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Algorithms in Genome Research


392109/10 Jens Stoye Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 ekvv/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 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 Number 1
05.11.2010 De-novo HTS assembly Number 2
15.11.2010, 18:00 Comparative HTS assembly, re-sequencing Number 3
19.11.2010 mRNA analysis, RNA sequencing Number 4
26.11.2010 Analysis of mass spectra Number 5
03.12.2010 Computational metabolomics, systems biology Number 6
10.12.2010 Computational metagenomics Number 7
17.12.2010 Genome alignment Number 8
14.01.2011 Genome rearrangements Number 9
21.01.2011 Gene cluster detection Number 10
28.01.2011 Haplotype inference, SNP disease association mapping 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 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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