@article{Wrzodek2010,
  author    = {Wrzodek, Clemens and Schr\"oder, Adrian and Dr\"ager, Andreas and Wanke, Dierk and
    Berendzen, Kenneth W. and Kronfeld, Marcel and Harter, Klaus and Zell, Andreas},
  title     = {{ModuleMaster}: A new tool to decipher transcriptional regulatory networks},
  journal   = {Biosystems},
  year      = {2010},
  volume    = {99},
  pages     = {79--81},
  number    = {1},
  month     = jan,
  abstract  = {In this article we present ModuleMaster, a novel application for finding
    \emph{cis}-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a
    newly developed method which not only considers transcription factor binding information but
    also multivariate functional relationships between regulators and target genes to improve the
    detection of CRMs. Given only the results of a microarray and a subsequent clustering
    experiment, the program includes all necessary data and algorithms to perform every step to find
    CRMs. This workbench possesses an easy-to-use graphical user interface, together with
    job-processing and command-line options, making ModuleMaster a sophisticated program for
    large-scale batch processing. The detected CRMs can be visualized and evaluated in various ways,
    i.e., generating GraphML- and R-based whole regulatory network visualizations or generating SBML
    files for subsequent analytical processing and dynamic modeling.
    Availability: ModuleMaster is freely available to academics as a webstart application and for
    download at \url{http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/}, including
    comprehensive documentation.},
  comment   = {http://www.cogsys.cs.uni-tuebingen.de/software/ModuleMaster/},
  doi       = {10.1016/j.biosystems.2009.09.005},
  issn      = {0303-2647},
  keywords  = {Gene regulation, Cis-regulatory modules, Regulatory sequence analysis, Matrix scan,
    Transcription factors},
  pdf       = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/wrzodek2010_ModuleMaster.pdf},
  publisher = {Elsevier},
  url       = {https://doi.org/10.1016/j.biosystems.2009.09.005}
}