This group is a subgroup of Life Sciences.
Coordinator of this subgroup: Gunnar Klau
We work on algorithmic solutions to problems from molecular biology and medicine. We develop mathematical models and novel methods for the analysis of biological and biomedical data and theoretical results resulting from these applications. Current research includes comparing and aligning proteins, RNA molecules, and biological networks as well as integrating high-throughput data and network topology in the context of cancer research. We cooperate closely with partners from biology and medicine.
Caption: The group in September 2009
Even if many of the problems we investigate turn out to be NP-hard, we first develop exact algorithms, which compute provably optimal solutions. The aim is to achieve reasonable computation time for practically relevant instance sizes. To this end, we use methods from discrete optimization, often in combination with classical algorithmics and graph theory. We make use of algorithm engineering techniques to come up with practical software implementations, which we make freely available as part of our planet-lisa library. For particularly large-scale problems we use the national supercomputing facilities.
Current research projects
- Multiple structural alignment of RNA and proteins
- Alignment, comparison, and query problems in biological networks
- Identifying functional modules in protein-protein interaction networks
- Subnetwork module construction for improved diagnostic classification and subtyping
- Partitioning molecules in charge groups for molecular dynamics simulations
- Tree matching for cell-tracking in live cell videos
- Robustness of the genectic code
- Breeding schedule optimization
- Flux optimization in metabolic networks
- Next-generation sequencing: Structural variations, transcript isoforms, haplotype inference
Other current and previous research of our group includes: side chain placement in the context of protein design, de novo peptide sequencing in proteomics, RNA structure prediction, identification of gene clusters, oligonucleotide probe selection for microarray experiments, and clustering and hierarchical disease classification by graph editing.
Researchers
- Gunnar Klau (group leader)
- Christine Staiger (joint PhD student with Dutch Cancer Institute)
- Mohammed El-Kebir (joint PhD student with Centre for Integrative Bioinformatics, VU Amsterdam)
- Murray Patterson (ERCIM postdoc)
- Joana Gonçalves (ERCIM postdoc)
- Cristina-Iulia Bucur (MSc student, VU Amsterdam, July 2012 - Feb 2013, Sep 2013 - )
- Marina Milo (MSc student, VU Amsterdam, Sep 2013 - )
Former group members
- Stefan Canzar (postdoctoral researcher, now Johns Hopkins University, Baltimore)
- Inken Wohlers (PhD student, now postdoc at University Duisburg-Essen)
- Leonardos Mageiros (MSc student, VU Amsterdam)
- Marlies van der Wees (MSc student, VU Amsterdam, now PhD student at UvA)
Guests
- Samira Jaeger (PhD student/EMBO short term fellowship programme, 19 Jan 2009 - 17 Apr 2009)
- Nora Toussaint (PhD student/CWI intern, 1 Sep 2009 - 1 Dec 2009
- Sandro Andreotti (PhD student, FU Berlin, 12 Feb 2010 - 18 Apr 2010 and July 2011 - October 2011)
- Xin Wang (PhD student, University of Cambridge/UK), October 2011, CWI intern 2012)
- Jialu Hu (PhD student, FU Berlin, December 2011)
- Thomas Bellitto (intern, ENS Cachan, COST Seqahead short term scientific mission, Mar - Jul 2013)
