MicrorarrayDetection: Detecting biological agents with DNA Micorarray
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.
Members: Alexander Schliep, Alexander Schliep, Jonas Heise. Collaborators: Knut Reinert (Freie Universitaet Berlin, Algorithmic Bioinformatics), Sven Rahmann (Bielefeld University, Computational Methods for Emerging Technologies), David C. Torney (Los Alamos National Laboratory, Theoretical Biology and Biophysics (T-10)), Gunnar Klau (Centrum Wiskunde & Informatica).
PublicationsMacula et al.. New, improved, and practical k-stem sequence similarity measures for probe design. J. Comput. Biol. 2008, 15, 525–534. Klau et al.. Integer linear programming approaches for non-unique probe selection. Discrete Appl. Math. 2007, 155:6-7, 840–856. Schliep et al.. Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. Bioinformatics 2006, 22:14, e424–e430. Klau et al.. Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics 2004, 20 Suppl 1, i186–i193. Schliep et al.. Group testing with DNA chips: generating designs and decoding experiments. Proc IEEE Comput Soc Bioinform Conf 2003, 2, 84–91. Heise. Selection of Family-Specific Probes for Microarrays. Bachelor's Thesis, Freie Universität Berlin, 2003. Kaderali et al.. Selecting signature oligonucleotides to identify organisms using DNA arrays. Bioinformatics 2002, 18:10, 1340–1349. Kaderali. Selecting target specific probes for DNA arrays. Master's Thesis, University of Cologne, 2001. Kaderali et al.. A new Algorithm for Accelerating Pair-Wise Computations of Melting Temperature. In Electron. Notes Discret. Math., 8, 46–49, 2001. Extended Abstract, 1st Cologne-Twente Workshop on Graphs and Combinatorial Optimization.