Research Cooperations

The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is not complete, also consult the AG ABI Projects Website.

Cooperations Within SPP1307

We are collaborating with the group of Prof. Dr. Ernst Mayr at TU Munich and their Practical Approximate Pattern Matching with Index Structures project within the DFG priority program SPP1307. Johannes Krugel is working on index data structures and integrates them directly in SeqAn, our software library for sequence analysis. Furthermore, we are planning a more direct collaboration on a simulator for genome evolution for a whole genome comparison benchmark.

We are collaborating with the group of Prof. Dr. Ulrich Meyer at Goethe Universität Frankfurt am Main and their Algorithms for Modern Hardware: Flash Memory project. Since Bioinformatics has to deal with large amounts of data, external memory algorithms are necessary. We are planning to investigate external memory algorithms for processing large graphs in context with our hierarchical sequence alignment methods, such as external memory breadth first search. Furthermore, the Ulrich Meyer's group is currently working on the STXXL library for external memory algorithms and we are investigating on how to benefit from the STXXL from within the SeqAn library.