We develop data-driven models and algorithmic methods to better understand biological processes. A particular focus lies on network biology, where major steps are to construct high-quality networks, to compare them, to derive network modules from high-throughput data, and to study their properties and their enrichment. Interesting challenges lie in the reconstruction of metagenomic network modules and the integrative analysis of host-microbe interaction networks.
Furthermore, we work on new methods for genotype/phenotype studies, for rational growth media design with flux balance analysis models and for reconstructing haplotypes of polyploid organisms.
- Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF (2016) Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy. Scientific Reports 6:36812.
- Computational Pan-Genomics Consortium (2016) Computational pan-genomics: status, promises and challenges. Brief Bioinform doi: 10.1093/bib/bbw089.
- Canzar S, Andreotti S, Weese D, Reinert K, Klau GW (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biol 17:16.
- Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schonhuth A (2015) WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. J Comput Biol 22(6):498-509.
- El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Muller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW (2015) xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics 31(19):3147-3155.
- Canzar S, El-Kebir M, Pool R, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW (2013) Charge group partitioning in biomolecular simulation. J Comput Biol 20(3):188-198.
- Staiger C, Cadot S, Kooter R, Dittrich M, Muller T, Klau GW, Wessels LF (2012) A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PloS One 7(4):e34796.
- Beisser D, Klau GW, Dandekar T, Muller T, Dittrich MT (2010) BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics 26(8):1129-1130.
- Klau GW (2009) A new graph-based method for pairwise global network alignment. BMC Bioinformatics 10 Suppl 1:S59.
- Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24(13):i223-231.