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

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=361003922|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=361004033|10]] | Stoye | Winter 2022/23 | 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** |
| 14.10.2022 | -- | -- |
| 21.10.2022 | -- | -- |
| 28.10.2022 | -- | -- |
| 04.11.2022 | Introduction, logistics | -- |
| 11.11.2022 | Physical mapping | {{:teaching:2022winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| 18.11.2022 | Genome assembly I | {{:teaching:2022winter:alggr:exercises02Assembly1.pdf|Exercises 2}} |
| 25.11.2022 | Genome assembly II | {{:teaching:2022winter:alggr:exercises03Assembly2.pdf|Exercises 3}} |
| 02.12.2022 | Sequence alignment | {{:teaching:2022winter:alggr:exercises04Alignment.pdf|Exercises 4}} |
| 09.12.2022 | Genome annotation | {{:teaching:2022winter:alggr:exercises05GenomeAnnotation.pdf|Exercises 5}} |
| 16.12.2022 | -- | -- |
| 13.01.2023 | Transcriptomics (RNA sequencing) | {{:teaching:2022winter:alggr:exercises06RNASeq.pdf|Exercises 6}} |
| Winter break |||
| 13.01.2023 | Proteomics, Metabolomics (analysis of mass spectra) | {{:teaching:2022winter:alggr:exercises07MassSpec.pdf|Exercises 7}} |
| **19.01.2023** | Haplotype inference | {{:teaching:2022winter:alggr:exercises08Haplotypes.pdf|Exercises 8}} |
| 20.01.2023 | SNP-disease association mapping | {{:teaching:2022winter:alggr:exercises09AssociationMapping.pdf|Exercises 9}} |
| 27.01.2023 | Computational pangenomics | {{:teaching:2022winter:alggr:exercises10Pangenomics.pdf|Exercises 10}} |
| 03.02.2023 | -- | -- |
| **08.02.2023** | Computational metagenomics |  |

==== Examination dates ====
Oral exams will be on 27 February 2023 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 2023. Please contact Heike Samuel if you are interested.