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

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=423644090|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=423653637|10]] | Stoye, Dias Vieira Braga | Winter 2023/24 | 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** |
| 13.10.2023 | -- | -- |
| 20.10.2023 | -- | -- |
| 27.10.2023 | Introduction, logistics | -- |
| 03.11.2023 | Physical mapping | {{:teaching:2023winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| <del>10.11.2023</del> | <del>Epigenomics</del> | |
| 17.11.2023 | Genome assembly I (M) | {{:teaching:2023winter:alggr:exercises03Assembly1.pdf|Exercises 3}} |
| 24.11.2023 | Genome assembly II (M) | {{:teaching:2023winter:alggr:exercises04Assembly2.pdf|Exercises 4}} |
| 01.12.2023 | Genome annotation I | {{:teaching:2023winter:alggr:exercises05GeneFinding.pdf|Exercises 5}} |
| 08.12.2023 | Genome annotation II | {{:teaching:2023winter:alggr:exercises06NonCoding.pdf|Exercises 6}} |
| 15.12.2023 | Transcriptomics | {{:teaching:2023winter:alggr:exercises07RNASeq.pdf|Exercises 7}} |
| 22.12.2023 | Proteomics (mass spectrometry) | {{:teaching:2023winter:alggr:exercises08MassSpec.pdf|Exercises 8}} |
| Winter break |||
| 12.01.2024 | Haplotype inference | {{:teaching:2023winter:alggr:exercises09Haplotypes.pdf|Exercises 9}} |
| 19.01.2024 | SNP-disease association mapping | {{:teaching:2023winter:alggr:exercises10AssociationMapping.pdf|Exercises 10}} |
| 26.01.2024 | Comparative genomics (M/L) | {{:teaching:2023winter:alggr:exercise11.pdf|Exercises 11}} |
| 02.02.2024 | Pangenomics, metagenomics | -- |

==== Examination dates ====
Oral exams will be on 16 February 2024 or later. Please make an appointment with the secretary in U10-151, [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=65856&lang=EN|Heike Samuel]].

A second oral exam can be taken in March 2024. Please contact Heike Samuel if you are interested.