Prof Dubitzky

Werner Dubitzky Ph.D. MSc
Professor of Bioinformatics, Head of the Bioinformatics research group
Scool of Biomedical Sciences, Coleraine, UU

Positions and Qualifications

  2002 — present: Chair of Bioinformatics and Head of Bioinformatics Group at Univeristy of Ulster, Coleraine, Northern Ireland
  2000 — 2001: Head of Data Mining Group, Intelligent Bioinformatics Research Group at the German Cancer Research Centre, Heidelberg, Germany
  1999: Project Leader (Biology-Inspired Knowledge Management), Research Centre for Knowledge Processing, Ulm, Germany
  1999: Lecturer in Informatics, Faculty of Informatics, University of Ulster, Jordanstown, Northern Ireland
  1997: Ph.D. (Artificial Intelligence), University of Ulster, Jordanstown, Northern Ireland
  1991: MSc Electrical Engineering, Fachhochschule Augsburg, Augsburg, Germany

Editorial Board Membership and Committees

  Briefings in Bioinformatics
  Online Journal of Bioinformatics
  Physics of Life, Virtual Journal on the Interface of Physics and Life Science

Current research:

Analysis and interpretation methods for biological data using data mining and statistics (high-throughput data from genomics and proteomics and imaging data);
Methods for integrating, managing, and sharing of biomedical information and resources using database, data/text mining, data warehousing, grid technology and Web services;
Processing, segmentation and analysis methods for large, multi-dimensional imaging data sets (e.g. from microscopy) and subsequent 3-D reconstruction algorithms for extracting biological structures and processes from these images using computational geometry (e.g., angiogenesis);
Methods for system-level modeling and simulation (e.g., gene networks, kinase/phosphatase interaction networks, protein unfolding simulations, bile acid/xenobiotic interaction system);
Methods for analysis and interpretation of scientific articles and texts using text mining and natural language processing technologies (annotation of microarray data, discovery of macromolecular interaction);
Grid and Web services technologies in bioinformatics and systems biology.
Ontology-driven applications to support functional prediction tasks (Dr Francisco Azuaje, UUJ).

Current grants:

?	Volume: ca. €2 800 000 (University of Ulster: €247 500)
?	Funding source: European Commission, Framework Programme VI, IST Call 5
?	Role: Principal Investigator. University of Ulster is coordinator organization
?	Project period: September 2006 – February 2009

Grid Services Based Environment to Enable Innovative Research (Chemomentum)

?	Volume: ca. €2 590 809 (University of Ulster: €215 791)
?	Funding source: European Commission, Framework Programme VI, IST Call 5
?	Role: Principal Investigator
?	Project period: July 2006 – December 2008

Bioinformatics Strategic Capability Fund

?	Volume: ca, €1 400 000
?	Funding source: Department of Education and Learning, Northern Ireland
?	Role: Principal Investigator
?	Project period: August 2004 – July 2007

A Regional Network for Post-Genomics and Systems Biology (SB(R)Net)

?	Volume: €85 000
?	Funding source: The Engineering and Physical Sciences Research Council, UK
?	Role: Principal Investigator
?	Project period: October 2004 – September 2007

Data Mining Tools and Services for Grid Computing Environments (DataMiningGrid)

?	Volume: €1 883 000 (University of Ulster: €347 000)
?	Funding source: European Commission, Framework Programme VI
?	Role: Principle Investigator and Project Co-ordinator
?	Project period: September 2004 – November 2006

Recent Publications:
Natarajan, J., Berrar, D., Dubitzky, W., Hack, C., Zhang, Y., DeSesa, C., Van Brocklyn, J.R., and Bremer, E.G., Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasivity of a glioblastoma cell line, BMC Bioinformatics, 7:373, 2006.

Fuß, H., Dubitzky, W., Downes, C.S., Kurth, M.J., Bistable Switching and Excitable Behaviour in the Activation of Src at Mitosis, Bioinformatics, Vol. 22(14), e158-e165, 2006

Mandel J.J., Plafreyman N.M., Dubitzky W., Codependence in Biological Systems, IEE Systems Biology (in press)

Berrar D., Bradbury I., Dubitzky W., Instance-based concept learning from multiclass DNA microarray data, BMC Bioinformatics, 7:73, 2006.

Berrar D., Bradbury I., Dubitzky W., Avoiding model selection bias in small-sample genomic data sets, Bioinformatics, 22(10), pp1245-1250, 2006. doi:10.1093/bioinformatics/btl066

McCourt D., Lopez J., Benfenati E., Mazzatorta P., Romberg M., Schuller B., and Dubitzky W., Towards an Intelligent Data Type for Toxicity, Proc. of International Conference on Artificial Intelligence, US, pp328-334, 2003.

Ragg T., Granzow M., Menzel W., Dubitzky W., Filtering Nonlinear Intensity Dependencies in cDNA-Microarray Experiments, Proc. of International Conference on Artificial Intelligence, US, pp335-341, 2003.

Berrar D., Downes C.S. and Dubitzky W., A Probabilistic Neural Network for Gene Selection and Classification of High-dimensional Microarray Data, Proc. of International Conference on Artificial Intelligence, US, pp342-349, 2003.

Sturgeon B., McCourt D., Cowper J., Palmer F., McClean S., Dubitzky W., Can the Grid Help to Solve the Data Integration Problems in Molecular Biology?, Proc. of the 3rd IEEE/ACM Int’l Symposium on Cluster Computing and the Grid, Biogrid 2003, pp588-593, 2003.

Berrar D., Downes C.S., Dubitzky W., Multiclass cancer classification using gene expression profiling and probabilistic neural networks, Proceedings of the Pacific Symposium on Biocomputing 8, World Scientific, New Jersey/London/Singapore/Hong Kong, pp5-16, 2003.