[Next-Generation Sequencing Book]
  • [Photo] Joerg Schultz • July 17, 2007

    BACKGROUND

    To date, most freely-available programs for the analysis of gene
    expression data are split into two parts: In the first, statistical
    methods are used to identify lists of 'interesting' genes, in the
    second these lists are searched for biological relevance. To overcome
    this separation, we have developed GEPAT. GEPAT provides gene
    annotation for the probes on the microarray and allows the
    visualization of analysis results on metabolic pathways and gene
    interaction networks. It includes different biological databases,
    making them directly usable in data analysis and
    interpretation. Defining and working with different subsets for any
    kind of analysis and interpretation is one of the main concepts of
    GEPAT.
    GEPAT is freely available under the LGPL open source license for
    academic and commercial users at http://gepat.sourceforge.net . An
    installation available for academic users can be found at
    http://gepat.bioapps.biozentrum.uni-wuerzburg.de. The core features
    have been published in Weniger M, Engelmann JC, Schultz J. Genome
    Expression Pathway Analysis Tool--analysis and visualization of
    microarray gene expression data under genomic, proteomic and metabolic
    context. BMC Bioinformatics. 8:179.

    RESPONSIBILITIES

    • Development of algorithms for the detection of de-regulated networks
    • Integration of information about diseases and drugs
    • Integration of microRNA Target information and development of
    algorithms for the detection of microRNA co-regulated genes
    • Extension of GEPAT to cover additional organisms
    The long run vision is to transform GEPAT from Gene Expression data
    analysis to a general tool for the annotation and explorative analysis
    of gene sets.

    REQUIREMENTS

    • in-depth Java knowledge
    • strong know-how and experience in programming internet tools with
    Apache Tomcat, Java Servlets, JSPs, JavaServer Faces
    • general experience in programming internet applications (HTML,
    JavaScript, CSS)
    • working experience with LinuX

    PREFERENCES

    • SQL
    • R, Bioconductor
    • biological background, experience in Microarray-Analysis

    TERMS

    2 years PostDoc position financed by a DFG grant.

    LOCALE

    University of Wuerzburg, Biocenter
    Department of Bioinformatics
    The department of bioinformatics located at the biocenter consists of
    interactive groups focussing on statistics and mathematical biology,
    evolutionary biology and phylogenetics, proteomics and genomics,
    sequence analysis, function and structure prediction, as well as on
    networks and pathway analysis.
    Further information about our group can be found at:
    http://www.biozentrum.uni-wuerzburg.de/joerg_schultz.html

    COMPENSATION

    The positions will be paid as BatIIa (or equivalent / full position)
    according to the German pay scale.

    HOW TO APPLY

    Applicants should send a PDF file with a statement of interest,
    Curriculum vitae and the contact information for at least two referees
    to:
    Joerg.Schultz[at]biozentrum.uni-wuerzburg.de

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