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

|[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=102495220|392109]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=102495331|10]] | Stoye | Fr 10:30-12:00/9:15-10:30 and 12:00-12:15 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**                                                                                                                                                                                                                                         |
| 13.10.2017   | Introduction, logistics                                                                                   | --                                                                                                                                                                                                                                                    |
| 20.10.2017   | Physical mapping                                                                                          | {{:teaching:2017winter:alggr:exercises01PhysicalMapping.pdf|Exercises 01}}                                                                                                                                                                            |
| 27.10.2017   | Genome assembly, re-sequencing                                                                            | {{:teaching:2017winter:alggr:exercises02Assembly.pdf|Exercises 02}}                                                                                                                                                                                   |
| 03.11.2017   | Hybrid genome assembly                                                                                    | {{:teaching:2017winter:alggr:exercises03HybridAssembly.pdf|Exercises 03}}                                                                                                                                                                             |
| 10.11.2017   | Haplotype inference                                                                                       | {{:teaching:2017winter:alggr:exercises04HaplotypeInference.pdf|Exercises 04}}                                                                                                                                                                         |
| 17.11.2017   | SNV-disease association mapping                                                                           | {{:teaching:2017winter:alggr:exercises05Associationmapping.pdf|Exercises 05}}                                                                                                                                                                         |
| 24.11.2017   | Gene finding (tRNAs, protein-coding genes)                                                                | {{:teaching:2017winter:alggr:exercises06GeneFinding.pdf|Exercises 06}}                                                                                                                                                                                |
| 01.12.2017   | Finding patterns in non-coding regions                                                                    | {{:teaching:2017winter:alggr:exercises07Noncoding.pdf|Exercises 07}}                                                                                                                                                                                  |
| 08.12.2017   | RNA-seq                                                                                                   | {{:teaching:2017winter:alggr:exercises08RNASeq.pdf|Exercises 08}}                                                                                                                                                                                     |
| 15.12.2017   | Proteomics: analysis of mass spectra                                                                      | {{:teaching:2017winter:alggr:exercises09MassSpec.pdf|Exercises 09}}                                                                                                                                                                                   |
| 22.12.2017   | --                                                                                                        | --                                                                                                                                                                                                                                                    |
| X-mas break                                                                                                                                                                                                                                                                                                                                                                    |||
| 12.01.2018   | Subclonal composition reconstruction (Linda Sundermann)                                                   | {{:teaching:2017winter:alggr:motivation.pdf|Motivation}}, {{:teaching:2017winter:alggr:exercise10_subclonal_reconstruction.pdf|Exercises 10}}                                                                                                         |
| 19.01.2018   | Reconstruction of ancestral genomes (Roland Wittler)                                                      | {{:teaching:2013winter:702lecture1-handout.pdf | Intro to Genome Rearrangements (Pedro Feijão, slides 1--14)}}, {{:teaching:2017winter:alggr:11ancestral_handout.pdf|handout}}, {{:teaching:2017winter:alggr:exercises11ancestral.pdf|Exercises 11}}  |
| 26.01.2018   | Synteny Hierarchies, or: PQ-Tree construction with Generating Families of Common Intervals (Daniel Dörr)  | {{:teaching:2017winter:alggr:exercise12.pdf|Exercises 12}}, {{:teaching:2017winter:alggr:lecture_notes12.txt |Lecture Notes}}                                                                                                                         |
| 02.02.2018   | Finding Gene Clusters by Discovering Common Intervals in Strings (Daniel Dörr)                            | {{:teaching:2017winter:alggr:lecture_notes13.txt |Lecture Notes}}, {{:teaching:2017winter:alggr:lecture13_slides.pdf |Slides}}                                                                                                                        |
==== Examination dates ====
Oral exams will be on 05.04.2018. Please make an appointment with the secretary in U10-151, Heike Samuel. 

A second oral exam can be taken on May 28. Please contact Heike Samuel if you are interested. 

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