@ARTICLE{Wrzodek2009,
  author = {Wrzodek, Clemens and Schr{\"o}der, Adrian and Dr{\"a}ger, 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 = {2009},
  volume = {In Press, Accepted Manuscript},
  pages = {-},
  month = {October},
  abstract = {Summary In this article we present ModuleMaster, a novel application
	for finding 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 programincludes
	all necessary data and algorithms to performevery step to find CRMs.
	This workbench possesses an easy-to-use graphical user interface,
	together with job processing and command line options, makingModuleMaster
	a sophisticated programfor 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.},
  doi = {10.1016/j.biosystems.2009.09.005},
  issn = {0303-2647},
  keywords = {Generegulation, Cis-regulatory modules, Regulatory sequence analysis,
	Matrix scan, Transcription factors},
  url = {http://www.sciencedirect.com/science/article/B6T2K-4XDMHNV-1/2/18278a8abb201e1792e9e68fbc976f7d}
}