09.01.2026 | Pangenomics and Variation Detection (JS) | {{:teaching:2025winter:alggr:exercises09Pangenomics.pdf|Exercises 9}} |
| 16.01.2026 | Comparative Genomics I - Breakpoint and SCJ distance (MDVB) | {{:teaching:2025winter:alggr:exercises10ComparativeGenomics1.pdf|Exercises 10}} |
| 23.01.2026 | Comparative Genomics II - DCJ distance and sorting (MDVB) | {{:teaching:2025winter:alggr:exercises11ComparativeGenomics2.pdf|Exercises 11}} |
| 30.01.2026 | Comparative Genomics III (MDVB) - Breakpoint and SCJ median |  {{:teaching:2025winter:alggr:exercises12ComparativeGenomics3.pdf|Exercises 12}} |
| 06.02.2026 | Computational Metagenomics (JS) | -- |

==== Examination dates ====
Oral exams will be in February/March 2026. Please make an appointment with Jens Stoye (by email).

A second oral exam can be taken until end of March 2026. Please contact Jens Stoye (by email) if you are interested.