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


|392109/10 | Jens Stoye | Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=19393956|ekvv]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=19394173|ekvv]] |

==== 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: ====
D. W. Mount. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory Press, 2001. 

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



==== Time table: ====

| **Date** | **Topic** | **Exercises** |
| 22.10.2010 | Introduction, logistics | (none) |
| 29.10.2010 | Patterns in non-coding regions | {{ 293exercises01Noncoding.pdf | Number 1 }}|
| 05.11.2010 | De-novo HTS assembly | {{ 293exercises02HtsAssembly.pdf | Number 2 }}|
| **15.11.2010, 18:00** | Comparative HTS assembly, re-sequencing | {{ 293exercises03ComparativeAssembly.pdf | Number 3 }}|
| 19.11.2010 | mRNA analysis, RNA sequencing | {{ 293exercises04MRNAs.pdf | Number 4 }}|
| 26.11.2010 | Analysis of mass spectra | {{ 293exercises05MassSpec.pdf | Number 5 }}|
| 03.12.2010 | Computational metabolomics, systems biology | {{ 293exercises06SystemsBiology.pdf | Number 6 }}|
| 10.12.2010 | Computational metagenomics | {{ 293exercises07Metagenomics.pdf | Number 7 }}|
| 17.12.2010 | Genome alignment | {{ 293exercises08GenomeAlignment.pdf | Number 8 }}|
| 14.01.2011 | Genome rearrangements | {{ 293exercises09Dcj.pdf | Number 9 }}|
| 21.01.2011 | Gene cluster detection | {{ 293exercises10GeneClusters.pdf | Number 10 }}|
| 28.01.2011 | Haplotype inference, SNP disease association mapping | {{ 293exercises11AssociationMapping.pdf | Number 11 }}|
| 04.02.2011 | Q&As | |

==== Organisational Matters: ====
Together with the practical course "Bioinformatics Applications in Genome Research" in the following summer semester, this lecture forms the master module [[http://www.zfl.uni-bielefeld.de/studium/module/techfak/modulhandbuch/#algorithmen_genomforschung|Algorithms in Genome Research]].\\ The exercises will not be corrected or graded, but presence and activity during the exercise hours is expected. Credit points will be given based on an oral exam at the end of the semester. 

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