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


|392107 |Jens Stoye |Winter 2008/2009 |Fr. 10-12 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=8231802|ekvv]] |

==== Organisational Matters ====
Together with the practical course "Bioinformatische Anwendungen in der Genomforschung" 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. 



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



==== Timetable ====

  * 17.10.2008: Organizational matters, overview 
  * 24.10.2008: -- no class-- 
  * 31.10.2008: Sequence assembly I: traditional, whole-genome shotgun 
  * 07.11.2008: Sequence assembly II: short-read assembly, re-sequencing 
  * 14.11.2008: Gene finding (tRNAs, pro and eu) 
  * 21.11.2008: Patterns in non-coding regions 
  * 28.11.2008: Transcriptomics I: DNA microarray design 
  * 05.12.2008: Transcriptomics II: DNA microarray analysis 
  * 12.12.2008: Proteomics I: 2D gels 
  * 19.12.2008: Proteomics II: Analysis of mass spectra 
  * 09.01.2009: Genome rearrangement I: Introduction 
  * 16.01.2009: Genome rearrangement II: DCJ distance and sorting 
  * 23.01.2009 at 9:00: Genome rearrangement III: HP distance 
  * 23.01.2009 at 10:15: Genome rearrangement IV: Genome halving (by Marvin Meinold) 
  * 30.01.2009: -- no class -- 
  * 06.02.2009: Gene clusters 


==== Exercises: Fr. 8:45 - 10:15 a.m. in U10-146 ====

  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises01assembly.pdf|Number 1]], Discussion: 2008 November 07 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises02htsAssembly.pdf|Number 2]], Discussion: 2008 November 14 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises03genefinding.pdf|Number 3]], Discussion: 2008 November 21 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises04noncoding.pdf|Number 4]], Discussion: 2008 November 28 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises05microarrayDesign.pdf|Number 5]], Discussion: 2008 December 05 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises06microarrayAnalysis.pdf|Number 6]], Discussion: 2008 December 12 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises07twoDgels.pdf|Number 7]], Discussion: 2008 December 19 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises08massSpec.pdf|Number 8]], Discussion: 2009 January 09 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises09dcj.pdf|Number 9]], Discussion: 2009 January 16 
  * [[http://gi.cebitec.uni-bielefeld.de/teaching/2008winter/alggf/exercises10hp.pdf|Number 10]], Discussion: 2009 February 06 
Back to [[:teaching|Teaching]]