Max Planck Institute for Molecular Genetics
Department of Computational Molecular Biology
DNA-Microarrays, well known for measuring gene expression levels, can be used for detecting presence or absence of biological targets (viruses of bacteria) from hybridization patterns of oligonucleotide probes and genomic DNA of agents. Due to sequence similarity of possible targets the use of non-unique oligonucleotides becomes necessary. With use of statistical group testing and phylogenetic information about targets, even the detection of novel targets becomes viable.
Macula, A.J. and Schliep, A. and Bishop, M.A. and Renz, T.E.. New, improved, and practical k-stem sequence similarity measures for probe design (2008) [details]
Hafemeister, Christoph. Efficient Computation of Probe Qualities (2008) [details]
Klau, Gunnar W. and Rahmann, Sven and Schliep, Alexander and Vingron, Martin and Reinert, Knut. Integer linear programming approaches for non-unique probe selection (2007) [details]
Schliep, Alexander and Rahmann, Sven. Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree (2006) [details]
Klau, Gunnar W. and Rahmann, Sven and Schliep, Alexander and Vingron, Martin and Reinert, Knut. Optimal robust non-unique probe selection using Integer Linear Programming (2004) [details]
Heise, Jonas. Selection of Family-Specific Probes for Microarrays (2003) [details]
Schliep, Alexander and Torney, David C. and Rahmann, Sven. Group testing with DNA chips: generating designs and decoding experiments (2003) [details]
Kaderali, Lars and Schliep, Alexander. Selecting signature oligonucleotides to identify organisms using DNA arrays (2002) [details]
Kaderali, Lars. Selecting target specific probes for DNA arrays (2001) [details]
Contact: Alexander Schliep (alexander.schliep@molgen.mpg.de).