Algorithms in Genome Research

392107

Jens Stoye

Winter 2008/2009

Fr. 10-12 in U10-146

Organisational Matters

Together with the practical course “Bioinformatische Anwendungen in der Genomforschung” in the following summer semester, this lecture forms the master module 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 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

Number 1, Discussion: 2008 November 07
Number 2, Discussion: 2008 November 14
Number 3, Discussion: 2008 November 21
Number 4, Discussion: 2008 November 28
Number 5, Discussion: 2008 December 05
Number 6, Discussion: 2008 December 12
Number 7, Discussion: 2008 December 19
Number 8, Discussion: 2009 January 09
Number 9, Discussion: 2009 January 16
Number 10, Discussion: 2009 February 06

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