Bioinformatics

Efficient clustering algorithms for genome-wide expression analysis

Contact: Dr. J. Ernst

Material available online:

BFAM Workshop Hohenkammer 2004 (talk), Powerpoint

Analysis of biological networks

For the analysis of biological networks heterogenous data and knowledge from different fields of molecular biology, biochemistry and medicine has to be merged, often resulting in large networks like protein-protein-interaction-, metabolic or regulatory networks. Within this project we aim at developing methods for the structural analysis, comparison and visualization of such (biological) networks.

Contacts: Jan Griebsch, Arno Buchner

Material available online:

BFAM Workshop Hohenkammer 2004 (slides), Powerpoint

German Conference on Bioinformatics 2004 (poster), pdf

Proteinsearch in large databases

A novel approach for fast searching in huge structural databases like the PDB. The data structure is based on an adaption of the generalized suffix tree and relies on an translation- and rotation-invariant representation of the protein backbone.

Contacts: Hanjo Täubig, Jan Griebsch, Arno Buchner

Material available online:

Talk at the GCB 2004 (slides), Powerpoint

Pattern matching

Main topics of interest are the design and analysis of indexing structures for large texts or collections thereof. We are also interested in approximate (i.e., fault tolerant) methods. The analysis considers worst-case as well as average-case behavior.

Contacts: Moritz Maaß, Johannes Nowak

Material available online:

Average-case Analysis of Approximate Trie Search. Slides of talk at CPM04 (see also material on personal home page)

Linear Bidirectional On-line Construction of Affix Trees Slides of talk at CPM00 (see also material on personal home page)

Exact algorithms for hard problems in computational biology and bioinformatics

Contacts: Sebastian Wernicke

Material available online:

Diploma Thesis, pdf

Partners

Computer-Chemie-Centrum, University of Erlangen-Nürnberg
Dr. Stuempflen, MIPS

Letzte Änderung: Jan Griebsch am 11.11.2004