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

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=475088078|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=475088242|10]] | Stoye, Robidou | Winter 2024/25 | 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** |
| 11.10.2024 | Introduction, logistics | -- |
| 18.10.2024 | Physical mapping (JS) | {{:teaching:2024winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| 25.10.2024 | Sequence analysis (LR) | -- |
| 01.11.2024 | (holiday) ||
| 08.11.2024 | Comparative genomics I (JS) | {{:teaching:2024winter:alggr:exercises03GeneClusters.pdf|Exercises 3}} |
| 15.11.2024 | Comparative genomics II (JS) | {{:teaching:2024winter:alggr:exercises04GenomeRearrangement.pdf|Exercises 4}} |
| 22.11.2024 | Genome assembly I (LR) | |
| 29.11.2024 | Genome assembly II (LR) | |
| 06.12.2024 | Genome assembly III (LR) | |
| 13.12.2024 | Transcriptomics (JS) | {{:teaching:2024winter:alggr:exercises08RNASeq.pdf|Exercises 8}} |
| 20.12.2024 | Proteomics (mass spectrometry) (JS) | {{:teaching:2024winter:alggr:exercises09MassSpec.pdf|Exercises 9}} |
| Winter break |||
| 10.01.2025 | Haplotype inference (JS) | {{:teaching:2024winter:alggr:exercises10Haplotypes.pdf|Exercises 10}} |
| 17.01.2025 | SNP-disease association mapping (JS) | {{:teaching:2024winter:alggr:exercises11AssociationMapping.pdf|Exercises 11}} |
| 24.01.2025 | Pangenomics (LR) | {{:teaching:2024winter:alggr:exercises12Pangenomes.pdf|Exercises 12}} |
| 31.01.2025 | Metagenomics (LR) | -- |

==== Examination dates ====
Oral exams will be on 17 February 2025 or later. Please make an appointment with our team assistants [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=473967687|Nicole Schellenberg]] or [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=493099163|Verena Uhlig]].

A second oral exam can be taken in March 2025. Please contact one of the team assistants if you are interested.